Is CDK20 p.Arg39Pro (c.116G>C) pathogenic?

CDK20 p.Arg39Pro (c.116G>C) is classified Uncertain significance in CDK20 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-12). AlphaMissense: ambiguous (0.4015); Rare (popmax 0.201%, sas).

How common is CDK20 p.Arg39Pro (c.116G>C) in the general population?

CDK20 p.Arg39Pro (c.116G>C) is rare (popmax 0.201%, sas) (gnomAD).

What do computational predictors say about CDK20 p.Arg39Pro (c.116G>C)?

AlphaMissense predicts ambiguous (score 0.4015) — an in-silico prediction, not a clinical call.

CDK20 p.Arg39Pro

c.116G>C · rs200054133 · VCV2388215

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4015 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.201%, sas)

Computational evidence

Protein change
AlphaMissense	0.4015	ambiguous
REVEL	0.307	indeterminate
SaProt	LLR -8.98	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3	GERP 1.5, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,981 bp · p 0.0053 · regional, not allelic
Overall
CADD	24.5	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 0.201% South Asian · 183/91,088 alleles

Filtering AF 0.177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.168%

Overall 0.0142% 229/1,614,178 alleles · rare exomes 220/1,461,862 · genomes 9/152,316 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.201%	498
Middle Eastern	0.066%	1,516
Remaining individualsnot grpmax-eligible	0.0144%	6,946
Admixed American	0.00333%	30,014
European (non-Finnish)	0.00263%	38,066

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.Arg39Pro
Coding: c.116G>C
MANE Select: NM_001039803
dbSNP: rs200054133
Type: single nucleotide variant
Location: chr9:87973995 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 39: the protein kinase domain

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

Similar variants

CDK20 p.Arg39Gln Uncertain significance ★ ⚠ same residue
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

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-arg39pro (accessed [today's date]).

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