CASK p.Gln124=
c.372G>A · rs1162518702 · VCV756948
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00176%, afr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 9.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00176%
African / African-American · 1/56,972 alleles
Overall
9.5e-05%
1/1,052,646 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CASK
- Protein
- p.Gln124=
- Coding
- c.372G>A
- MANE Select
- NM_001367721
- dbSNP
- rs1162518702
- Type
- single nucleotide variant
- Location
- chrX:41739441 (GRCh38)
- Structure
- AlphaFold pLDDT 79.45 · 22 PDB
- Residue 124
- the protein kinase domain; a UniProt-annotated variant site (found in a patient with epilepsy and pontocerebellar hypoplasia; likely pathogenic); an α-helix
Similar variants
- CASK p.Ala300Thr Uncertain significance ★★ same condition
- CASK p.Arg560Trp Uncertain significance ★★ ⚠ same condition
- CASK p.Arg766Trp Uncertain significance ★★ same condition
- CASK p.Asn31Ser Uncertain significance ★★ ⚠ same condition
- CASK p.Asp330Gly Uncertain significance ★★ ⚠ same condition
- CASK p.Asp498Gly Uncertain significance ★★ ⚠ same condition
- CASK p.Glu662Asp Uncertain significance ★★ ⚠ same condition
- CASK p.Gly21Asp Uncertain significance ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cask-p-gln124 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown