CASK c.1015+1G>C
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | Δ1.00 | donor loss · deltas |
| Pangolin | Δ0.87 | loss · gain 0.24 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.7, phastCons 1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 35.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CASK
- Coding
- c.1015+1G>C
- MANE Select
- NM_001367721
- dbSNP
- rs1569350501
- Type
- single nucleotide variant
- Location
- chrX:41626603 (GRCh38)
- Structure
- AlphaFold pLDDT 79.45 · 22 PDB
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-c-1015-plus-1g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown