CASK p.Phe720fs
c.2160del · VCV4822516
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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 23 of 27 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CASK
- Protein
- p.Phe720fs
- Coding
- c.2160del
- MANE Select
- NM_001367721
- Type
- Deletion
- Location
- chrX:41534969 (GRCh38)
- Structure
- AlphaFold pLDDT 79.45 · 22 PDB
- Residue 720
- a UniProt-annotated variant site (found in a patient with epilepsy and pontocerebellar hypoplasia; likely pathogenic); the 'required for interaction with nrxn1 (via c-terminal tail)' region
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-p-phe720fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown