CASK c.429+4del
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,121,908)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2, phastCons 1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,121,908). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CASK
- Coding
- c.429+4del
- MANE Select
- NM_001367721
- dbSNP
- rs797045434
- Type
- Deletion
- Location
- chrX:41739380 (GRCh38)
- Structure
- AlphaFold pLDDT 79.45 · 22 PDB
Similar variants
- CASK p.Thr548fs Pathogenic/Likely pathogenic ★★ same type
- CASK p.Val292del Likely pathogenic ★★ same type
- CASK c.1504-6del Benign/Likely benign ★★ same type
- CASK c.1669-6del Benign/Likely benign ★★ same type
- CASK c.2521-11del Benign ★★ same type
- CASK c.533-99_533-84del Benign ★★ same type
- CASK c.116_117delCA Pathogenic ★ same type
- CASK c.1504-2_1504-1del Likely pathogenic ★ same type
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-429-plus-4del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown