Is CASK p.Lys706del (c.2113AAG[1]) pathogenic?

CASK p.Lys706del (c.2113AAG[1]) is classified Uncertain significance in CASK (ClinVar, Single submitter, 1 submitter; last evaluated 2020-09-01). No gnomAD frequency available for this variant; Associated with Intellectual disability, CASK-related, X-linked.

What condition is associated with CASK p.Lys706del (c.2113AAG[1])?

CASK p.Lys706del (c.2113AAG[1]) is associated with Intellectual disability, CASK-related, X-linked (ClinVar).

How common is CASK p.Lys706del (c.2113AAG[1]) in the general population?

CASK p.Lys706del (c.2113AAG[1]) is no gnomAD frequency available for this variant (gnomAD).

CASK p.Lys706del

c.2113AAG[1] · rs2147111902 · VCV1054601

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

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.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1

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.Lys706del
Coding: c.2113AAG[1]
MANE Select: NM_001367721
dbSNP: rs2147111902
Type: Microsatellite
Location: chrX:41542728 (GRCh38)
Structure: AlphaFold pLDDT 79.45 · 22 PDB
Residue 706: a UniProt-annotated variant site (found in a patient with epilepsy and pontocerebellar hypoplasia; likely pathogenic); 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

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

Similar variants

CASK c.430-27_430-20del Benign/Likely benign ★★ same condition
CASK c.430-31TGTT[2] Benign ★★ same condition
CASK c.1314+5_1314+8del Conflicting classifications of pathogenicity ★ same condition
CASK c.430-31TGTT[4] Likely benign ★ same condition
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

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-lys706del (accessed [today's date]).

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