Is CDK20 p.Leu269= (c.807T>G) pathogenic?

CDK20 p.Leu269= (c.807T>G) is classified Likely benign in CDK20 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-11). Very rare (popmax 0.00439%, sas).

How common is CDK20 p.Leu269= (c.807T>G) in the general population?

CDK20 p.Leu269= (c.807T>G) is very rare (popmax 0.00439%, sas) (gnomAD).

CDK20 p.Leu269=

c.807T>G · rs753946529 · VCV2610547

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00439%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.185	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.59	phastCons 0.001
Overall
CADD	2.064	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00439% South Asian · 4/91,092 alleles

Filtering AF 0.00143% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.00031% 5/1,613,924 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00439%	22,773
African / African-American	0.00134%	74,888

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.Leu269=
Coding: c.807T>G
MANE Select: NM_001039803
dbSNP: rs753946529
Type: single nucleotide variant
Location: chr9:87969230 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 269: 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-leu269 (accessed [today's date]).

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