CASK p.Ile137fs
c.410_411del · VCV4950080
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
CASK-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 27 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CASK
- Protein
- p.Ile137fs
- Coding
- c.410_411del
- MANE Select
- NM_001367721
- Type
- Deletion
- Location
- chrX:41739402 (GRCh38)
- Structure
- AlphaFold pLDDT 79.45 · 22 PDB
- Residue 137
- the protein kinase domain; a UniProt-annotated variant site (found in a patient with epilepsy and pontocerebellar hypoplasia; likely pathogenic)
Disease context
CASK-related disorder
Similar variants
- CASK p.Thr548fs Pathogenic/Likely pathogenic ★★ same condition
- CASK c.1504-2_1504-1del Likely pathogenic ★ same condition
- CASK p.Ala814fs Likely pathogenic ★ same condition
- CASK p.His520fs Likely pathogenic ★ same condition
- CASK p.Lys393fs Likely pathogenic ★ same condition
- CASK p.Lys877del Uncertain significance same condition
- CASK p.Arg28Ter Pathogenic ★★ same condition
- CASK p.Arg489Trp Pathogenic/Likely pathogenic ★★ 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-ile137fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown