Is CDK13 p.Glu775fs (c.2322_2325del) pathogenic?

CDK13 p.Glu775fs (c.23222325del) is classified Likely pathogenic in CDK13 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-28). Absent from gnomAD; Associated with congenital heart defects, dysmorphic facial features, and intellectual developmental disorder.

How common is CDK13 p.Glu775fs (c.2322_2325del) in the general population?

CDK13 p.Glu775fs (c.2322_2325del) is absent from gnomAD (gnomAD).

CDK13 p.Glu775fs

Q: What condition is associated with CDK13 p.Glu775fs (c.2322_2325del)?

CDK13 p.Glu775fs (c.2322_2325del) is associated with congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (ClinVar).

Q: How is CDK13-related developmental delay-intellectual disability-facial dysmorphism-congenital heart defects syndrome inherited?

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

c.2322_2325del · rs2116327857 · VCV1302013

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

congenital heart defects, dysmorphic facial features, and intellectual developmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 5 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.8	GERP -1.3, phastCons 1

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

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: CDK13
Protein: p.Glu775fs
Coding: c.2322_2325del
MANE Select: NM_003718
dbSNP: rs2116327857
Type: Deletion
Location: chr7:40001998 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 775: the protein kinase domain

Full CDK13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital heart defects, dysmorphic facial features, and intellectual developmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For CDK13-related developmental delay-intellectual disability-facial dysmorphism-congenital heart defects syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood, Infancy

Similar variants

CDK13 p.Leu61fs Pathogenic/Likely pathogenic ★★ same condition
CDK13 p.Ser662del Uncertain significance ★★ same condition
CDK13 p.Arg110fs Likely pathogenic ★ same condition
CDK13 p.Phe809fs Likely pathogenic ★ same condition
CDK13 p.Ala633del Uncertain significance ★ same condition
CDK13 p.Glu195_Arg200del Uncertain significance ★ same condition
CDK13 p.Glu769_Ile770insTer Uncertain significance ★ same condition
CDK13 p.Ser269fs 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/cdk13-p-glu775fs (accessed [today's date]).

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