Is CASK p.Val732del (c.2191GTA[1]) pathogenic?

CASK p.Val732del (c.2191GTA[1]) is classified Pathogenic in CASK (ClinVar, Single submitter, 1 submitter; last evaluated 2018-10-23). Absent from gnomAD.

How common is CASK p.Val732del (c.2191GTA[1]) in the general population?

CASK p.Val732del (c.2191GTA[1]) is absent from gnomAD (gnomAD).

CASK p.Val732del

c.2191GTA[1] · rs1064796488 · VCV423552

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.2	GERP 0.47, phastCons 1

Population frequency

dbSNP / gnomAD

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.Val732del
Coding: c.2191GTA[1]
MANE Select: NM_001367721
dbSNP: rs1064796488
Type: Microsatellite
Location: chrX:41534933 (GRCh38)
Structure: AlphaFold pLDDT 79.45 · 22 PDB
Residue 732: 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

Full CASK gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CASK p.Asp95fs Pathogenic ★★ same type
CASK c.430-27_430-20del Benign/Likely benign ★★ same type
CASK c.430-31TGTT[2] Benign ★★ same type
CASK c.278+2_278+3del Pathogenic ★ same type
CASK p.Glu849fs Pathogenic ★ same type
CASK p.Ile755fs Likely pathogenic ★ same type
CASK p.Thr893fs Likely pathogenic ★ same type
CASK c.1314+5_1314+8del Conflicting classifications of pathogenicity ★ 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-val732del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown