CASK p.Glu13fs
c.38_39del · rs2520195542 · VCV2627876
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 1 of 27 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. 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
- Protein
- p.Glu13fs
- Coding
- c.38_39del
- MANE Select
- NM_001367721
- dbSNP
- rs2520195542
- Type
- Deletion
- Location
- chrX:41922950 (GRCh38)
- Structure
- AlphaFold pLDDT 79.45 · 22 PDB
- Residue 13
- the protein kinase domain; a β-strand
Similar variants
- CASK p.Glu13Ter Pathogenic ★ same residue
- CASK p.Gly751fs Pathogenic ★ same condition
- CASK c.172+1G>A Uncertain significance ★ same condition
- 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
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-glu13fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown