Is CASK p.Arg613fs (c.1838del) pathogenic?

CASK p.Arg613fs (c.1838del) is classified Likely pathogenic in CASK (ClinVar, Single submitter, 1 submitter). Associated with syndromic X-linked intellectual disability Najm type.

What condition is associated with CASK p.Arg613fs (c.1838del)?

CASK p.Arg613fs (c.1838del) is associated with syndromic X-linked intellectual disability Najm type (ClinVar).

How is X-linked intellectual disability, Najm type inherited?

Typically X-linked dominant (Orphanet). A genetic counselor can assess individual risk for a family.

CASK p.Arg613fs

c.1838del · VCV4531271

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

syndromic X-linked intellectual disability Najm type

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 20 of 27
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.2	GERP 1.7, phastCons 1

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

Variant & gene context

Gene: CASK
Protein: p.Arg613fs
Coding: c.1838del
MANE Select: NM_001367721
Type: Deletion
Location: chrX:41555604 (GRCh38)
Structure: AlphaFold pLDDT 79.45 · 22 PDB
Residue 613: a UniProt-annotated variant site (found in a patient with epilepsy and pontocerebellar hypoplasia; likely pathogenic); the sh3 domain; 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

Disease context

syndromic X-linked intellectual disability Najm type — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked intellectual disability, Najm type (Orphanet):

Inheritance: X-linked dominant
Onset: Infancy, Neonatal

Similar variants

CASK p.Arg613Ter Pathogenic/Likely pathogenic ★★ same residue
CASK p.Thr548fs Pathogenic/Likely pathogenic ★★ same condition
CASK p.Val292del Likely pathogenic ★★ same condition
CASK c.116_117delCA Pathogenic ★ same condition
CASK c.173-1145_278+7387del Likely pathogenic ★ same condition
CASK p.Asp98fs Pathogenic ★ same condition
CASK p.Cys205fs Likely pathogenic ★ same condition
CASK p.Ile649fs Likely pathogenic ★ 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-arg613fs (accessed [today's date]).

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