Is CDK20 p.Val91Met (c.271G>A) pathogenic?

CDK20 p.Val91Met (c.271G>A) is classified Uncertain significance in CDK20 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-01-26). AlphaMissense: likely benign (0.3114); Rare (popmax 0.214%, mid); Associated with CDK20-related disorder.

What condition is associated with CDK20 p.Val91Met (c.271G>A)?

CDK20 p.Val91Met (c.271G>A) is associated with CDK20-related disorder (ClinVar).

How common is CDK20 p.Val91Met (c.271G>A) in the general population?

CDK20 p.Val91Met (c.271G>A) is rare (popmax 0.214%, mid) (gnomAD).

What do computational predictors say about CDK20 p.Val91Met (c.271G>A)?

AlphaMissense predicts likely benign (score 0.3114) — an in-silico prediction, not a clinical call.

CDK20 p.Val91Met

c.271G>A · rs564653137 · VCV3029878

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3114 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.214%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CDK20-related disorder

Computational evidence

Protein change
AlphaMissense	0.3114	likely benign
REVEL	0.228	benign-leaning
SaProt	LLR -8.07	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.7	GERP 1.4, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,981 bp · p 0.0053 · regional, not allelic
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.214% Middle Eastern · 13/6,062 alleles

Filtering AF 0.127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.101%

Overall 0.000929% 15/1,614,158 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.214%	466
Remaining individualsnot grpmax-eligible	0.0016%	62,510
South Asian	0.0011%	91,080

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: CDK20
Protein: p.Val91Met
Coding: c.271G>A
MANE Select: NM_001039803
dbSNP: rs564653137
Type: single nucleotide variant
Location: chr9:87971254 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 91: the protein kinase domain

Full CDK20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CDK20-related disorder

Similar variants

CDK20 p.Tyr215His Uncertain significance ★ ⚠ same condition
CDK20 c.190-6C>A Likely benign same condition
CDK20 c.-10C>T Likely benign same condition
CDK20 p.Ala95= Likely benign same condition
CDK20 p.Arg158Cys Likely benign same condition
CDK20 p.Arg179Cys Likely benign ⚠ same condition
CDK20 p.Asp256= Likely benign same condition
CDK20 p.Glu345= Likely benign 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/cdk20-p-val91met (accessed [today's date]).

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