Is CDK20 p.Phe83= (c.249C>T) pathogenic?

CDK20 p.Phe83= (c.249C>T) is classified Likely benign in CDK20 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-02-03). Ultra-rare (popmax 0.0183%, amr); Associated with CDK20-related disorder.

What condition is associated with CDK20 p.Phe83= (c.249C>T)?

CDK20 p.Phe83= (c.249C>T) is associated with CDK20-related disorder (ClinVar).

How common is CDK20 p.Phe83= (c.249C>T) in the general population?

CDK20 p.Phe83= (c.249C>T) is ultra-rare (popmax 0.0183%, amr) (gnomAD).

CDK20 p.Phe83=

c.249C>T · rs373884873 · VCV3054527

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0183%, amr)

Conditions

CDK20-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.4	GERP 0.41, phastCons 1
Overall
CADD	8.593	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0183% Admixed American · 11/59,980 alleles

Filtering AF 0.0102% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00786%

Overall 0.00273% 44/1,613,940 alleles · ultra-rare exomes 36/1,461,766 · genomes 8/152,174 · joint denominator

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0811%	1,234
Admixed Americangrpmax	0.0183%	5,453
Remaining individualsnot grpmax-eligible	0.0048%	20,828
African / African-American	0.00133%	74,934
European (non-Finnish)	0.000424%	235,998

Ashkenazi Jewish 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.Phe83=
Coding: c.249C>T
MANE Select: NM_001039803
dbSNP: rs373884873
Type: single nucleotide variant
Location: chr9:87971276 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 83: 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.Arg179Cys Likely benign same condition
CDK20 p.Asp256= 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-phe83 (accessed [today's date]).

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