Is CDK20 p.Ala261Glu (c.782C>A) pathogenic?

CDK20 p.Ala261Glu (c.782C>A) is classified Uncertain significance in CDK20 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-28). AlphaMissense: ambiguous (0.5158); Very rare (popmax 6.84e-05%).

How common is CDK20 p.Ala261Glu (c.782C>A) in the general population?

CDK20 p.Ala261Glu (c.782C>A) is very rare (popmax 6.84e-05%) (gnomAD).

What do computational predictors say about CDK20 p.Ala261Glu (c.782C>A)?

AlphaMissense predicts ambiguous (score 0.5158) — an in-silico prediction, not a clinical call.

CDK20 p.Ala261Glu

c.782C>A · rs779975575 · VCV2340411

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5158 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 6.84e-05%)

Computational evidence

Protein change
AlphaMissense	0.5158	ambiguous
REVEL	0.565	indeterminate
SaProt	LLR -11.18	damaging
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>A here scores Δ0.96 · evaluated, not missing
Constraint at this position
Conservation	phyloP 8.3	phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,981 bp · p 0.0053 · regional, not allelic
Overall
CADD	25.0	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 6.84e-05%

Overall 6.84e-05% 1/1,461,814 alleles · very rare

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.Ala261Glu
Coding: c.782C>A
MANE Select: NM_001039803
dbSNP: rs779975575
Type: single nucleotide variant
Location: chr9:87969255 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 261: the protein kinase domain

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

Similar variants

CDK20 p.Phe204Leu Uncertain significance ★★ ⚠ same type
CDK20 c.189+23G>C Benign ★★ same type
CDK20 c.378+19C>T Benign ★★ same type
CDK20 c.564-44C>T Benign ★★ same type
CDK20 c.688-214G>A Benign ★★ same type
CDK20 c.76-20G>T Benign ★★ same type
CDK20 c.76-66T>C Benign ★★ same type
CDK20 c.*153C>T Benign ★★ 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/cdk20-p-ala261glu (accessed [today's date]).

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