Is CDK13 p.Ala970Val (c.2909C>T) pathogenic?

CDK13 p.Ala970Val (c.2909C>T) is classified Uncertain significance in CDK13 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-20). AlphaMissense: likely benign (0.1154); Very rare (popmax 0.002%, amr); Associated with Inborn genetic diseases.

What condition is associated with CDK13 p.Ala970Val (c.2909C>T)?

CDK13 p.Ala970Val (c.2909C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CDK13 p.Ala970Val (c.2909C>T) in the general population?

CDK13 p.Ala970Val (c.2909C>T) is very rare (popmax 0.002%, amr) (gnomAD).

What do computational predictors say about CDK13 p.Ala970Val (c.2909C>T)?

AlphaMissense predicts likely benign (score 0.1154) — an in-silico prediction, not a clinical call.

CDK13 p.Ala970Val

c.2909C>T · rs1440361300 · VCV2809332

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1154 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.002%, amr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1154	likely benign
REVEL	0.344	indeterminate
SaProt	LLR -10.07	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.31 · evaluated, not missing
Constraint at this position
Conservation	phyloP 7.7	GERP 2.3, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 129 bp · p 0.11 · regional, not allelic
Overall
CADD	27.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.002% Admixed American · 1/50,002 alleles

Overall 6.65e-05% 1/1,504,188 alleles · very rare exomes 1/1,352,246 · genomes 0/151,942 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CDK13
Protein: p.Ala970Val
Coding: c.2909C>T
MANE Select: NM_003718
dbSNP: rs1440361300
Type: single nucleotide variant
Location: chr7:40078731 (GRCh38)
Gene constraint: LOEUF 0.434 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 50.59 · 2 PDB
Residue 970: the protein kinase domain; an α-helix

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

Similar variants

CDK13 p.Ala1301Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala134Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala182Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala331Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Ala504Val Uncertain significance ★★ ⚠ same condition
CDK13 p.Arg1366Cys Uncertain significance ★★ ⚠ same condition
CDK13 p.Arg197Ser Uncertain significance ★★ ⚠ same condition
CDK13 p.Arg199Cys 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-ala970val (accessed [today's date]).

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