Is CDK20 p.Arg179Cys (c.535C>T) pathogenic?

CDK20 p.Arg179Cys (c.535C>T) is classified Likely benign in CDK20 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-01-16). AlphaMissense: likely benign (0.1353); Rare (popmax 0.206%, nfe); Associated with CDK20-related disorder.

What condition is associated with CDK20 p.Arg179Cys (c.535C>T)?

CDK20 p.Arg179Cys (c.535C>T) is associated with CDK20-related disorder (ClinVar).

How common is CDK20 p.Arg179Cys (c.535C>T) in the general population?

CDK20 p.Arg179Cys (c.535C>T) is rare (popmax 0.206%, nfe) (gnomAD).

What do computational predictors say about CDK20 p.Arg179Cys (c.535C>T)?

AlphaMissense predicts likely benign (score 0.1353) — an in-silico prediction, not a clinical call.

CDK20 p.Arg179Cys

c.535C>T · rs138822378 · VCV3055815

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1353 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.206%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

CDK20-related disorder

Computational evidence

Protein change
AlphaMissense	0.1353	likely benign
REVEL	0.467	indeterminate
SaProt	LLR -8.22	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 3.1	phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,981 bp · p 0.0053 · regional, not allelic
Overall
CADD	26.9	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 0.206% European (non-Finnish) · 2,432/1,180,006 alleles

Filtering AF 0.199% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.196%

Overall 0.178% 2,872/1,614,070 alleles · rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.53%	189
European (non-Finnish)grpmax	0.206%	485
Amishnot grpmax-eligible	0.11%	912
Remaining individualsnot grpmax-eligible	0.0944%	1,059
Admixed American	0.03%	3,334
African / African-American	0.028%	3,573
Middle Eastern	0.0165%	6,062
South Asian	0.0011%	91,084

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Arg179Cys
Coding: c.535C>T
MANE Select: NM_001039803
dbSNP: rs138822378
Type: single nucleotide variant
Location: chr9:87970596 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 179: 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.Arg158Cys 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-arg179cys (accessed [today's date]).

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