CASK c.532+2dup
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +2 | canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone |
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 1.6, phastCons 1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CASK
- Coding
- c.532+2dup
- MANE Select
- NM_001367721
- Type
- Duplication
- Location
- chrX:41671425 (GRCh38)
- Structure
- AlphaFold pLDDT 79.45 · 22 PDB
Similar variants
- CASK c.1504-6dup Benign/Likely benign ★★ same type
- CASK c.1806+17dup Likely benign ★★ same type
- CASK c.2521-11dup Benign/Likely benign ★★ same type
- CASK c.1156-4408_1503+2676dup Likely pathogenic ★ same type
- CASK c.1315-4_1315-1dup Likely pathogenic ★ same type
- CASK p.Ala187fs Likely pathogenic ★ same type
- CASK p.Asn666fs Pathogenic ★ same type
- CASK p.Asn757fs 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-532-plus-2dup (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown