Is CDK20 p.Arg158Cys (c.472C>T) pathogenic?

CDK20 p.Arg158Cys (c.472C>T) is classified Likely benign in CDK20 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-12-18). AlphaMissense: likely benign (0.1255); Rare (popmax 0.133%, afr); Associated with CDK20-related disorder.

What condition is associated with CDK20 p.Arg158Cys (c.472C>T)?

CDK20 p.Arg158Cys (c.472C>T) is associated with CDK20-related disorder (ClinVar).

How common is CDK20 p.Arg158Cys (c.472C>T) in the general population?

CDK20 p.Arg158Cys (c.472C>T) is rare (popmax 0.133%, afr) (gnomAD).

What do computational predictors say about CDK20 p.Arg158Cys (c.472C>T)?

AlphaMissense predicts likely benign (score 0.1255) — an in-silico prediction, not a clinical call.

CDK20 p.Arg158Cys

c.472C>T · rs138173042 · VCV3054204

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1255 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.133%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

CDK20-related disorder

Computational evidence

Protein change
AlphaMissense	0.1255	likely benign
REVEL	0.368	indeterminate
SaProt	LLR -6.65	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.7	phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,981 bp · p 0.0053 · regional, not allelic
Overall
CADD	24.2	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 0.133% African / African-American · 100/74,966 alleles

Filtering AF 0.112% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.104%

Overall 0.0101% 163/1,614,006 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.133%	750
Middle Eastern	0.0495%	2,021
Remaining individualsnot grpmax-eligible	0.0128%	7,813
Admixed American	0.00833%	12,002
European (non-Finnish)	0.00356%	28,095
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,606
Finnishnot grpmax-eligible	0.00312%	32,016
South Asian	0.0022%	45,537

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.Arg158Cys
Coding: c.472C>T
MANE Select: NM_001039803
dbSNP: rs138173042
Type: single nucleotide variant
Location: chr9:87970804 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 158: 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 p.Val91Met 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.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-arg158cys (accessed [today's date]).

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