BCLAF3 and CSNK1E

[hdashnow]

Status: Proposed/Limited/Provisional?

Paper: https://www.nature.com/articles/s41467-024-50159-6 (quoted below)

BCLAF3

A single proband with developmental and epileptic encephalopathy (DEE) and a methylation signal. Absent in controls.

Possible coordinates in hg38
chrX:19990245-19991021
chrX:19990922-19990973

Motif: CCG

One male proband with uDEE displayed de novo outlier hypermethylation in a region annotated as intergenic on the GRCh37/hg19 genome build and at the 5’UTR of BCLAF3 on the GRCh38/hg38 genome build. Using ONT long-read sequencing, we discovered a novel CGG repeat expansion in exon 1 of BCLAF3 in this proband inherited from his unaffected mother. The mother’s long-read data displayed skewed X-inactivation against the expanded allele. Skewed X-inactivation may explain why the mother does not have a detectable DNA methylation abnormality at this locus and could provide a mechanism for her to circumvent any functional consequences of the BCLAF3 abnormality. While BCLAF3 has been previously predicted to be a potential disorder-associated gene on chrX58, little is known about its function or disease associations. Thus, further work is needed to investigate whether this abnormality is present in other individuals and if loss of this gene on chrX in males could cause a DEE.

Supp.

BCLAF3 hypermethylation/repeat expansion: Individual 33109 Individual 33109 was found to harbor hypermethylation in exon 1 of BLCAF3 due to an underlying repeat expansion. Individual 33109 is a male with focal developmental and epileptic encephalopathy, moderate intellectual disability, and autism spectrum disorder. He had normal development until seizure onset with tonic-clonic seizures at 3 years when development slowed. He had developmental regression at 4 years. He had drug-resistant epilepsy, including convulsive status epilepticus (3 years 10 months), focal tonic seizures and focal clonic seizures (4 years 2 months), atypical absence seizures (4 years), atonic seizures (5 years 8 months), and focal impaired awareness seizure (7 years). EEG showed a slow background with multifocal discharges. In a previous sequencing analysis, an inherited SCN1A variant (NM_001165963.4:c.4096G>A, NP_001159435.1:p.Val1366Ile) was detected in 33109, his affected brother, and his unaffected mother. His 7-year-old brother had drug-responsive tonicclonic seizures between 3 and 5 years of age with a normal EEG and MRI. He has normal cognition with autistic features. As the proband's mother is unaffected, the proband and his brother's phenotype are not consistent with SCN1A, and the variant is present in 5 individuals in gnomAD, it is thought that the SCN1A variant alone is not the cause of 33109’s phenotype.

CSNK1E

Possible coordinates in hg38:
chr22:38316204-38317449
chr22:38317282-38317306

Motif GCC

We detected two individuals with uDEEs and two control individuals with hypermethylation spanning the 5’UTR and intron 1 of the Casein kinase 1 isoform epsilon (CSNK1E, MIM:600863, Fig. 3A) gene. Although present in one control and reported in 6/23,116 controls17, an individual with DEE and probable haploinsufficiency due to a de novo splicing variant (c.885+1 G > A) in CSNK1E has been reported34, suggesting further study is warranted to determine if variation in this gene causes DEE. Segregation analysis revealed that the hypermethylation in one proband was maternally inherited (Family 1, Supplementary Fig. 8), whereas the other arose de novo (Family 2). After validation of hypermethylation with targeted EM-seq for both probands (Supplementary Fig. 5), long-read sequencing of the proband (genome, ~ 1500–3000 bp) and mother (targeted, ~ 1500 bp) from Family 1 and the proband from Family 2 (genome, ~ 1100–3200 bp) confirmed the presence of an expanded CGG motif in both (Fig. 3C), as previously reported in individuals with hypermethylation of CSNK1E at fragile site FRA22A and reduced expression in lymphoblastoid cells17. Through GeneMatcher35, we identified Family 3 consisting of a proband with the same CSNK1E hypermethylated DMR and CGG repeat expansion (genome, ~ 1300–2100 bp) inherited from his mother (genome, ~ 270 –3500 bp), who is mildly affected by learning, speech, and sleep difficulties (Supplementary Phenotype data). Expression analysis in available fibroblasts from Families 2 and 3 showed that individuals with CSNK1E hypermethylation had decreased expression of CSNK1E compared to hypermethylation-negative controls (Fig. 3B). Analysis using the OUTRIDER algorithm36 confirmed “drop-out” of CSNK1E (ENSG00000213923) expression compared to publicly available fibroblast controls37 (Fig. 3B, Supplementary Fig. 9). Thus, we report 3 individuals with uDEEs harboring inherited and de novo CSNK1E hypermethylation due to an underlying repeat expansion (n = 4 LRS) that leads to approximately 50% reduction in CSNK1E expression (n = 3 RNA-seq drop-out). No other candidate gene variants for these 3 probands were found by trio GS analysis. However, due to finding this abnormality in seemingly unaffected individuals, one control and one mother (Family 1) in our cohort and others17, further work is required to determine whether variations in CSNK1E cause or contribute to the DEEs.

See also, Supp. "CSNK1E hypermethylation/repeat expansion". page 2 for phenotypes

[hdashnow]

There was a possible update on BCLAF3 at @christylaflamme ASHG 2025 poster with several additional patients a hint of a preprint to come 🤞