Is CASK p.Ile65= (c.195C>T) pathogenic?

CASK p.Ile65= (c.195C>T) is classified Benign/Likely benign in CASK (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-11). Ultra-rare (popmax 0.0235%, mid); Associated with Intellectual disability, CASK-related, X-linked.

What condition is associated with CASK p.Ile65= (c.195C>T)?

CASK p.Ile65= (c.195C>T) is associated with Intellectual disability, CASK-related, X-linked (ClinVar).

How common is CASK p.Ile65= (c.195C>T) in the general population?

CASK p.Ile65= (c.195C>T) is ultra-rare (popmax 0.0235%, mid) (gnomAD).

CASK p.Ile65=

c.195C>T · rs769320891 · VCV589660

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0235%, mid)

Conditions

Intellectual disability, CASK-related, X-linked

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Overall
CADD	13.39	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0235% Middle Eastern · 1/4,261 alleles

Filtering AF 0.00237% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00126%

Overall 0.000851% 10/1,175,611 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0235%	4,261
East Asian	0.00893%	11,199
African / African-American	0.0053%	18,881
Remaining individualsnot grpmax-eligible	0.0043%	23,232
European (non-Finnish)	0.000116%	864,020

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.Ile65=
Coding: c.195C>T
MANE Select: NM_001367721
dbSNP: rs769320891
Type: single nucleotide variant
Location: chrX:41787261 (GRCh38)
Structure: AlphaFold pLDDT 79.45 · 22 PDB
Residue 65: the protein kinase domain; a UniProt-annotated variant site (found in a patient with epilepsy and pontocerebellar hypoplasia; likely pathogenic); 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 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-ile65 (accessed [today's date]).

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