Is CASK p.Val11fs (c.29_30dup) pathogenic?

CASK p.Val11fs (c.2930dup) is classified Pathogenic in CASK (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-23). Absent from gnomAD; Associated with Intellectual disability, CASK-related, X-linked.

What condition is associated with CASK p.Val11fs (c.29_30dup)?

CASK p.Val11fs (c.29_30dup) is associated with Intellectual disability, CASK-related, X-linked (ClinVar).

How common is CASK p.Val11fs (c.29_30dup) in the general population?

CASK p.Val11fs (c.29_30dup) is absent from gnomAD (gnomAD).

CASK p.Val11fs

c.29_30dup · rs2148116120 · VCV1377857

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Intellectual disability, CASK-related, X-linked

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 5.8	GERP 2.8, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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.Val11fs
Coding: c.29_30dup
MANE Select: NM_001367721
dbSNP: rs2148116120
Type: Duplication
Location: chrX:41922958 (GRCh38)
Structure: AlphaFold pLDDT 79.45 · 22 PDB
Residue 11: an α-helix

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

Disease context

Intellectual disability, CASK-related, X-linked — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CASK c.1504-6dup Benign/Likely benign ★★ same condition
CASK c.1806+17dup Likely benign ★★ same condition
CASK p.Gln553fs Pathogenic ★ same condition
CASK p.Leu820fs Pathogenic ★ same condition
CASK p.Lys277Ter Pathogenic ★ same condition
CASK c.1155+2dup Uncertain significance ★ same condition
CASK c.1669-6dup Conflicting classifications of pathogenicity ★ same condition
CASK c.1234-3dup Benign ★ same condition

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-val11fs (accessed [today's date]).

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