Is CDK13 p.Leu61fs (c.181del) pathogenic?

CDK13 p.Leu61fs (c.181del) is classified Pathogenic/Likely pathogenic in CDK13 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-08-16). Absent from gnomAD; Associated with Inborn genetic diseases.

What condition is associated with CDK13 p.Leu61fs (c.181del)?

CDK13 p.Leu61fs (c.181del) is associated with Inborn genetic diseases, congenital heart defects, dysmorphic facial features, and intellectual developmental disorder (ClinVar).

How common is CDK13 p.Leu61fs (c.181del) in the general population?

CDK13 p.Leu61fs (c.181del) is absent from gnomAD (gnomAD).

CDK13 p.Leu61fs

c.181del · rs1554317002 · VCV521173

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

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 1 of 14
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.3	GERP 0.57, phastCons 1
Region caveats
Repeat context	tandem	(GCC)n simple repeat · ambiguous alignment · confidence, not pathogenicity

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.Leu61fs
Coding: c.181del
MANE Select: NM_003718
dbSNP: rs1554317002
Type: Deletion
Location: chr7:39950821 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB

Full CDK13 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

Also linked: congenital heart defects, dysmorphic facial features, and intellectual developmental disorder

Similar variants

CDK13 p.Ser662del Uncertain significance ★★ same condition
CDK13 p.Ala561fs Pathogenic ★ same condition
CDK13 p.Arg110fs Likely pathogenic ★ same condition
CDK13 p.Arg301fs Pathogenic ★ same condition
CDK13 p.Glu654fs Pathogenic ★ same condition
CDK13 p.Glu775fs Likely pathogenic ★ same condition
CDK13 p.Phe809fs Likely pathogenic ★ same condition
CDK13 p.Ala633del 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/cdk13-p-leu61fs (accessed [today's date]).

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