Is CDK13 p.Ala344fs (c.1021_1028dup) pathogenic?

CDK13 p.Ala344fs (c.10211028dup) is classified Uncertain significance in CDK13 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-09-11). Absent from gnomAD.

How common is CDK13 p.Ala344fs (c.1021_1028dup) in the general population?

CDK13 p.Ala344fs (c.1021_1028dup) is absent from gnomAD (gnomAD).

CDK13 p.Ala344fs

c.1021_1028dup · rs2116069714 · VCV1312067

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 7.7	GERP 1.4, 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.Ala344fs
Coding: c.1021_1028dup
MANE Select: NM_003718
dbSNP: rs2116069714
Type: Duplication
Location: chr7:39951659 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 344: the 'disordered' region

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

Similar variants

CDK13 p.Ser177fs Pathogenic/Likely pathogenic ★★ same type
CDK13 p.Pro51_Pro52insGlnLeuLeuGlnPro Uncertain significance ★★ same type
CDK13 p.Leu87fs Pathogenic ★ same type
CDK13 p.Ser385fs Pathogenic ★ same type
CDK13 p.Thr174fs Pathogenic ★ same type
CDK13 p.Val564Ter Pathogenic ★ same type
CDK13 c.2354-15885_2781-6387dup Uncertain significance ★ same type
CDK13 p.Ala162fs Conflicting classifications of pathogenicity ★ ⚠ same type

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-ala344fs (accessed [today's date]).

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