Is CDK20 p.Asp256= (c.768C>T) pathogenic?

CDK20 p.Asp256= (c.768C>T) is classified Likely benign in CDK20 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-07-07). Rare (popmax 0.147%, sas); Associated with CDK20-related disorder.

What condition is associated with CDK20 p.Asp256= (c.768C>T)?

CDK20 p.Asp256= (c.768C>T) is associated with CDK20-related disorder (ClinVar).

How common is CDK20 p.Asp256= (c.768C>T) in the general population?

CDK20 p.Asp256= (c.768C>T) is rare (popmax 0.147%, sas) (gnomAD).

CDK20 p.Asp256=

c.768C>T · rs546971086 · VCV3048333

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.147%, sas)

Conditions

CDK20-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.179	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -7.2
Overall
CADD	0.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.147% South Asian · 134/91,082 alleles

Filtering AF 0.127% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.119%

Overall 0.00954% 154/1,613,994 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.147%	680
Remaining individualsnot grpmax-eligible	0.0096%	10,416
Admixed American	0.00667%	15,002
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,600
East Asian	0.00223%	44,860
European (non-Finnish)	0.000678%	147,490

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.Asp256=
Coding: c.768C>T
MANE Select: NM_001039803
dbSNP: rs546971086
Type: single nucleotide variant
Location: chr9:87969269 (GRCh38)
Gene constraint: LOEUF 1.342 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.08
Residue 256: 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.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-asp256 (accessed [today's date]).

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