Is CASK p.Glu194= (c.582G>A) pathogenic?

CASK p.Glu194= (c.582G>A) is classified Likely benign in CASK (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-11-25). Very rare (popmax 0.00884%, nfe); Associated with Inborn genetic diseases.

What condition is associated with CASK p.Glu194= (c.582G>A)?

CASK p.Glu194= (c.582G>A) is associated with Inborn genetic diseases (ClinVar).

How common is CASK p.Glu194= (c.582G>A) in the general population?

CASK p.Glu194= (c.582G>A) is very rare (popmax 0.00884%, nfe) (gnomAD).

CASK p.Glu194=

c.582G>A · rs774107615 · VCV589499

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00884%, nfe)

Conditions

Inborn genetic diseases

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 1.8	GERP -0.12, phastCons 1
Overall
CADD	9.701	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00884% European (non-Finnish) · 79/893,778 alleles

Filtering AF 0.00721% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00667%

Overall 0.00695% 84/1,208,084 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00884%	11,314
African / African-American	0.00525%	19,057
Remaining individualsnot grpmax-eligible	0.00421%	23,768

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.Glu194=
Coding: c.582G>A
MANE Select: NM_001367721
dbSNP: rs774107615
Type: single nucleotide variant
Location: chrX:41665403 (GRCh38)
Structure: AlphaFold pLDDT 79.45 · 22 PDB
Residue 194: the protein kinase domain; a UniProt-annotated variant site (found in a patient with epilepsy and pontocerebellar hypoplasia; likely pathogenic)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CASK p.Ala300Thr Uncertain significance ★★ ⚠ same condition
CASK p.Arg560Trp Uncertain significance ★★ ⚠ same condition
CASK p.Arg766Trp Uncertain significance ★★ ⚠ same condition
CASK p.Asn31Ser Uncertain significance ★★ ⚠ same condition
CASK p.Asp330Gly Uncertain significance ★★ ⚠ same condition
CASK p.Asp498Gly Uncertain significance ★★ ⚠ same condition
CASK p.Glu662Asp Uncertain significance ★★ ⚠ same condition
CASK p.Gly21Asp 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-glu194 (accessed [today's date]).

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