Is CDK2 p.Val79Gly (c.236T>G) pathogenic?

CDK2 p.Val79Gly (c.236T>G) is classified Uncertain significance in CDK2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-10). AlphaMissense: likely pathogenic (0.9572); Very rare (popmax 0.00668%, afr).

How common is CDK2 p.Val79Gly (c.236T>G) in the general population?

CDK2 p.Val79Gly (c.236T>G) is very rare (popmax 0.00668%, afr) (gnomAD).

What do computational predictors say about CDK2 p.Val79Gly (c.236T>G)?

AlphaMissense predicts likely pathogenic (score 0.9572) — an in-silico prediction, not a clinical call.

CDK2 p.Val79Gly

c.236T>G · rs369617221 · VCV2326489

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9572 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00668%, afr)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9572	likely pathogenic
REVEL	0.854	moderately pathogenic-leaning
SaProt	LLR -14.30	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 2.3, phastCons 1
Regional constraint	o/e 0.34	constrained · MANE · 1,122 bp · p 7e-12 · regional, not allelic
Overall
CADD	30.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% African / African-American · 5/74,892 alleles

Filtering AF 0.00255% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00162%

Overall 0.00124% 20/1,613,946 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00668%	14,978
European (non-Finnish)	0.00127%	78,665

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: CDK2
Protein: p.Val79Gly
Coding: c.236T>G
MANE Select: NM_001798
dbSNP: rs369617221
Type: single nucleotide variant
Location: chr12:55968090 (GRCh38)
Gene constraint: LOEUF 0.39 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 88.55 · 523 PDB
Residue 79: the protein kinase domain; a β-strand

Full CDK2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDK2 p.Arg199His Uncertain significance ★ ⚠ same type
CDK2 p.Arg200Gln Uncertain significance ★ ⚠ same type
CDK2 p.Arg200Trp Uncertain significance ★ ⚠ same type
CDK2 p.Arg214Gln Uncertain significance ★ ⚠ same type
CDK2 p.Asp288His Uncertain significance ★ ⚠ same type
CDK2 p.Cys191Arg Uncertain significance ★ ⚠ same type
CDK2 p.Glu57Ala Uncertain significance ★ ⚠ same type
CDK2 p.His268Leu Uncertain significance ★ ⚠ 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/cdk2-p-val79gly (accessed [today's date]).

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