Is CASK p.Ala311Thr (c.931G>A) pathogenic?

CASK p.Ala311Thr (c.931G>A) is classified Uncertain significance in CASK (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-30). AlphaMissense: likely pathogenic (0.9161); Very rare (popmax 0.000116%, nfe); Associated with Intellectual disability, CASK-related, X-linked.

What condition is associated with CASK p.Ala311Thr (c.931G>A)?

CASK p.Ala311Thr (c.931G>A) is associated with Intellectual disability, CASK-related, X-linked (ClinVar).

How common is CASK p.Ala311Thr (c.931G>A) in the general population?

CASK p.Ala311Thr (c.931G>A) is very rare (popmax 0.000116%, nfe) (gnomAD).

What do computational predictors say about CASK p.Ala311Thr (c.931G>A)?

AlphaMissense predicts likely pathogenic (score 0.9161) — an in-silico prediction, not a clinical call.

CASK p.Ala311Thr

c.931G>A · rs2519038111 · VCV2699628

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9161 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000116%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Intellectual disability, CASK-related, X-linked

Computational evidence

Protein change
AlphaMissense	0.9161	likely pathogenic
REVEL	0.313	indeterminate
SaProt	LLR -7.80	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.9, phastCons 1
Regional constraint	o/e 0.50	unconstrained · MANE · 77 kb · p 1.9e-13 · regional, not allelic
Overall
CADD	24.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000116% European (non-Finnish) · 1/864,649 alleles

Overall 9.4e-05% 1/1,064,270 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CASK
Protein: p.Ala311Thr
Coding: c.931G>A
MANE Select: NM_001367721
dbSNP: rs2519038111
Type: single nucleotide variant
Location: chrX:41626688 (GRCh38)
Structure: AlphaFold pLDDT 79.45 · 22 PDB
Residue 311: a UniProt-annotated variant site (found in a patient with epilepsy and pontocerebellar hypoplasia; likely pathogenic); an α-helix; the 'calmodulin-binding' region

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 p.Arg489Gln Pathogenic/Likely pathogenic ★★ same condition
CASK p.Ala359Val Uncertain significance ★★ ⚠ same condition
CASK p.Ala833Thr Uncertain significance ★★ ⚠ same condition
CASK p.Arg130Cys Uncertain significance ★★ ⚠ same condition
CASK p.Arg572His Uncertain significance ★★ ⚠ same condition
CASK p.Arg61Trp Uncertain significance ★★ ⚠ same condition
CASK p.Asp424Gly Uncertain significance ★★ ⚠ same condition
CASK p.Asp445Asn Uncertain significance ★★ ⚠ 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-ala311thr (accessed [today's date]).

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