diff --git a/CITATION.cff b/CITATION.cff
index c04c0aa6..58c6e1af 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,5 +1,5 @@
title: STRchive
-version: 2.15.0
+version: 2.16.0
date-released: "2026-1-21"
url: https://github.com/dashnowlab/STRchive
authors:
diff --git a/data/STRchive-citations.json b/data/STRchive-citations.json
index 443cec4b..cf5a055b 100644
--- a/data/STRchive-citations.json
+++ b/data/STRchive-citations.json
@@ -156116,240 +156116,6 @@
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@@ -157372,12 +157138,6 @@
"language": "en",
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@@ -157510,12 +157270,6 @@
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+ "id": "genereviews:NBK1427",
+ "manubot_success": true,
+ "link": "http://www.ncbi.nlm.nih.gov/books/NBK1427/",
+ "title": "Congenital Central Hypoventilation Syndrome",
+ "type": "chapter",
+ "doi": "",
+ "authors": [
+ ["Debra E.", "Weese-Mayer"],
+ ["Casey M.", "Rand"],
+ ["Ilya", "Khaytin"],
+ ["Susan M.", "Slattery"],
+ ["Kai Lee", "Yap"],
+ ["Mary L.", "Marazita"],
+ ["Elizabeth M.", "Berry-Kravis"]
+ ],
+ "publisher": "GeneReviews\u00ae",
+ "issn": "",
+ "date": "1993-01-01",
+ "abstract": "Congenital central hypoventilation syndrome (CCHS) represents the extreme manifestation of autonomic nervous system dysregulation (ANSD) with the hallmark of disordered respiratory control. The age of initial recognition of CCHS ranges from neonatal onset (i.e., in the first 30 days of life) to (less commonly) later onset (from 1 month to adulthood). Neonatal-onset CCHS is characterized by apparent hypoventilation with monotonous respiratory rates and shallow breathing either during sleep only or while awake as well as asleep; ANSD including decreased heart rate beat-to-beat variability and sinus pauses; altered temperature regulation; and altered pupillary response to light. Some children have altered development of neural crest-derived structures (i.e., Hirschsprung disease, altered esophageal motility/dysphagia, and severe constipation even in the absence of Hirschsprung disease) and/or tumors of neural crest origin (neuroblastoma, ganglioneuroma, and ganglioneuroblastoma). Neurocognitive delay is variable, and possibly influenced by cyanotic breath holding, prolonged sinus pauses, need for 24-hour/day artificial ventilation, and seizures. Later-onset CCHS is characterized by alveolar hypoventilation during sleep and attenuated manifestations of ANSD., The diagnosis of CCHS is established in a proband with suggestive findings and a heterozygous PHOX2B pathogenic variant identified on molecular genetic testing., Treatment of manifestations: Management by multidisciplinary specialists, including pediatric pulmonology, sleep medicine, cardiology, oncology, ophthalmology, gastroenterology, neurodevelopmental psychology, and neurology, is recommended. The treatment goals for CCHS are to secure the airway and to use chronic artificial ventilatory support at home to compensate for the hypoventilation and the altered/absent ventilatory responses to hypoxemia and hypercarbia. Prolonged transient asystoles that may present as syncope and/or staring spells and are of significant duration (\u22653.0 seconds) may warrant placement of a cardiac pacemaker; abnormal pupillary reactivity may necessitate protective eye wear given the amount of light exposure in daily life from LED lights, and screen time in educational settings, computer-based work environments, and mobile devices. Other findings treated as per standard practice include Hirschsprung disease and other gastrointestinal motility issues; tumors of neural crest origin; and cognitive impairment/delay. Surveillance: Assess every six months for the first three years, then annually thereafter: (1) in a pediatric respiratory physiology laboratory spontaneous breathing awake (in varied age-appropriate activities of daily living during the daytime and before sleep) and asleep, with recording of respiratory inductance plethysmography of the chest and abdomen, hemoglobin saturation with pulse waveform, end-tidal carbon dioxide level with visible waveform, electrocardiogram, blood pressure, cerebral regional blood flow/oxygenation, and appropriate sleep state staging measures; (2) hemoglobin/hematocrit and reticulocyte count for polycythemia; (3) 72-hour Holter recording for abrupt, prolonged asystoles; (4) echocardiogram changes consistent with right ventricular hypertrophy and cor pulmonale; (5) neurocognitive assessment/educational needs; and (6) comprehensive age-appropriate noninvasive autonomic testing. Agents/circumstances to avoid: Swimming and breath-holding contests (risk of asphyxia, death); alcohol (respiratory depression), recreational drugs (varied effects including death), and prescription as well as non-prescription medications/sedatives/anesthetics that could induce respiratory depression. Evaluation of relatives at risk: It is appropriate to clarify the genetic status of parents, sibs, and offspring of an individual with CCHS in order to identify as early as possible family members who would benefit from prompt initiation of treatment, surveillance, and awareness of agents/circumstances to avoid., CCHS is typically inherited in an autosomal dominant manner (CCHS caused by biallelic reduced penetrance PHOX2B pathogenic variants has been reported in two families). The majority of affected individuals have the disorder as the result of a de novo pathogenic variant. Somatic/germline mosaicism is present in 5%-25% of asymptomatic parents. If a parent of the proband is known to be heterozygous for the PHOX2B pathogenic variant identified in the proband, the risk to the sibs of inheriting the pathogenic variant is 50%. Once the PHOX2B pathogenic variant has been identified in an affected family member, prenatal testing for a pregnancy at increased risk and preimplantation genetic testing are possible (because of the high frequency of parental mosaicism in CCHS, a fetus should be considered at risk for CCHS even if the PHOX2B pathogenic variant detected in the proband was not identified in either parent).",
+ "language": "eng",
+ "note": "PMID: 20301600\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1427"
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+ "manubot_success": false,
+ "link": "https://omim.org/entry/607136",
+ "note": "WARNING: Manubot does not support url:https://omim.org/entry/607136. Skipping"
+},
+{
+ "id": "omim:187500",
+ "manubot_success": false,
+ "link": "https://omim.org/entry/187500",
+ "note": "WARNING: Manubot does not support url:https://omim.org/entry/187500. Skipping"
+},
+{
+ "id": "omim:613267",
+ "manubot_success": false,
+ "link": "https://omim.org/entry/613267",
+ "note": "WARNING: Manubot does not support url:https://omim.org/entry/613267. Skipping"
+},
+{
+ "id": "omim:619216",
+ "manubot_success": false,
+ "link": "https://omim.org/entry/619216",
+ "note": "WARNING: Manubot does not support url:https://omim.org/entry/619216. Skipping"
+},
+{
+ "id": "omim:600223",
+ "manubot_success": false,
+ "link": "https://omim.org/entry/600223",
+ "note": "WARNING: Manubot does not support url:https://omim.org/entry/600223. Skipping"
+},
+{
+ "id": "omim:314390",
+ "manubot_success": false,
+ "link": "https://omim.org/entry/314390",
+ "note": "WARNING: Manubot does not support url:https://omim.org/entry/314390. Skipping"
+},
+{
+ "id": "omim:616181",
+ "manubot_success": false,
+ "link": "https://omim.org/entry/616181",
+ "note": "WARNING: Manubot does not support url:https://omim.org/entry/616181. Skipping"
+},
+{
+ "id": "malacard:KNS007",
+ "manubot_success": false,
+ "link": "https://www.malacards.org/card/KNS007",
+ "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.malacards.org/card/KNS007']' timed out after 3 seconds"
+},
+{
+ "id": "genereviews:NBK1491",
+ "manubot_success": false,
+ "link": "https://www.ncbi.nlm.nih.gov/books/NBK1491",
+ "note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1491']' timed out after 3 seconds"
+},
{
"id": "genereviews:NBK1466",
"manubot_success": false,
@@ -157626,31 +157631,26 @@
"link": "https://www.ncbi.nlm.nih.gov/books/NBK1126",
"note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'url:https://www.ncbi.nlm.nih.gov/books/NBK1126']' timed out after 3 seconds"
},
-{
- "id": "genereviews:NBK1427",
- "manubot_success": true,
- "link": "http://www.ncbi.nlm.nih.gov/books/NBK1427/",
- "title": "Congenital Central Hypoventilation Syndrome",
- "type": "chapter",
- "doi": "",
- "authors": [
- ["Debra E.", "Weese-Mayer"],
- ["Casey M.", "Rand"],
- ["Ilya", "Khaytin"],
- ["Susan M.", "Slattery"],
- ["Kai Lee", "Yap"],
- ["Mary L.", "Marazita"],
- ["Elizabeth M.", "Berry-Kravis"]
- ],
- "publisher": "GeneReviews\u00ae",
- "issn": "",
- "date": "1993-01-01",
- "abstract": "Congenital central hypoventilation syndrome (CCHS) represents the extreme manifestation of autonomic nervous system dysregulation (ANSD) with the hallmark of disordered respiratory control. The age of initial recognition of CCHS ranges from neonatal onset (i.e., in the first 30 days of life) to (less commonly) later onset (from 1 month to adulthood). Neonatal-onset CCHS is characterized by apparent hypoventilation with monotonous respiratory rates and shallow breathing either during sleep only or while awake as well as asleep; ANSD including decreased heart rate beat-to-beat variability and sinus pauses; altered temperature regulation; and altered pupillary response to light. Some children have altered development of neural crest-derived structures (i.e., Hirschsprung disease, altered esophageal motility/dysphagia, and severe constipation even in the absence of Hirschsprung disease) and/or tumors of neural crest origin (neuroblastoma, ganglioneuroma, and ganglioneuroblastoma). Neurocognitive delay is variable, and possibly influenced by cyanotic breath holding, prolonged sinus pauses, need for 24-hour/day artificial ventilation, and seizures. Later-onset CCHS is characterized by alveolar hypoventilation during sleep and attenuated manifestations of ANSD., The diagnosis of CCHS is established in a proband with suggestive findings and a heterozygous PHOX2B pathogenic variant identified on molecular genetic testing., Treatment of manifestations: Management by multidisciplinary specialists, including pediatric pulmonology, sleep medicine, cardiology, oncology, ophthalmology, gastroenterology, neurodevelopmental psychology, and neurology, is recommended. The treatment goals for CCHS are to secure the airway and to use chronic artificial ventilatory support at home to compensate for the hypoventilation and the altered/absent ventilatory responses to hypoxemia and hypercarbia. Prolonged transient asystoles that may present as syncope and/or staring spells and are of significant duration (\u22653.0 seconds) may warrant placement of a cardiac pacemaker; abnormal pupillary reactivity may necessitate protective eye wear given the amount of light exposure in daily life from LED lights, and screen time in educational settings, computer-based work environments, and mobile devices. Other findings treated as per standard practice include Hirschsprung disease and other gastrointestinal motility issues; tumors of neural crest origin; and cognitive impairment/delay. Surveillance: Assess every six months for the first three years, then annually thereafter: (1) in a pediatric respiratory physiology laboratory spontaneous breathing awake (in varied age-appropriate activities of daily living during the daytime and before sleep) and asleep, with recording of respiratory inductance plethysmography of the chest and abdomen, hemoglobin saturation with pulse waveform, end-tidal carbon dioxide level with visible waveform, electrocardiogram, blood pressure, cerebral regional blood flow/oxygenation, and appropriate sleep state staging measures; (2) hemoglobin/hematocrit and reticulocyte count for polycythemia; (3) 72-hour Holter recording for abrupt, prolonged asystoles; (4) echocardiogram changes consistent with right ventricular hypertrophy and cor pulmonale; (5) neurocognitive assessment/educational needs; and (6) comprehensive age-appropriate noninvasive autonomic testing. Agents/circumstances to avoid: Swimming and breath-holding contests (risk of asphyxia, death); alcohol (respiratory depression), recreational drugs (varied effects including death), and prescription as well as non-prescription medications/sedatives/anesthetics that could induce respiratory depression. Evaluation of relatives at risk: It is appropriate to clarify the genetic status of parents, sibs, and offspring of an individual with CCHS in order to identify as early as possible family members who would benefit from prompt initiation of treatment, surveillance, and awareness of agents/circumstances to avoid., CCHS is typically inherited in an autosomal dominant manner (CCHS caused by biallelic reduced penetrance PHOX2B pathogenic variants has been reported in two families). The majority of affected individuals have the disorder as the result of a de novo pathogenic variant. Somatic/germline mosaicism is present in 5%-25% of asymptomatic parents. If a parent of the proband is known to be heterozygous for the PHOX2B pathogenic variant identified in the proband, the risk to the sibs of inheriting the pathogenic variant is 50%. Once the PHOX2B pathogenic variant has been identified in an affected family member, prenatal testing for a pregnancy at increased risk and preimplantation genetic testing are possible (because of the high frequency of parental mosaicism in CCHS, a fetus should be considered at risk for CCHS even if the PHOX2B pathogenic variant detected in the proband was not identified in either parent).",
- "language": "eng",
- "note": "PMID: 20301600\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1427"
-},
{
"id": "isbn:978-3-031-66932-3",
"manubot_success": false,
"note": "WARNING: Manubot could not generate citation: Command '['manubot', 'cite', 'isbn:978-3-031-66932-3']' timed out after 3 seconds"
+},
+{
+ "id": "pmid:25101480",
+ "manubot_success": false,
+ "link": "https://pubmed.ncbi.nlm.nih.gov/25101480",
+ "note": "WARNING: Couldn't parse Manubot response: list index out of range"
+},
+{
+ "id": "pmid:29939637",
+ "manubot_success": false,
+ "link": "https://pubmed.ncbi.nlm.nih.gov/29939637",
+ "note": "WARNING: Couldn't parse Manubot response: list index out of range"
+},
+{
+ "id": "pmid:39666847",
+ "manubot_success": false,
+ "link": "https://pubmed.ncbi.nlm.nih.gov/39666847",
+ "note": "WARNING: Couldn't parse Manubot response: list index out of range"
}]
\ No newline at end of file
diff --git a/data/STRchive-loci.json b/data/STRchive-loci.json
index be8f38ee..6e82f7fc 100644
--- a/data/STRchive-loci.json
+++ b/data/STRchive-loci.json
@@ -72,12 +72,12 @@
"stop_hg19": 147582273,
"start_t2t": 146765190,
"stop_t2t": 146765342,
- "disease": "Fragile X syndrome, FRAXE type",
+ "disease": "Intellectual developmental disorder, Fragile X intellectual disability",
"inheritance": ["XR"],
- "disease_description": "A nonsyndromic X-linked mental retardation (NS-XLMR) characterized by mild intellectual deficit. FRAXE is the most common form of NS-XLMR [@mondo:0010659].",
- "hpo_terms": null,
+ "disease_description": "A nonsyndromic X-linked intellectual development disorder characterized by mild intellectual deficit. FRAXE is the most common form of non-syndromic X-linked disability [@mondo:0010659].",
+ "hpo_terms": ["HP:0000718 Aggressive behavior", "HP:0000713 Agitation", "HP:0000729 Autistic behavior", "HP:0002312 Clumsiness", "HP:0000722 Compulsive behaviors", "HP:0000750 Delayed speech and language development", "HP:0001249 Intellectual disability"],
"prevalence": "2/50000",
- "prevalence_details": "1-4/100,000 males [@url:medlineplus.gov/genetics/condition/fragile-xe-syndrome]; 1/50-100,000 males, more than 50 families [@pmid:11246464]. Found in populations around the globe, including in the UK, US, Canada, Taiwan, Germany, Greece, Cyprus, Spain, and Finland [@pmid:11246464].",
+ "prevalence_details": "1-4/100,000 males [@url:medlineplus.gov/genetics/condition/fragile-xe-syndrome]; 1/50-100,000 males, more than 50 families 11246464]. Found in populations around the globe, including in the UK, US, Canada, Taiwan, Germany, Greece, Cyprus, Spain, and Finland [@pmid:11246464].",
"age_onset": "Typical: 2-10 [@pmid:11246464]. Range: 1-10; developmental delays without physical features can make onset difficult to detect until schooling [@omim:309548].",
"age_onset_min": 1.0,
"age_onset_max": 10.0,
@@ -926,8 +926,8 @@
"benign_min": 2,
"benign_max": 23,
"intermediate_min": 24,
- "intermediate_max": 60,
- "pathogenic_min": 251,
+ "intermediate_max": 30,
+ "pathogenic_min": 31,
"pathogenic_max": 4088,
"motif_len": 6,
"ref_copies": 10.8,
@@ -1634,10 +1634,10 @@
"gene_strand": "-",
"reference_motif_reference_orientation": ["GAA"],
"pathogenic_motif_reference_orientation": ["GAA"],
- "benign_motif_reference_orientation": ["GAAGGA", "GAAGAAGAAGAAGCA"],
+ "benign_motif_reference_orientation": ["GGA", "GCA"],
"unknown_motif_reference_orientation": [],
"pathogenic_motif_gene_orientation": ["CTT"],
- "benign_motif_gene_orientation": ["CCTTCT", "CTGCTTCTTCTTCTT"],
+ "benign_motif_gene_orientation": ["CCT", "CTG"],
"unknown_motif_gene_orientation": [],
"locus_structure": [],
"benign_min": 8,
@@ -1679,7 +1679,7 @@
"stop_t2t": 146176769,
"disease": "Fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1",
"inheritance": ["XD"],
- "disease_description": "A genetic syndrome caused by mutations in the FMR1 gene which is responsible for the expression of the fragile X mental retardation 1 protein. This protein participates in neural development. This syndrome is manifested with mental, emotional, behavioral, physical, and learning disabilities.; Any primary ovarian failure in which the cause of the disease is a mutation in the FMR1 gene.; Fragile X-associated tremor/ataxia syndrome (FXTAS) is a rare neurodegenerative disorder characterized by adult-onset progressive intention tremor and gait ataxia [@mondo:0010383; @mondo:0010706; @mondo:0010382].",
+ "disease_description": "A genetic syndrome caused by mutations in the FMR1 gene which is responsible for the expression of the fragile X messenger ribonucleoprotein 1 (FMR1) protein. This protein participates in neural development. This syndrome is manifested with mental, emotional, behavioral, physical, and learning disabilities.; Any primary ovarian failure in which the cause of the disease is a mutation in the FMR1 gene.; Fragile X-associated tremor/ataxia syndrome (FXTAS) is a rare neurodegenerative disorder characterized by adult-onset progressive intention tremor and gait ataxia [@mondo:0010383; @mondo:0010706; @mondo:0010382].",
"hpo_terms": null,
"prevalence": "14/100000",
"prevalence_details": "Incidence of full mutation in males 19/100,000; prevalence 14/100,000 [@genereviews:NBK1384]. Female prevalence 9/100,000 [@pmid:24700618]. Known carrier frequency is approximately 300-500/100,000 but detected was 11/100,000 [@pmid:29100084]. FXS prevalence 1:7000 males, 1:11,000 females; FX premutation carriers 1:290-855 males, 1:148-300 females [@isbn:978-3-031-66932-3]. Found worldwide [@genereviews:NBK1384]. In Thailand, 1 in 600 women carry a premutation, and 1 in 400 carry a 'gray zone' allele [@pmid:39320553].",
@@ -1688,9 +1688,9 @@
"age_onset_max": 78.0,
"typ_age_onset_min": 1.0,
"typ_age_onset_max": 65.0,
- "details": "Intermediate or 'gray zone' occur at 45-54 alleles and may be unstable enough to expand into the premutation range, as well as associate with parkinsonism [@pmid:32463542; @genereviews:NBK1384]. FXTAS/POI occurs at 55-200 repeats, FXS >200, late onset; AGG and CTG interruptions documented [@genereviews:NBK1384; @pmid:29868108].",
+ "details": "Intermediate or 'gray zone' occur at 45-54 alleles and may be unstable enough to expand into the premutation range, as well as associate with parkinsonism [@pmid:32463542; @genereviews:NBK1384]. FXTAS/POI occurs at 55-200 repeats, FXS >200, late onset; AGG and CTG interruptions documented [@genereviews:NBK1384; @pmid:29868108]. Women with the premutation have been reported showing episodic memory deficits, similar to those seen in AD [@pmid:41555826].",
"mechanism": "LoF/GoF",
- "mechanism_detail": "Loss of function via transcriptional silencing in FXS, RNA gain of function in FXTAS/FXPOI [@pmid:16205714; @pmid:36169768].",
+ "mechanism_detail": "Loss of function via transcriptional silencing in FXS, RNA gain of function in FXTAS/FXPOI [@pmid:16205714; @pmid:36169768]. *PRKGG* appears to modulate neurotoxicity [@pmid:41507195].",
"year": "1992 [@pmid:1605194]; causative gene discovered in 1991 [@pmid:1710175]",
"location_in_gene": "5' UTR",
"gene_strand": "+",
@@ -1884,9 +1884,9 @@
"age_onset_max": 70.0,
"typ_age_onset_min": 20.0,
"typ_age_onset_max": 34.0,
- "details": "Benign repeats range from absent [@gnomad:GIPC1] to 32 [@genereviews:NBK535148], while pathogenic alleles range from 73-164 repeats [@pmid:38876750; @genereviews:NBK535148]. Intermediate alleles have undetermined significance but may represent a phenotypic spectrum [@pmid:32413282]. Interruptions documented: CGA [@pmid:35245110]. Interruptions proposed but not confirmed in primary literature: TCG/CCT/TTG [@pmid:38467784].",
+ "details": "Benign repeats range from absent [@gnomad:GIPC1] to 32 [@genereviews:NBK535148], while pathogenic alleles range from 73-164 repeats [@pmid:38876750; @genereviews:NBK535148]. Findings suggest that alternative initiation sites and an upstream CTG codon serve as the initiation site for RAN translation [@pmid:41121761]. Intermediate alleles have undetermined significance but may represent a phenotypic spectrum [@pmid:32413282]. Interruptions documented: CGA [@pmid:35245110]. Interruptions proposed but not confirmed in primary literature: TCG/CCT/TTG [@pmid:38467784].",
"mechanism": "LoF/GoF?",
- "mechanism_detail": "RNA mediated toxicity hypothesized [@omim:618940], still unknown [@pmid:36169768].",
+ "mechanism_detail": "Findings suggest that the mechanism is likely not LoF, but the mechanism is otherwise unknown [@pmid:41121761]. This expansion appears to be predominantly RAN translated into a toxic protein [@pmid:41121761]. This protein has been reported to impair cell proliferation, induce cytotoxicity and apoptosis in multiple cell lines, and caused phenotypic defects in a zebrafish model [@pmid:41121761].",
"year": "2020 [@pmid:32413282]",
"location_in_gene": "5' UTR",
"gene_strand": "-",
@@ -2838,9 +2838,9 @@
"stop_hg19": 145209354,
"start_t2t": 148519695,
"stop_t2t": 148519738,
- "disease": "Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3",
+ "disease": "Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3, hereditary essential tremor type 6",
"inheritance": ["AD"],
- "disease_description": "Neuronal intranuclear inclusion disease (NIID) is a very rare multisystem neurodegenerative disorder characterized by the presence of eosinophilic intranuclear inclusions in neuronal and glial cells, and neuronal loss [@mondo:0011327].",
+ "disease_description": "Neuronal intranuclear inclusion disease (NIID) is a very rare multisystem neurodegenerative disorder characterized by the presence of eosinophilic intranuclear inclusions in neuronal and glial cells, and neuronal loss [@mondo:0011327]. Due to overlapping phenotypes and the shared locus, it is unclear whether these four diseases are comorbid, synonymous, or entirely separate.",
"hpo_terms": null,
"prevalence": null,
"prevalence_details": ">400 patients reported in literature [@pmid:37371433]. Found in individuals of East Asian ancestry [@pmid:38876750].",
@@ -2851,7 +2851,7 @@
"typ_age_onset_max": 70.0,
"details": "Benign alleles are less than 38 repeats, while pathogenic alleles contain 66+ repeats [@genereviews:NBK535148]. Intermediate alleles may be associated with a phenotypic spectrum, and even pathogenic cases can have variable phenotype [@pmid:39055960; @pmid:39496005]: NOTCH2NLC expansions have been linked Alzheimer's disease and Parkinson's disease, leading to a potential role in NIID-related disorders [@pmid:31178126]. Age of onset inversely related to allele size [@pmid:38377026]. Motif variation in controls: (AGG)(CGG)n(AGG)0-3(CGG)0-2. GGA and AGC interruptions may influence phenotype [@pmid:34718964]. Interruptions documented: GGA, GGG [@pmid:35245110]; ACCGAGAAGATGCCCGCCCTGC interruption proposed but not confirmed [@pmid:38467784]. Detection may be challenging due to parology between genes: C253572.1, NOTCH2, NOTCH2NL, NBPF14, NBPF19.",
"mechanism": "GoF",
- "mechanism_detail": "Polyglycine expansion; may relate to methylation or RNA pathogenicity [@omim:603472; @pmid:36169768; @pmid:38467784]. The polyglycine-containing protein sequesters a key subunit of transcription factor NF-κB in nuclear inclusions, leading to impaired autophagy [@doi:10.1186/s12964-025-02079-1].",
+ "mechanism_detail": "Polyglycine expansion; may relate to methylation or RNA pathogenicity [@omim:603472; @pmid:36169768; @pmid:38467784]. The polyglycine-containing protein sequesters a key subunit of transcription factor NF-κB in nuclear inclusions, leading to impaired autophagy [@doi:10.1186/s12964-025-02079-1]. Tau pathology is evident, changes in p-tau levels and tau deposition have been reported [@pmid:41539185].",
"year": "2019 [@pmid:31332380]",
"location_in_gene": "5' UTR",
"gene_strand": "+",
@@ -3026,7 +3026,7 @@
"stop_t2t": 41719805,
"disease": "Congenital central hypoventilation syndrome",
"inheritance": ["AD"],
- "disease_description": "A rare disease due to a severely impaired central autonomic control of breathing and dysfunction of the autonomous nervous system. The incidence is estimated to be at 1 of 200 000 livebirths. A heterozygous mutation of PHOX-2B gene is found in 90% of the patients. Association with a Hirschsprung's disease is observed in 16% of the cases (adapted from Mondo) [@mondo:0800026].",
+ "disease_description": "A rare disease due to a severely impaired central autonomic control of breathing and dysfunction of the autonomous nervous system. The incidence is estimated to be at 1 of 200 000 livebirths. A heterozygous mutation of PHOX-2B gene is found in 90% of the patients. Association with a Hirschsprung's disease is observed in 16% of the cases (adapted from Mondo) [@mondo:0800026]. Hyperinsulinism has been observed in patients [@pmid:41531556].",
"hpo_terms": null,
"prevalence": null,
"prevalence_details": "Incidence is 1:148000-200000 births (Estimated, may include mild/undiagnosed or be overestimated globally) [@genereviews:NBK1427]. Rare, but reported worldwide [@pmid:15121777].",
@@ -3583,12 +3583,12 @@
"location_in_gene": "Intron 2",
"gene_strand": "-",
"reference_motif_reference_orientation": ["AAAAG"],
- "pathogenic_motif_reference_orientation": ["AAGGG", "ACAGG", "AGGGC", "AAGGC", "AGAGG"],
- "benign_motif_reference_orientation": ["AAAAG", "AAAGG", "AAGAG", "AAAGGG"],
- "unknown_motif_reference_orientation": ["AAAAA", "AAAAC", "AACGG", "AAGAC", "AAGGT", "AGAAC", "AGGGG", "GAAAC", "GGGAC", "GTGAG", "AAAAGA", "AAAGGA", "GGAAAG"],
- "pathogenic_motif_gene_orientation": ["CCCTT", "CCTGT", "CCCTG", "CCTTG", "CCTCT"],
- "benign_motif_gene_orientation": ["CTTTT", "CCTTT", "CTCTT", "CCCTTT"],
- "unknown_motif_gene_orientation": ["TTTTT", "GTTTT", "CCGTT", "CTTGT", "ACCTT", "CTGTT", "CCCCT", "CGTTT", "CCCGT", "ACCTC", "CTTTTT", "CCTTTT", "CCCTTT"],
+ "pathogenic_motif_reference_orientation": ["AAGGG", "ACAGG", "AAAGG", "AGGGC"],
+ "benign_motif_reference_orientation": ["AAAAG", "AAAGGG"],
+ "unknown_motif_reference_orientation": ["AAAAA", "AAAAC", "AACGG", "AAGAC", "AAGGT", "AGGGG", "AAGAG", "AAAAGG", "AAACG", "AACAG", "AGGTG", "ACGGG", "AAAAAG", "AAGGC"],
+ "pathogenic_motif_gene_orientation": ["CCCTT", "CCTGT", "CCTTT", "CCCTG"],
+ "benign_motif_gene_orientation": ["CTTTT", "CCCTTT"],
+ "unknown_motif_gene_orientation": ["TTTTT", "GTTTT", "CCGTT", "CTTGT", "ACCTT", "CCCCT", "CTCTT", "CCTTTT", "CGTTT", "CTGTT", "ACCTC", "CCCGT", "CTTTTT", "CCTTG"],
"locus_structure": [
{
"motif": "AAAAG",
@@ -3823,8 +3823,8 @@
"additional_literature": ["pmid:41426430", "pmid:41219789", "pmid:38961870", "pmid:38467733", "pmid:38059543", "pmid:37592133", "pmid:36740228", "pmid:36622139", "pmid:36092952", "pmid:33791773", "pmid:33721773", "pmid:33681653", "pmid:33501421", "pmid:33040085", "pmid:32973343", "pmid:32203200", "pmid:32194077", "pmid:32174879", "pmid:31664039", "pmid:31483537", "pmid:30559482", "pmid:30351492", "pmid:30194086"]
},
{
- "id": "XLMR_SOX3",
- "disease_id": "XLMR",
+ "id": "XLID_SOX3",
+ "disease_id": "XLID, PHP",
"gene": "SOX3",
"chrom": "chrX",
"start_hg38": 140504316,
@@ -3833,7 +3833,7 @@
"stop_hg19": 139586526,
"start_t2t": 138816203,
"stop_t2t": 138816248,
- "disease": "X-linked panhypopituitarism ; X-linked mental retardation with isolated growth hormone",
+ "disease": "X-linked intellectual developmental disorder with isolated growth hormone deficiency; X-linked panhypopituitarism",
"inheritance": ["XR"],
"disease_description": "X-linked isolated growth hormone deficiency (GHD) or combined pituitary hormone deficiency (CPHD) patients with or without intellectual disability [@pmid:24346842].",
"hpo_terms": null,
diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed
index 192ac6d9..b5c535c4 100644
--- a/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed
+++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.TRGT.bed
@@ -13,7 +13,7 @@ chr3 131917482 131917635 ID=DM2_CNBP;MOTIFS=CAGG,CAGA,CA;STRUC=
chr3 141687011 141687054 ID=BPES_FOXL2;MOTIFS=NGC;STRUC=
chr3 186521667 186521706 ID=FAME4_YEATS2;MOTIFS=TTTTA,TTTCA;STRUC=
chr4 3073603 3073723 ID=HD_HTT;MOTIFS=CAG,CCG;STRUC=
-chr4 39318077 39318136 ID=CANVAS_RFC1;MOTIFS=AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAGG,AAGAG,AAAGGG;STRUC=
+chr4 39318077 39318136 ID=CANVAS_RFC1;MOTIFS=AAAAG,AAGGG,ACAGG,AAAGG,AGGGC,AAAGGG;STRUC=
chr4 41719745 41719805 ID=CCHS_PHOX2B;MOTIFS=GCN;STRUC=
chr4 162693303 162693405 ID=FAME7_RAPGEF2;MOTIFS=TTTTA,TTTCA;STRUC=
chr5 10295525 10295593 ID=FAME3_MARCHF6;MOTIFS=TTTTA,TTTCA;STRUC=
@@ -38,7 +38,7 @@ chr12 111575873 111575940 ID=SCA2_ATXN2;MOTIFS=CTG;STRUC=
chr12 123532573 123532603 ID=OPDM4_RILPL1;MOTIFS=GGC;STRUC=
chr13 69361213 69361270 ID=SCA8_ATXN8OS;MOTIFS=CTA,CTG;STRUC=
chr13 99196358 99196404 ID=HPE5_ZIC2;MOTIFS=GCN;STRUC=
-chr13 101377549 101377792 ID=SCA27B_FGF14;MOTIFS=GAA,GAAGGA,GAAGAAGAAGAAGCA;STRUC=
+chr13 101377549 101377792 ID=SCA27B_FGF14;MOTIFS=GAA,GGA,GCA;STRUC=
chr14 17522488 17522519 ID=OPMD_PABPN1;MOTIFS=GCN;STRUC=
chr14 86300519 86300603 ID=SCA3_ATXN3;MOTIFS=CTG;STRUC=
chr15 20458510 20458536 ID=ALS1_NIPA1;MOTIFS=GCG;STRUC=
@@ -70,6 +70,6 @@ chrX 30882677 30882751 ID=DMD_DMD;MOTIFS=TTC,T;STRUC=
chrX 65975147 65975250 ID=SBMA_AR;MOTIFS=GCA;STRUC=
chrX 69887153 69887230 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC=
chrX 135876774 135876804 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC=
-chrX 138816203 138816248 ID=XLMR_SOX3;MOTIFS=NGC;STRUC=
+chrX 138816203 138816248 ID=XLID_SOX3;MOTIFS=NGC;STRUC=
chrX 146176677 146176769 ID=FXS_FMR1;MOTIFS=CGG;STRUC=
chrX 146765190 146765342 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=
diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed
index 86e42039..15894f9a 100644
--- a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed
+++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed
@@ -82,6 +82,6 @@ chrX 30882743 30882751 T 1 DMD_DMD_flank
chrX 65975147 65975250 GCA 3 SBMA_AR
chrX 69887153 69887230 AGAGGG 6 XDP_TAF1
chrX 135876774 135876804 GCN 3 VACTERLX_ZIC3
-chrX 138816203 138816248 NGC 3 XLMR_SOX3
+chrX 138816203 138816248 NGC 3 XLID_SOX3
chrX 146176677 146176769 CGG 3 FXS_FMR1
chrX 146765190 146765342 GCC 3 FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz
index abee0b5a..6311b1db 100644
Binary files a/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz and b/data/catalogs/STRchive-disease-loci.T2T-chm13.atarva.bed.gz differ
diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed
index 41339dcd..a9e41721 100644
--- a/data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed
+++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.general.bed
@@ -2,7 +2,7 @@
chr1 870158 870178 HMNR7_VWA1 VWA1 GGCGCGGAGC GGCGCGGAGC 1 AR Neuronopathy, distal hereditary motor, autosomal recessive 7
chr1 57245935 57245973 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar ataxia type 37
chr1 94266544 94266567 OPDM5_ABCD3 ABCD3 GCC GCC 118 AD Oculopharyngodistal myopathy type 5
-chr1 148519695 148519738 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3
+chr1 148519695 148519738 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3, hereditary essential tremor type 6
chr1 154328121 154330802 ADTKD_MUC1 MUC1 GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG GCCCACGGTGTCACCTCGGCCCCGGACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCA None AD Autosomal dominant tubulointerstitial kidney disease
chr1 155728131 155728159 NME_NAXE NAXE GGGCC GGGCC 200 AR NAXE-related mitochondrial encephalopathy
chr2 96703674 96703732 FAME2_STARD7 STARD7 AAAAT AAATG 274 AD Familial adult myoclonic epilepsy 2
@@ -14,7 +14,7 @@ chr3 131917482 131917557 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic dystrophy type 2
chr3 141687011 141687054 BPES_FOXL2 FOXL2 NGC NGC 15 AD,AR Blepharophimosis, epicanthus inversus, and ptosis
chr3 186521667 186521706 FAME4_YEATS2 YEATS2 TTTTA TTTCA 1000 AD Familial adult myoclonic epilepsy 4
chr4 3073603 3073687 HD_HTT HTT CAG CAG 36 AD Huntington disease
-chr4 39318077 39318136 CANVAS_RFC1 RFC1 AAAAG AAGGG,ACAGG,AGGGC,AAGGC,AGAGG 400 AR Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome
+chr4 39318077 39318136 CANVAS_RFC1 RFC1 AAAAG AAGGG,ACAGG,AAAGG,AGGGC 400 AR Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome
chr4 41719745 41719805 CCHS_PHOX2B PHOX2B GCN GCN 26 AD Congenital central hypoventilation syndrome
chr4 162693303 162693405 FAME7_RAPGEF2 RAPGEF2 TTTTA TTTCA 60 AD Familial adult myoclonic epilepsy type 7
chr5 10295525 10295593 FAME3_MARCHF6 MARCHF6 TTTTA TTTCA 650 AD Familial adult myoclonic epilepsy type 3
@@ -28,7 +28,7 @@ chr7 27335912 27335954 HFG_HOXA13-I HOXA13 NGC NGC 22 AD Hand-foot-genital syndr
chr7 56047900 56047939 FRA7A_ZNF713 ZNF713 GCG GCG 450 AD Autism spectrum disorder associated with fragile site FRA7A
chr8 105716409 105716441 OPDM1_LRP12 LRP12 CGC CGC 85 AD Oculopharyngodistal myopathy type 1
chr8 119495247 119495353 FAME1_SAMD12 SAMD12 TAAAA TGAAA 105 AD Familial adult myoclonic epilepsy type 1
-chr9 27584063 27584155 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 251 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
+chr9 27584063 27584155 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 31 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
chr9 81210834 81210861 FRDA_FXN FXN GAA GAA 56 AR Friedreich ataxia
chr9 142886568 142886595 HSAN-VIII_PRDM12 PRDM12 GCC GCC 18 AR Hereditary sensory and autonomic neuropathy type VIII
chr10 80695718 80695748 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharyngeal myopathy with leukoencephalopathy 1
@@ -71,6 +71,6 @@ chrX 30882677 30882743 DMD_DMD DMD TTC TTC 59 XR Duchenne muscular dystrophy
chrX 65975147 65975250 SBMA_AR AR GCA GCA 38 XR Spinal and bulbar muscular atrophy, Kennedy Disease
chrX 69887153 69887230 XDP_TAF1 TAF1 AGAGGG AGAGGG 35 XR X-linked dystonia-parkinsonism (XDP) a.k.a. Dystonia 3, torsion, X-linked (DYT3)
chrX 135876774 135876804 VACTERLX_ZIC3 ZIC3 GCN GCN 12 XR X-linked VACTERL syndrome
-chrX 138816203 138816248 XLMR_SOX3 SOX3 NGC NGC 22 XR X-linked panhypopituitarism ; X-linked mental retardation with isolated growth hormone
+chrX 138816203 138816248 XLID_SOX3 SOX3 NGC NGC 22 XR X-linked intellectual developmental disorder with isolated growth hormone deficiency; X-linked panhypopituitarism
chrX 146176677 146176769 FXS_FMR1 FMR1 CGG CGG 201 XD Fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1
-chrX 146765190 146765342 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type
+chrX 146765190 146765342 FRAXE_AFF2 AFF2 GCC GCC 201 XR Intellectual developmental disorder, Fragile X intellectual disability
diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed
index c36c8a4d..f5b2f6ad 100644
--- a/data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed
+++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.longTR.bed
@@ -13,7 +13,7 @@ chr3 131917483 131917557 CAGG DM2_CNBP
chr3 141687012 141687054 NGC BPES_FOXL2
chr3 186521668 186521706 TTTCA,TTTTA FAME4_YEATS2
chr4 3073604 3073687 CAG HD_HTT
-chr4 39318078 39318136 AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAAG,AAAGG,AAGAG,AAAGGG CANVAS_RFC1
+chr4 39318078 39318136 AAGGG,ACAGG,AAAGG,AGGGC,AAAAG,AAAGGG CANVAS_RFC1
chr4 41719746 41719805 GCN CCHS_PHOX2B
chr4 162693304 162693405 TTTCA,TTTTA FAME7_RAPGEF2
chr5 10295526 10295593 TTTCA,TTTTA FAME3_MARCHF6
@@ -38,7 +38,7 @@ chr12 111575874 111575940 CTG SCA2_ATXN2
chr12 123532574 123532603 GGC OPDM4_RILPL1
chr13 69361244 69361270 CTG SCA8_ATXN8OS
chr13 99196359 99196404 GCN HPE5_ZIC2
-chr13 101377550 101377792 GAA,GAAGGA,GAAGAAGAAGAAGCA SCA27B_FGF14
+chr13 101377550 101377792 GAA,GGA,GCA SCA27B_FGF14
chr14 17522489 17522519 GCN OPMD_PABPN1
chr14 86300520 86300603 CTG SCA3_ATXN3
chr15 20458511 20458536 GCG ALS1_NIPA1
@@ -70,6 +70,6 @@ chrX 30882678 30882743 TTC DMD_DMD
chrX 65975148 65975250 GCA SBMA_AR
chrX 69887154 69887230 AGAGGG XDP_TAF1
chrX 135876775 135876804 GCN VACTERLX_ZIC3
-chrX 138816204 138816248 NGC XLMR_SOX3
+chrX 138816204 138816248 NGC XLID_SOX3
chrX 146176678 146176769 CGG FXS_FMR1
chrX 146765191 146765342 GCC FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed b/data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed
index 2f601147..b5c06f5e 100644
--- a/data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed
+++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.straglr.bed
@@ -80,6 +80,6 @@ chrX 30882743 30882751 T DMD_DMD DMD_DMD_T
chrX 65975147 65975250 GCA SBMA_AR SBMA_AR
chrX 69887153 69887230 AGAGGG XDP_TAF1 XDP_TAF1
chrX 135876774 135876804 GCN VACTERLX_ZIC3 VACTERLX_ZIC3
-chrX 138816203 138816248 NGC XLMR_SOX3 XLMR_SOX3
+chrX 138816203 138816248 NGC XLID_SOX3 XLID_SOX3
chrX 146176677 146176769 CGG FXS_FMR1 FXS_FMR1
chrX 146765190 146765342 GCC FRAXE_AFF2 FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json b/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json
index c24a0a9d..b5e34c0d 100644
--- a/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json
+++ b/data/catalogs/STRchive-disease-loci.T2T-chm13.stranger.json
@@ -393,7 +393,7 @@
"DisplayRU": "GGCCCC",
"Disease": "FTDALS1",
"NormalMax": 23,
- "PathologicMin": 251,
+ "PathologicMin": 31,
"Gene": "C9orf72"
},
{
@@ -961,14 +961,14 @@
"Gene": "ZIC3"
},
{
- "LocusId": "XLMR_SOX3",
+ "LocusId": "XLID_SOX3",
"ReferenceRegion": "chrX:138816203-138816248",
"LocusStructure": "(NGC)*",
"VariantType": "Repeat",
"HGNCId": null,
"InheritanceMode": ["XR"],
"DisplayRU": "NGC",
- "Disease": "XLMR",
+ "Disease": "XLID, PHP",
"NormalMax": 15,
"PathologicMin": 22,
"Gene": "SOX3"
diff --git a/data/catalogs/STRchive-disease-loci.hg19.TRGT.bed b/data/catalogs/STRchive-disease-loci.hg19.TRGT.bed
index ab47340c..257f76ba 100644
--- a/data/catalogs/STRchive-disease-loci.hg19.TRGT.bed
+++ b/data/catalogs/STRchive-disease-loci.hg19.TRGT.bed
@@ -13,7 +13,7 @@ chr3 128891419 128891577 ID=DM2_CNBP;MOTIFS=CAGG,CAGA,CA;STRUC=
chr3 138664861 138664904 ID=BPES_FOXL2;MOTIFS=NGC;STRUC=
chr3 183429975 183430014 ID=FAME4_YEATS2;MOTIFS=TTTTA,TTTCA;STRUC=
chr4 3076603 3076696 ID=HD_HTT;MOTIFS=CAG,CCG;STRUC=
-chr4 39350044 39350103 ID=CANVAS_RFC1;MOTIFS=AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAGG,AAGAG,AAAGGG;STRUC=
+chr4 39350044 39350103 ID=CANVAS_RFC1;MOTIFS=AAAAG,AAGGG,ACAGG,AAAGG,AGGGC,AAAGGG;STRUC=
chr4 41747989 41748049 ID=CCHS_PHOX2B;MOTIFS=GCN;STRUC=
chr4 160263678 160263770 ID=FAME7_RAPGEF2;MOTIFS=TTTTA,TTTCA;STRUC=
chr5 10356455 10356523 ID=FAME3_MARCHF6;MOTIFS=TTTTA,TTTCA;STRUC=
@@ -38,7 +38,7 @@ chr12 112036753 112036823 ID=SCA2_ATXN2;MOTIFS=CTG;STRUC=
chr12 124018267 124018297 ID=OPDM4_RILPL1;MOTIFS=GGC;STRUC=
chr13 70713485 70713561 ID=SCA8_ATXN8OS;MOTIFS=CTA,CTG;STRUC=
chr13 100637702 100637748 ID=HPE5_ZIC2;MOTIFS=GCN;STRUC=
-chr13 102813924 102814076 ID=SCA27B_FGF14;MOTIFS=GAA,GAAGGA,GAAGAAGAAGAAGCA;STRUC=
+chr13 102813924 102814076 ID=SCA27B_FGF14;MOTIFS=GAA,GGA,GCA;STRUC=
chr14 23790681 23790712 ID=OPMD_PABPN1;MOTIFS=GCN;STRUC=
chr14 92537354 92537396 ID=SCA3_ATXN3;MOTIFS=CTG;STRUC=
chr15 23086363 23086389 ID=ALS1_NIPA1;MOTIFS=GCG;STRUC=
@@ -70,6 +70,6 @@ chrX 31302674 31302730 ID=DMD_DMD;MOTIFS=TTC,T;STRUC=
chrX 66765158 66765261 ID=SBMA_AR;MOTIFS=GCA;STRUC=
chrX 70672904 70672981 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC=
chrX 136648985 136649015 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC=
-chrX 139586481 139586526 ID=XLMR_SOX3;MOTIFS=NGC;STRUC=
+chrX 139586481 139586526 ID=XLID_SOX3;MOTIFS=NGC;STRUC=
chrX 146993567 146993629 ID=FXS_FMR1;MOTIFS=CGG;STRUC=
chrX 147582124 147582273 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=
diff --git a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed
index 78f66ecc..9ee8cc08 100644
--- a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed
+++ b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed
@@ -82,6 +82,6 @@ chrX 31302722 31302730 T 1 DMD_DMD_flank
chrX 66765158 66765261 GCA 3 SBMA_AR
chrX 70672904 70672981 AGAGGG 6 XDP_TAF1
chrX 136648985 136649015 GCN 3 VACTERLX_ZIC3
-chrX 139586481 139586526 NGC 3 XLMR_SOX3
+chrX 139586481 139586526 NGC 3 XLID_SOX3
chrX 146993567 146993629 CGG 3 FXS_FMR1
chrX 147582124 147582273 GCC 3 FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz
index 98a3a488..8fbc9ad3 100644
Binary files a/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz and b/data/catalogs/STRchive-disease-loci.hg19.atarva.bed.gz differ
diff --git a/data/catalogs/STRchive-disease-loci.hg19.general.bed b/data/catalogs/STRchive-disease-loci.hg19.general.bed
index 0dddc18d..aed1196a 100644
--- a/data/catalogs/STRchive-disease-loci.hg19.general.bed
+++ b/data/catalogs/STRchive-disease-loci.hg19.general.bed
@@ -2,7 +2,7 @@
chr1 1371178 1371198 HMNR7_VWA1 VWA1 GGCGCGGAGC GGCGCGGAGC 1 AR Neuronopathy, distal hereditary motor, autosomal recessive 7
chr1 57832715 57832793 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar ataxia type 37
chr1 94883977 94884000 OPDM5_ABCD3 ABCD3 GCC GCC 118 AD Oculopharyngodistal myopathy type 5
-chr1 145209323 145209354 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3
+chr1 145209323 145209354 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3, hereditary essential tremor type 6
chr1 155160981 155162030 ADTKD_MUC1 MUC1 GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG GCCCACGGTGTCACCTCGGCCCCGGACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCA None AD Autosomal dominant tubulointerstitial kidney disease
chr1 156561557 156561575 NME_NAXE NAXE GGGCC GGGCC 200 AR NAXE-related mitochondrial encephalopathy
chr2 96862804 96862862 FAME2_STARD7 STARD7 AAAAT AAATG 274 AD Familial adult myoclonic epilepsy 2
@@ -14,7 +14,7 @@ chr3 128891419 128891499 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic dystrophy type 2
chr3 138664861 138664904 BPES_FOXL2 FOXL2 NGC NGC 15 AD,AR Blepharophimosis, epicanthus inversus, and ptosis
chr3 183429975 183430014 FAME4_YEATS2 YEATS2 TTTTA TTTCA 1000 AD Familial adult myoclonic epilepsy 4
chr4 3076603 3076660 HD_HTT HTT CAG CAG 36 AD Huntington disease
-chr4 39350044 39350103 CANVAS_RFC1 RFC1 AAAAG AAGGG,ACAGG,AGGGC,AAGGC,AGAGG 400 AR Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome
+chr4 39350044 39350103 CANVAS_RFC1 RFC1 AAAAG AAGGG,ACAGG,AAAGG,AGGGC 400 AR Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome
chr4 41747989 41748049 CCHS_PHOX2B PHOX2B GCN GCN 26 AD Congenital central hypoventilation syndrome
chr4 160263678 160263770 FAME7_RAPGEF2 RAPGEF2 TTTTA TTTCA 60 AD Familial adult myoclonic epilepsy type 7
chr5 10356455 10356523 FAME3_MARCHF6 MARCHF6 TTTTA TTTCA 650 AD Familial adult myoclonic epilepsy type 3
@@ -28,7 +28,7 @@ chr7 27239543 27239585 HFG_HOXA13-I HOXA13 NGC NGC 22 AD Hand-foot-genital syndr
chr7 55955293 55955332 FRA7A_ZNF713 ZNF713 GCG GCG 450 AD Autism spectrum disorder associated with fragile site FRA7A
chr8 105601198 105601227 OPDM1_LRP12 LRP12 CGC CGC 85 AD Oculopharyngodistal myopathy type 1
chr8 119379051 119379157 FAME1_SAMD12 SAMD12 TAAAA TGAAA 105 AD Familial adult myoclonic epilepsy type 1
-chr9 27573482 27573544 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 251 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
+chr9 27573482 27573544 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 31 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
chr9 71652202 71652220 FRDA_FXN FXN GAA GAA 56 AR Friedreich ataxia
chr9 133556992 133557028 HSAN-VIII_PRDM12 PRDM12 GCC GCC 18 AR Hereditary sensory and autonomic neuropathy type VIII
chr10 81586139 81586160 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharyngeal myopathy with leukoencephalopathy 1
@@ -71,6 +71,6 @@ chrX 31302674 31302722 DMD_DMD DMD TTC TTC 59 XR Duchenne muscular dystrophy
chrX 66765158 66765261 SBMA_AR AR GCA GCA 38 XR Spinal and bulbar muscular atrophy, Kennedy Disease
chrX 70672904 70672981 XDP_TAF1 TAF1 AGAGGG AGAGGG 35 XR X-linked dystonia-parkinsonism (XDP) a.k.a. Dystonia 3, torsion, X-linked (DYT3)
chrX 136648985 136649015 VACTERLX_ZIC3 ZIC3 GCN GCN 12 XR X-linked VACTERL syndrome
-chrX 139586481 139586526 XLMR_SOX3 SOX3 NGC NGC 22 XR X-linked panhypopituitarism ; X-linked mental retardation with isolated growth hormone
+chrX 139586481 139586526 XLID_SOX3 SOX3 NGC NGC 22 XR X-linked intellectual developmental disorder with isolated growth hormone deficiency; X-linked panhypopituitarism
chrX 146993567 146993629 FXS_FMR1 FMR1 CGG CGG 201 XD Fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1
-chrX 147582124 147582273 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type
+chrX 147582124 147582273 FRAXE_AFF2 AFF2 GCC GCC 201 XR Intellectual developmental disorder, Fragile X intellectual disability
diff --git a/data/catalogs/STRchive-disease-loci.hg19.longTR.bed b/data/catalogs/STRchive-disease-loci.hg19.longTR.bed
index 3ba18238..80681770 100644
--- a/data/catalogs/STRchive-disease-loci.hg19.longTR.bed
+++ b/data/catalogs/STRchive-disease-loci.hg19.longTR.bed
@@ -13,7 +13,7 @@ chr3 128891420 128891499 CAGG DM2_CNBP
chr3 138664862 138664904 NGC BPES_FOXL2
chr3 183429976 183430014 TTTCA,TTTTA FAME4_YEATS2
chr4 3076604 3076660 CAG HD_HTT
-chr4 39350045 39350103 AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAAG,AAAGG,AAGAG,AAAGGG CANVAS_RFC1
+chr4 39350045 39350103 AAGGG,ACAGG,AAAGG,AGGGC,AAAAG,AAAGGG CANVAS_RFC1
chr4 41747990 41748049 GCN CCHS_PHOX2B
chr4 160263679 160263770 TTTCA,TTTTA FAME7_RAPGEF2
chr5 10356456 10356523 TTTCA,TTTTA FAME3_MARCHF6
@@ -38,7 +38,7 @@ chr12 112036754 112036823 CTG SCA2_ATXN2
chr12 124018268 124018297 GGC OPDM4_RILPL1
chr13 70713516 70713561 CTG SCA8_ATXN8OS
chr13 100637703 100637748 GCN HPE5_ZIC2
-chr13 102813925 102814076 GAA,GAAGGA,GAAGAAGAAGAAGCA SCA27B_FGF14
+chr13 102813925 102814076 GAA,GGA,GCA SCA27B_FGF14
chr14 23790682 23790712 GCN OPMD_PABPN1
chr14 92537355 92537396 CTG SCA3_ATXN3
chr15 23086364 23086389 GCG ALS1_NIPA1
@@ -70,6 +70,6 @@ chrX 31302675 31302722 TTC DMD_DMD
chrX 66765159 66765261 GCA SBMA_AR
chrX 70672905 70672981 AGAGGG XDP_TAF1
chrX 136648986 136649015 GCN VACTERLX_ZIC3
-chrX 139586482 139586526 NGC XLMR_SOX3
+chrX 139586482 139586526 NGC XLID_SOX3
chrX 146993568 146993629 CGG FXS_FMR1
chrX 147582125 147582273 GCC FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.hg19.straglr.bed b/data/catalogs/STRchive-disease-loci.hg19.straglr.bed
index 9e52fca2..d6b33f29 100644
--- a/data/catalogs/STRchive-disease-loci.hg19.straglr.bed
+++ b/data/catalogs/STRchive-disease-loci.hg19.straglr.bed
@@ -80,6 +80,6 @@ chrX 31302722 31302730 T DMD_DMD DMD_DMD_T
chrX 66765158 66765261 GCA SBMA_AR SBMA_AR
chrX 70672904 70672981 AGAGGG XDP_TAF1 XDP_TAF1
chrX 136648985 136649015 GCN VACTERLX_ZIC3 VACTERLX_ZIC3
-chrX 139586481 139586526 NGC XLMR_SOX3 XLMR_SOX3
+chrX 139586481 139586526 NGC XLID_SOX3 XLID_SOX3
chrX 146993567 146993629 CGG FXS_FMR1 FXS_FMR1
chrX 147582124 147582273 GCC FRAXE_AFF2 FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.hg19.stranger.json b/data/catalogs/STRchive-disease-loci.hg19.stranger.json
index 9da2ed04..7fcafa58 100644
--- a/data/catalogs/STRchive-disease-loci.hg19.stranger.json
+++ b/data/catalogs/STRchive-disease-loci.hg19.stranger.json
@@ -393,7 +393,7 @@
"DisplayRU": "GGCCCC",
"Disease": "FTDALS1",
"NormalMax": 23,
- "PathologicMin": 251,
+ "PathologicMin": 31,
"Gene": "C9orf72"
},
{
@@ -961,14 +961,14 @@
"Gene": "ZIC3"
},
{
- "LocusId": "XLMR_SOX3",
+ "LocusId": "XLID_SOX3",
"ReferenceRegion": "chrX:139586481-139586526",
"LocusStructure": "(NGC)*",
"VariantType": "Repeat",
"HGNCId": null,
"InheritanceMode": ["XR"],
"DisplayRU": "NGC",
- "Disease": "XLMR",
+ "Disease": "XLID, PHP",
"NormalMax": 15,
"PathologicMin": 22,
"Gene": "SOX3"
diff --git a/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed b/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed
index 75c81b02..e1be0ca7 100644
--- a/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed
+++ b/data/catalogs/STRchive-disease-loci.hg38.TRGT.bed
@@ -13,7 +13,7 @@ chr3 129172576 129172734 ID=DM2_CNBP;MOTIFS=CAGG,CAGA,CA;STRUC=
chr3 138946019 138946062 ID=BPES_FOXL2;MOTIFS=NGC;STRUC=
chr3 183712187 183712226 ID=FAME4_YEATS2;MOTIFS=TTTTA,TTTCA;STRUC=
chr4 3074876 3074969 ID=HD_HTT;MOTIFS=CAG,CCG;STRUC=
-chr4 39348424 39348483 ID=CANVAS_RFC1;MOTIFS=AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAGG,AAGAG,AAAGGG;STRUC=
+chr4 39348424 39348483 ID=CANVAS_RFC1;MOTIFS=AAAAG,AAGGG,ACAGG,AAAGG,AGGGC,AAAGGG;STRUC=
chr4 41745972 41746032 ID=CCHS_PHOX2B;MOTIFS=GCN;STRUC=
chr4 159342526 159342618 ID=FAME7_RAPGEF2;MOTIFS=TTTTA,TTTCA;STRUC=
chr5 10356343 10356411 ID=FAME3_MARCHF6;MOTIFS=TTTTA,TTTCA;STRUC=
@@ -38,7 +38,7 @@ chr12 111598949 111599019 ID=SCA2_ATXN2;MOTIFS=CTG;STRUC=
chr12 123533720 123533750 ID=OPDM4_RILPL1;MOTIFS=GGC;STRUC=
chr13 70139353 70139429 ID=SCA8_ATXN8OS;MOTIFS=CTA,CTG;STRUC=
chr13 99985448 99985494 ID=HPE5_ZIC2;MOTIFS=GCN;STRUC=
-chr13 102161574 102161726 ID=SCA27B_FGF14;MOTIFS=GAA,GAAGGA,GAAGAAGAAGAAGCA;STRUC=
+chr13 102161574 102161726 ID=SCA27B_FGF14;MOTIFS=GAA,GGA,GCA;STRUC=
chr14 23321472 23321503 ID=OPMD_PABPN1;MOTIFS=GCN;STRUC=
chr14 92071010 92071052 ID=SCA3_ATXN3;MOTIFS=CTG;STRUC=
chr15 22786677 22786703 ID=ALS1_NIPA1;MOTIFS=GCG;STRUC=
@@ -70,6 +70,6 @@ chrX 31284557 31284613 ID=DMD_DMD;MOTIFS=TTC,T;STRUC=
chrX 67545316 67545419 ID=SBMA_AR;MOTIFS=GCA;STRUC=
chrX 71453054 71453131 ID=XDP_TAF1;MOTIFS=AGAGGG;STRUC=
chrX 137566826 137566856 ID=VACTERLX_ZIC3;MOTIFS=GCN;STRUC=
-chrX 140504316 140504361 ID=XLMR_SOX3;MOTIFS=NGC;STRUC=
+chrX 140504316 140504361 ID=XLID_SOX3;MOTIFS=NGC;STRUC=
chrX 147912049 147912111 ID=FXS_FMR1;MOTIFS=CGG;STRUC=
chrX 148500604 148500753 ID=FRAXE_AFF2;MOTIFS=GCC;STRUC=
diff --git a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed
index 8311febd..a681be25 100644
--- a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed
+++ b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed
@@ -82,6 +82,6 @@ chrX 31284605 31284613 T 1 DMD_DMD_flank
chrX 67545316 67545419 GCA 3 SBMA_AR
chrX 71453054 71453131 AGAGGG 6 XDP_TAF1
chrX 137566826 137566856 GCN 3 VACTERLX_ZIC3
-chrX 140504316 140504361 NGC 3 XLMR_SOX3
+chrX 140504316 140504361 NGC 3 XLID_SOX3
chrX 147912049 147912111 CGG 3 FXS_FMR1
chrX 148500604 148500753 GCC 3 FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz
index 23164d4e..dbffdc3a 100644
Binary files a/data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz and b/data/catalogs/STRchive-disease-loci.hg38.atarva.bed.gz differ
diff --git a/data/catalogs/STRchive-disease-loci.hg38.general.bed b/data/catalogs/STRchive-disease-loci.hg38.general.bed
index 961e3bab..d7aaf199 100644
--- a/data/catalogs/STRchive-disease-loci.hg38.general.bed
+++ b/data/catalogs/STRchive-disease-loci.hg38.general.bed
@@ -2,7 +2,7 @@
chr1 1435798 1435818 HMNR7_VWA1 VWA1 GGCGCGGAGC GGCGCGGAGC 1 AR Neuronopathy, distal hereditary motor, autosomal recessive 7
chr1 57367043 57367121 SCA37_DAB1 DAB1 AAAAT GAAAT 31 AD Spinocerebellar ataxia type 37
chr1 94418421 94418444 OPDM5_ABCD3 ABCD3 GCC GCC 118 AD Oculopharyngodistal myopathy type 5
-chr1 149390802 149390842 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3
+chr1 149390802 149390842 NIID_NOTCH2NLC NOTCH2NLC GGC GGC 66 AD Neuronal intranuclear inclusion disease, Alzheimer disease and parkinsonism phenotype, Oculopharyngodistal myopathy (OPDM) type 3, hereditary essential tremor type 6
chr1 155188505 155192239 ADTKD_MUC1 MUC1 GGCTNNGGGNGCGGTGGAGCCCGGGGCNGGNCTGNTNTCCGGGGCCGAGGTGACANCNTG GCCCACGGTGTCACCTCGGCCCCGGACACCAGGCCGGCCCCGGGCTCCACCGCCCCCCCCA None AD Autosomal dominant tubulointerstitial kidney disease
chr1 156591765 156591783 NME_NAXE NAXE GGGCC GGGCC 200 AR NAXE-related mitochondrial encephalopathy
chr2 96197066 96197124 FAME2_STARD7 STARD7 AAAAT AAATG 274 AD Familial adult myoclonic epilepsy 2
@@ -14,7 +14,7 @@ chr3 129172576 129172656 DM2_CNBP CNBP CAGG CAGG 75 AD Myotonic dystrophy type 2
chr3 138946019 138946062 BPES_FOXL2 FOXL2 NGC NGC 15 AD,AR Blepharophimosis, epicanthus inversus, and ptosis
chr3 183712187 183712226 FAME4_YEATS2 YEATS2 TTTTA TTTCA 1000 AD Familial adult myoclonic epilepsy 4
chr4 3074876 3074933 HD_HTT HTT CAG CAG 36 AD Huntington disease
-chr4 39348424 39348483 CANVAS_RFC1 RFC1 AAAAG AAGGG,ACAGG,AGGGC,AAGGC,AGAGG 400 AR Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome
+chr4 39348424 39348483 CANVAS_RFC1 RFC1 AAAAG AAGGG,ACAGG,AAAGG,AGGGC 400 AR Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome
chr4 41745972 41746032 CCHS_PHOX2B PHOX2B GCN GCN 26 AD Congenital central hypoventilation syndrome
chr4 159342526 159342618 FAME7_RAPGEF2 RAPGEF2 TTTTA TTTCA 60 AD Familial adult myoclonic epilepsy type 7
chr5 10356343 10356411 FAME3_MARCHF6 MARCHF6 TTTTA TTTCA 650 AD Familial adult myoclonic epilepsy type 3
@@ -28,7 +28,7 @@ chr7 27199924 27199966 HFG_HOXA13-I HOXA13 NGC NGC 22 AD Hand-foot-genital syndr
chr7 55887600 55887639 FRA7A_ZNF713 ZNF713 GCG GCG 450 AD Autism spectrum disorder associated with fragile site FRA7A
chr8 104588970 104588999 OPDM1_LRP12 LRP12 CGC CGC 85 AD Oculopharyngodistal myopathy type 1
chr8 118366812 118366918 FAME1_SAMD12 SAMD12 TAAAA TGAAA 105 AD Familial adult myoclonic epilepsy type 1
-chr9 27573484 27573546 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 251 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
+chr9 27573484 27573546 FTDALS1_C9orf72 C9orf72 GGCCCC GGCCCC 31 AD Frontotemporal dementia (FTD) and/or amyotrophic lateral sclerosis (ALS)
chr9 69037286 69037304 FRDA_FXN FXN GAA GAA 56 AR Friedreich ataxia
chr9 130681605 130681641 HSAN-VIII_PRDM12 PRDM12 GCC GCC 18 AR Hereditary sensory and autonomic neuropathy type VIII
chr10 79826383 79826404 OPML1_NUTM2B-AS1 NUTM2B-AS1 GGC GGC 161 AD Oculopharyngeal myopathy with leukoencephalopathy 1
@@ -71,6 +71,6 @@ chrX 31284557 31284605 DMD_DMD DMD TTC TTC 59 XR Duchenne muscular dystrophy
chrX 67545316 67545419 SBMA_AR AR GCA GCA 38 XR Spinal and bulbar muscular atrophy, Kennedy Disease
chrX 71453054 71453131 XDP_TAF1 TAF1 AGAGGG AGAGGG 35 XR X-linked dystonia-parkinsonism (XDP) a.k.a. Dystonia 3, torsion, X-linked (DYT3)
chrX 137566826 137566856 VACTERLX_ZIC3 ZIC3 GCN GCN 12 XR X-linked VACTERL syndrome
-chrX 140504316 140504361 XLMR_SOX3 SOX3 NGC NGC 22 XR X-linked panhypopituitarism ; X-linked mental retardation with isolated growth hormone
+chrX 140504316 140504361 XLID_SOX3 SOX3 NGC NGC 22 XR X-linked intellectual developmental disorder with isolated growth hormone deficiency; X-linked panhypopituitarism
chrX 147912049 147912111 FXS_FMR1 FMR1 CGG CGG 201 XD Fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and fragile X-associated primary ovarian insufficiency FXPOI/POF1
-chrX 148500604 148500753 FRAXE_AFF2 AFF2 GCC GCC 201 XR Fragile X syndrome, FRAXE type
+chrX 148500604 148500753 FRAXE_AFF2 AFF2 GCC GCC 201 XR Intellectual developmental disorder, Fragile X intellectual disability
diff --git a/data/catalogs/STRchive-disease-loci.hg38.longTR.bed b/data/catalogs/STRchive-disease-loci.hg38.longTR.bed
index 8a36b988..18313db9 100644
--- a/data/catalogs/STRchive-disease-loci.hg38.longTR.bed
+++ b/data/catalogs/STRchive-disease-loci.hg38.longTR.bed
@@ -13,7 +13,7 @@ chr3 129172577 129172656 CAGG DM2_CNBP
chr3 138946020 138946062 NGC BPES_FOXL2
chr3 183712188 183712226 TTTCA,TTTTA FAME4_YEATS2
chr4 3074877 3074933 CAG HD_HTT
-chr4 39348425 39348483 AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAAG,AAAGG,AAGAG,AAAGGG CANVAS_RFC1
+chr4 39348425 39348483 AAGGG,ACAGG,AAAGG,AGGGC,AAAAG,AAAGGG CANVAS_RFC1
chr4 41745973 41746032 GCN CCHS_PHOX2B
chr4 159342527 159342618 TTTCA,TTTTA FAME7_RAPGEF2
chr5 10356344 10356411 TTTCA,TTTTA FAME3_MARCHF6
@@ -38,7 +38,7 @@ chr12 111598950 111599019 CTG SCA2_ATXN2
chr12 123533721 123533750 GGC OPDM4_RILPL1
chr13 70139384 70139429 CTG SCA8_ATXN8OS
chr13 99985449 99985494 GCN HPE5_ZIC2
-chr13 102161575 102161726 GAA,GAAGGA,GAAGAAGAAGAAGCA SCA27B_FGF14
+chr13 102161575 102161726 GAA,GGA,GCA SCA27B_FGF14
chr14 23321473 23321503 GCN OPMD_PABPN1
chr14 92071011 92071052 CTG SCA3_ATXN3
chr15 22786678 22786703 GCG ALS1_NIPA1
@@ -70,6 +70,6 @@ chrX 31284558 31284605 TTC DMD_DMD
chrX 67545317 67545419 GCA SBMA_AR
chrX 71453055 71453131 AGAGGG XDP_TAF1
chrX 137566827 137566856 GCN VACTERLX_ZIC3
-chrX 140504317 140504361 NGC XLMR_SOX3
+chrX 140504317 140504361 NGC XLID_SOX3
chrX 147912050 147912111 CGG FXS_FMR1
chrX 148500605 148500753 GCC FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.hg38.straglr.bed b/data/catalogs/STRchive-disease-loci.hg38.straglr.bed
index 6b4a89c4..6dfa4fda 100644
--- a/data/catalogs/STRchive-disease-loci.hg38.straglr.bed
+++ b/data/catalogs/STRchive-disease-loci.hg38.straglr.bed
@@ -80,6 +80,6 @@ chrX 31284605 31284613 T DMD_DMD DMD_DMD_T
chrX 67545316 67545419 GCA SBMA_AR SBMA_AR
chrX 71453054 71453131 AGAGGG XDP_TAF1 XDP_TAF1
chrX 137566826 137566856 GCN VACTERLX_ZIC3 VACTERLX_ZIC3
-chrX 140504316 140504361 NGC XLMR_SOX3 XLMR_SOX3
+chrX 140504316 140504361 NGC XLID_SOX3 XLID_SOX3
chrX 147912049 147912111 CGG FXS_FMR1 FXS_FMR1
chrX 148500604 148500753 GCC FRAXE_AFF2 FRAXE_AFF2
diff --git a/data/catalogs/STRchive-disease-loci.hg38.stranger.json b/data/catalogs/STRchive-disease-loci.hg38.stranger.json
index 3231f70c..81a97f12 100644
--- a/data/catalogs/STRchive-disease-loci.hg38.stranger.json
+++ b/data/catalogs/STRchive-disease-loci.hg38.stranger.json
@@ -393,7 +393,7 @@
"DisplayRU": "GGCCCC",
"Disease": "FTDALS1",
"NormalMax": 23,
- "PathologicMin": 251,
+ "PathologicMin": 31,
"Gene": "C9orf72"
},
{
@@ -961,14 +961,14 @@
"Gene": "ZIC3"
},
{
- "LocusId": "XLMR_SOX3",
+ "LocusId": "XLID_SOX3",
"ReferenceRegion": "chrX:140504316-140504361",
"LocusStructure": "(NGC)*",
"VariantType": "Repeat",
"HGNCId": null,
"InheritanceMode": ["XR"],
"DisplayRU": "NGC",
- "Disease": "XLMR",
+ "Disease": "XLID, PHP",
"NormalMax": 15,
"PathologicMin": 22,
"Gene": "SOX3"
diff --git a/data/plots/age-onset.json b/data/plots/age-onset.json
index 5e202b61..e5848e2a 100644
--- a/data/plots/age-onset.json
+++ b/data/plots/age-onset.json
@@ -13,7 +13,7 @@
"orientation": "h",
"width": 0.2,
"x": [47.0, 32.0, 39.0, 52.0, 51.0, 44.0, 66.0, 71.0, 59.0, 0, 19.0, 46.0, 54.0, 57.0, 25.0, 56.0, 0, 53.0, 54.0, 72.0, 40.0, 23.0, 68.0, 40.0, 20.0, 75.0, 54.0, 60.0, 0, 61.0, 59.0, 57.0, 0, 0, 47.0, 56.0, 59.0, 10.0, 70.0, 84.0, 0, 0, 1.0, 84.0, 6.0, 0, 0, 73.0, 76.0, 72.0, 74.0, 0, 65.0, 0, 0, 3.0, 36.0, 0, 0],
- "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"type": "bar"
},
{
@@ -29,7 +29,7 @@
"orientation": "h",
"width": 0.2,
"x": [0, 0, 0, 0, 0, 0, 0, 0, 0, 57.0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 12.0, 0, 0, 0, 0, 0, 0, 0, 78.0, 2.0, 0, 0, 0, 0, 0.0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 10.0],
- "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"type": "bar"
},
{
@@ -45,7 +45,7 @@
"orientation": "h",
"width": 0.2,
"x": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 78.0, 0],
- "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"type": "bar"
},
{
@@ -61,7 +61,7 @@
"orientation": "h",
"width": 0.2,
"x": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 67.0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 75.0, 0, 0, 0, 0, 1.0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9.0, 0, 0, 0, 0, 0, 9.0, 0, 4.0, 4.0, 0, 0, 0, 0],
- "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"type": "bar"
},
{
@@ -78,7 +78,7 @@
"showlegend": false,
"width": 0.6,
"x": [19.0, 10.0, 20.0, 16.0, 0, 0, 28.0, 14.0, 19.0, 0, 0, 20.0, 0, 9.0, 0, 14.0, 0, 19.0, 22.0, 36.0, 0, 0, 40.0, 6.0, 12.0, 6.0, 24.0, 18.0, 0, 0, 20.0, 19.0, 0, 0, 0, 18.0, 29.0, 0, 39.0, 9.0, 0, 0, 0, 9.0, 0, 0, 0, 28.0, 29.0, 20.0, 20.0, 0, 44.0, 0, 0, 0, 2.0, 0, 0],
- "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"type": "bar"
},
{
@@ -95,7 +95,7 @@
"showlegend": false,
"width": 0.6,
"x": [0, 0, 0, 0, 0, 0, 0, 0, 0, 16.0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 9.0, 0, 0, 0, 0, 0, 0, 0, 5.0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2.0],
- "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"type": "bar"
},
{
@@ -112,7 +112,7 @@
"showlegend": false,
"width": 0.6,
"x": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 64.0, 0],
- "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"type": "bar"
},
{
@@ -129,7 +129,7 @@
"showlegend": false,
"width": 0.6,
"x": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 29.0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8.0, 0, 0, 0, 0, 0, 0, 0, 0.0, 0, 0, 0, 0, 0],
- "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "y": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"type": "bar"
},
{
@@ -727,7 +727,7 @@
"yaxis":
{
"tickmode": "array",
- "tickvals": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLMR", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
+ "tickvals": ["FECD3", "CJD", "SCA36", "ALS1", "FAME6", "MRUPAV", "SCA27B", "FTDALS1", "OPMD", "CANVAS", "FAME7", "SCA37", "ADTKD", "SCA6", "OPML1", "OPDM2", "XDP", "SCA4", "HDL2", "SCA10", "FAME3", "FAME4", "NIID", "OPDM5", "OPDM4", "SCA31", "SCA12", "FAME1", "SBMA", "FAME8", "OPDM1", "SCA1", "EPM1", "DMD", "SCA51", "FAME2", "SCA17", "EDM1, PSACH", "SCA3, MJD", "SCA2", "FRDA", "GDPAG", "FRA7A", "HD", "FRA2A", "FRAXE", "NME", "DM2", "SCA8", "DRPLA", "DM1", "XLID, PHP", "SCA7", "EIEE1", "PRTS", "FRA12A", "CCHS", "FXS, FXTAS, POF1", "HMNR7"],
"title":
{
"text": "Disease"
diff --git a/data/plots/path-size.json b/data/plots/path-size.json
index 825f367b..ad2ea57f 100644
--- a/data/plots/path-size.json
+++ b/data/plots/path-size.json
@@ -1,7 +1,7 @@
{
"data": [
{
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+ "base": [0, 50, 18, 2871, 0, 0, 15, 1, 0, 15, 252, 10, 24, 9, 18, 12, 15, 0, 0, 9, 24, 18, 9, 15, 44, 0, 20, 39, 1, 1, 45, 0, 21, 12, 33, 48, 15, 1, 18, 30, 15, 75, 18, 42, 60, 18, 96, 18, 27, 12, 18, 42, 27, 45, 45, 42, 24, 45, 45, 12, 36, 12, 36, 21, 30, 42, 0, 30, 30, 18, 15, 16, 20, 30],
"hovertemplate": "Disease: %{y} \u003cbr\u003e Range: %{base} - %{x} bp",
"legendgroup": "Benign",
"marker":
@@ -12,12 +12,12 @@
"offset": -0.3,
"orientation": "h",
"width": 0.6,
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+ "x": [0, 110, 66, 198, 0, 0, 99, 54, 0, 51, 780, 25, 513, 51, 51, 105, 117, 0, 0, 39, 12, 30, 123, 222, 60, 0, 220, 96, 95, 59, 105, 0, 90, 126, 99, 51, 84, 149, 78, 87, 87, 45, 87, 36, 54, 66, 0, 87, 75, 69, 60, 48, 33, 0, 0, 0, 30, 0, 0, 42, 0, 39, 0, 21, 18, 0, 0, 0, 0, 12, 0, 0, 0, 0],
+ "y": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHP", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
"type": "bar"
},
{
- "base": [0, 165, 90, 0, 0, 0, 0, 55, 144, 0, 126, 0, 0, 540, 0, 417, 120, 135, 0, 0, 0, 0, 0, 0, 240, 108, 0, 260, 0, 0, 0, 150, 0, 114, 135, 0, 102, 0, 120, 120, 105, 123, 108, 81, 0, 87, 0, 108, 108, 84, 81, 93, 63, 0, 0, 0, 0, 0, 0, 57, 0, 0, 0, 0, 0, 0, 0, 33, 33, 0, 0, 0, 0, 0],
+ "base": [0, 165, 90, 0, 0, 0, 0, 55, 0, 126, 0, 0, 540, 0, 417, 120, 135, 0, 0, 0, 0, 0, 0, 240, 108, 0, 260, 0, 0, 0, 150, 0, 114, 144, 135, 0, 102, 0, 120, 120, 105, 123, 108, 81, 0, 87, 0, 108, 108, 84, 81, 93, 63, 0, 0, 0, 0, 0, 0, 57, 0, 0, 0, 0, 0, 0, 0, 33, 33, 0, 0, 0, 0, 0],
"hovertemplate": "Disease: %{y} \u003cbr\u003e Range: %{base} - %{x} bp",
"legendgroup": "Intermediate",
"marker":
@@ -28,12 +28,12 @@
"offset": -0.3,
"orientation": "h",
"width": 0.6,
- "x": [0, 4085, 3804, 0, 0, 0, 0, 945, 216, 0, 129, 0, 0, 417, 0, 201, 480, 465, 0, 0, 0, 0, 0, 0, 60, 188, 0, 0, 0, 0, 0, 60, 0, 81, 42, 0, 63, 0, 27, 30, 42, 21, 33, 54, 0, 30, 0, 6, 3, 21, 24, 9, 12, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
- "y": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FTDALS1", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLMR", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
+ "x": [0, 4085, 3804, 0, 0, 0, 0, 945, 0, 129, 0, 0, 417, 0, 201, 480, 465, 0, 0, 0, 0, 0, 0, 60, 188, 0, 0, 0, 0, 0, 60, 0, 81, 36, 42, 0, 63, 0, 27, 30, 42, 21, 33, 54, 0, 30, 0, 6, 3, 21, 24, 9, 12, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
+ "y": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHP", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
"type": "bar"
},
{
- "base": [5000, 4000, 3900, 3663, 3300, 3250, 2040, 2000, 1506, 1370, 1350, 1260, 1000, 960, 900, 819, 603, 603, 550, 525, 483, 360, 360, 354, 303, 300, 300, 280, 255, 219, 216, 213, 210, 198, 180, 177, 168, 155, 153, 153, 150, 147, 144, 138, 135, 120, 120, 117, 114, 111, 108, 105, 78, 75, 75, 66, 66, 66, 66, 63, 60, 60, 54, 54, 51, 45, 45, 36, 36, 33, 18, 12, 10, 0],
+ "base": [5000, 4000, 3900, 3663, 3300, 3250, 2040, 2000, 1370, 1350, 1260, 1000, 960, 900, 819, 603, 603, 550, 525, 483, 360, 360, 354, 303, 300, 300, 280, 255, 219, 216, 213, 210, 198, 186, 180, 177, 168, 155, 153, 153, 150, 147, 144, 138, 135, 120, 120, 117, 114, 111, 108, 105, 78, 75, 75, 66, 66, 66, 66, 63, 60, 60, 54, 54, 51, 45, 45, 36, 36, 33, 18, 12, 10, 0],
"hovertemplate": "Disease: %{y} \u003cbr\u003e Range: %{base} - %{x} bp",
"legendgroup": "Pathogenic",
"marker":
@@ -44,8 +44,8 @@
"offset": -0.3,
"orientation": "h",
"width": 0.6,
- "x": [0, 18500, 11100, 1287, 0, 1925, 2460, 11750, 23022, 1420, 0, 294, 0, 1851, 0, 99, 5397, 5397, 3250, 17875, 1617, 1140, 231, 1728, 597, 43700, 10700, 40, 612, 273, 114, 3687, 102, 1353, 81, 69, 4932, 220, 81, 7647, 11850, 51, 135, 84, 165, 60, 264, 156, 90, 1269, 642, 1395, 21, 0, 0, 0, 30, 3, 12, 36, 0, 21, 0, 3, 30, 27, 1625, 18, 0, 135, 3, 0, 20, 0],
- "y": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FTDALS1", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLMR", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
+ "x": [0, 18500, 11100, 1287, 0, 1925, 2460, 11750, 1420, 0, 294, 0, 1851, 0, 99, 5397, 5397, 3250, 17875, 1617, 1140, 231, 1728, 597, 43700, 10700, 40, 612, 273, 114, 3687, 102, 1353, 24342, 81, 69, 4932, 220, 81, 7647, 11850, 51, 135, 84, 165, 60, 264, 156, 90, 1269, 642, 1395, 21, 0, 0, 0, 30, 3, 12, 36, 0, 21, 0, 3, 30, 27, 1625, 18, 0, 135, 3, 0, 20, 0],
+ "y": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHP", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
"type": "bar"
},
{
@@ -126,32 +126,6 @@
"y": ["CANVAS", "CANVAS"],
"type": "scatter"
},
- {
- "hoverinfo": "skip",
- "line":
- {
- "color": "#aeaeae",
- "dash": "dot"
- },
- "mode": "lines",
- "showlegend": false,
- "x": [138, 144],
- "y": ["FTDALS1", "FTDALS1"],
- "type": "scatter"
- },
- {
- "hoverinfo": "skip",
- "line":
- {
- "color": "#aeaeae",
- "dash": "dot"
- },
- "mode": "lines",
- "showlegend": false,
- "x": [360, 1506],
- "y": ["FTDALS1", "FTDALS1"],
- "type": "scatter"
- },
{
"hoverinfo": "skip",
"line":
@@ -529,6 +503,32 @@
"y": ["NIID", "NIID"],
"type": "scatter"
},
+ {
+ "hoverinfo": "skip",
+ "line":
+ {
+ "color": "#aeaeae",
+ "dash": "dot"
+ },
+ "mode": "lines",
+ "showlegend": false,
+ "x": [138, 144],
+ "y": ["FTDALS1", "FTDALS1"],
+ "type": "scatter"
+ },
+ {
+ "hoverinfo": "skip",
+ "line":
+ {
+ "color": "#aeaeae",
+ "dash": "dot"
+ },
+ "mode": "lines",
+ "showlegend": false,
+ "x": [180, 186],
+ "y": ["FTDALS1", "FTDALS1"],
+ "type": "scatter"
+ },
{
"hoverinfo": "skip",
"line":
@@ -1046,7 +1046,7 @@
"mode": "lines",
"showlegend": false,
"x": [45, 66],
- "y": ["XLMR", "XLMR"],
+ "y": ["XLID, PHP", "XLID, PHP"],
"type": "scatter"
},
{
@@ -1256,7 +1256,7 @@
"name": "Benign",
"showlegend": false,
"x": [96, 45, 45, 42, 45, 45, 36, 36, 42, 30, 30, 15, 16, 20, 30],
- "y": ["CJD", "TOF", "HPE5", "HFG-I", "SD5", "XLMR", "PRTS", "HFG-II", "BPES", "OPMD", "VACTERLX", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
+ "y": ["CJD", "TOF", "HPE5", "HFG-I", "SD5", "XLID, PHP", "PRTS", "HFG-II", "BPES", "OPMD", "VACTERLX", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
"type": "scatter"
},
{
@@ -1869,7 +1869,7 @@
"yaxis":
{
"tickmode": "array",
- "tickvals": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FTDALS1", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLMR", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
+ "tickvals": ["FAME4", "SCA10", "SCA36", "MRUPAV", "FAME6", "FAME3", "GDPAG", "CANVAS", "FAME2", "FRA7A", "CPUM", "NME", "SCA27B", "FRA2A", "FRA12A", "FRAXE", "FXS, FXTAS, POF1", "SCA31", "FAME1", "OPML1", "EPM1", "OPDM4", "OPDM5", "JBS", "DM2", "FAME7", "RCPS", "OPDM1", "OPDM2", "DBQD2, BSS", "SCA8", "XDP", "NIID", "FTDALS1", "SCA3, MJD", "DMD", "FRDA", "SCA37", "SCA12", "FECD3", "DM1", "SCA17", "DRPLA", "SCA4", "SCA51", "HDL2", "CJD", "SCA1", "SBMA", "SCA7", "HD", "SCA2", "CCHS", "TOF", "HPE5", "HFG-I", "HFG-III", "SD5", "XLID, PHP", "SCA6", "PRTS", "CCD", "HFG-II", "HSAN VIII", "EIEE1", "BPES", "FAME8", "OPMD", "VACTERLX", "ALS1", "EDM1, PSACH", "CHNG3", "HMNR7", "CPEO"],
"title":
{
"text": "Disease"
diff --git a/data/ref-alleles/ref-alleles.T2T-chm13.txt b/data/ref-alleles/ref-alleles.T2T-chm13.txt
index 1ce62e6a..8e9254b7 100644
--- a/data/ref-alleles/ref-alleles.T2T-chm13.txt
+++ b/data/ref-alleles/ref-alleles.T2T-chm13.txt
@@ -89,8 +89,8 @@ CAAGTCCTTC CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
CAAGTCCTTC CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CCG CCA CCG CCG CCG CCG CCG CCG CCG CCT CCTCAGCTTC
CANVAS_RFC1
-chr4 39318077 39318136 AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG STRchive
-chr4 39318077 39318136 AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAGG,AAGAG,AAAGGG TRGT
+chr4 39318077 39318136 AAAAG,AAGGG,ACAGG,AAAGG,AGGGC STRchive
+chr4 39318077 39318136 AAAAG,AAGGG,ACAGG,AAAGG,AGGGC,AAAGGG TRGT
TCTGTTTCAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA AGCATGTTCT
TCTGTTTCAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA AGCATGTTCT
@@ -240,7 +240,7 @@ CCTGTCCCCA GCG GCG GCG GCA GCG GCG GCG GCG GCT GCG GCG GCG GCG GCC GCG G TGTCCGC
SCA27B_FGF14
chr13 101377549 101377792 GAA STRchive
-chr13 101377549 101377792 GAA,GAAGGA,GAAGAAGAAGAAGCA TRGT
+chr13 101377549 101377792 GAA,GGA,GCA TRGT
AACTTTCTGT GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAATGTGTTT
AACTTTCTGT GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAATGTGTTT
@@ -430,7 +430,7 @@ chrX 135876774 135876804 GCN TRGT
CTCAACCCAC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC TTCAAGCTGA
CTCAACCCAC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC TTCAAGCTGA
-XLMR_SOX3
+XLID_SOX3
chrX 138816203 138816248 NGC STRchive
chrX 138816203 138816248 NGC TRGT
CCGGACTGCT GGC GGC AGC GGC TGC GGC CGC GGC AGC GGC GGC GGC GGC CGC GGC ACCGGGAGGC
diff --git a/data/ref-alleles/ref-alleles.hg19.txt b/data/ref-alleles/ref-alleles.hg19.txt
index 4571380e..b9ae4c34 100644
--- a/data/ref-alleles/ref-alleles.hg19.txt
+++ b/data/ref-alleles/ref-alleles.hg19.txt
@@ -89,8 +89,8 @@ CAAGTCCTTC CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
CAAGTCCTTC CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CCG CCA CCG CCG CCG CCG CCG CCG CCG CCT CCTCAGCTTC
CANVAS_RFC1
-chr4 39350044 39350103 AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG STRchive
-chr4 39350044 39350103 AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAGG,AAGAG,AAAGGG TRGT
+chr4 39350044 39350103 AAAAG,AAGGG,ACAGG,AAAGG,AGGGC STRchive
+chr4 39350044 39350103 AAAAG,AAGGG,ACAGG,AAAGG,AGGGC,AAAGGG TRGT
TCTGTTTCAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA AGCATGTTCT
TCTGTTTCAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA AGCATGTTCT
@@ -240,7 +240,7 @@ CCTGTCCCCA GCG GCG GCG GCA GCG GCG GCG GCG GCT GCG GCG GCG GCG GCC GCG G TGTCCGC
SCA27B_FGF14
chr13 102813924 102814076 GAA STRchive
-chr13 102813924 102814076 GAA,GAAGGA,GAAGAAGAAGAAGCA TRGT
+chr13 102813924 102814076 GAA,GGA,GCA TRGT
TGAAGAAAGA AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TAGAAATGTG
TGAAGAAAGA AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TAGAAATGTG
@@ -430,7 +430,7 @@ chrX 136648985 136649015 GCN TRGT
CTCAACCCAC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC TTCAAGCTGA
CTCAACCCAC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC TTCAAGCTGA
-XLMR_SOX3
+XLID_SOX3
chrX 139586481 139586526 NGC STRchive
chrX 139586481 139586526 NGC TRGT
CCGGACTGCT GGC GGC AGC GGC TGC GGC CGC GGC AGC GGC GGC GGC GGC CGC GGC ACCGGGAGGC
diff --git a/data/ref-alleles/ref-alleles.hg38.txt b/data/ref-alleles/ref-alleles.hg38.txt
index a7875038..67d9fac9 100644
--- a/data/ref-alleles/ref-alleles.hg38.txt
+++ b/data/ref-alleles/ref-alleles.hg38.txt
@@ -89,8 +89,8 @@ CAAGTCCTTC CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
CAAGTCCTTC CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAA CAG CCG CCA CCG CCG CCG CCG CCG CCG CCG CCT CCTCAGCTTC
CANVAS_RFC1
-chr4 39348424 39348483 AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG STRchive
-chr4 39348424 39348483 AAAAG,AAGGG,ACAGG,AGGGC,AAGGC,AGAGG,AAAGG,AAGAG,AAAGGG TRGT
+chr4 39348424 39348483 AAAAG,AAGGG,ACAGG,AAAGG,AGGGC STRchive
+chr4 39348424 39348483 AAAAG,AAGGG,ACAGG,AAAGG,AGGGC,AAAGGG TRGT
TCTGTTTCAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA AGCATGTTCT
TCTGTTTCAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA AGCATGTTCT
@@ -240,7 +240,7 @@ CCTGTCCCCA GCG GCG GCG GCA GCG GCG GCG GCG GCT GCG GCG GCG GCG GCC GCG G TGTCCGC
SCA27B_FGF14
chr13 102161574 102161726 GAA STRchive
-chr13 102161574 102161726 GAA,GAAGGA,GAAGAAGAAGAAGCA TRGT
+chr13 102161574 102161726 GAA,GGA,GCA TRGT
TGAAGAAAGA AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TAGAAATGTG
TGAAGAAAGA AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA TAGAAATGTG
@@ -430,7 +430,7 @@ chrX 137566826 137566856 GCN TRGT
CTCAACCCAC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC TTCAAGCTGA
CTCAACCCAC GCC GCC GCC GCC GCC GCC GCC GCC GCT GCC TTCAAGCTGA
-XLMR_SOX3
+XLID_SOX3
chrX 140504316 140504361 NGC STRchive
chrX 140504316 140504361 NGC TRGT
CCGGACTGCT GGC GGC AGC GGC TGC GGC CGC GGC AGC GGC GGC GGC GGC CGC GGC ACCGGGAGGC