Is CDK16 p.Ser119= (c.357A>G) pathogenic?

CDK16 p.Ser119= (c.357A>G) is classified Benign in CDK16 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-11). Common (popmax 25%, afr) — too common for a highly-penetrant pathogenic allele; Associated with CDK16-related disorder.

What condition is associated with CDK16 p.Ser119= (c.357A>G)?

CDK16 p.Ser119= (c.357A>G) is associated with CDK16-related disorder (ClinVar).

CDK16 p.Ser119=

Q: How common is CDK16 p.Ser119= (c.357A>G) in the general population?

CDK16 p.Ser119= (c.357A>G) is common (popmax 25%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.357A>G · rs5952422 · VCV3059606

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 25%, afr) — too common for a highly-penetrant pathogenic allele

Conditions

CDK16-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.007	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.7	GERP -3.7
Overall
CADD	0.15	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 25% African / African-American · 14,232/56,874 alleles

Filtering AF 24.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 24.5%

Overall 1.37% 16,529/1,209,531 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	25%	4
Remaining individualsnot grpmax-eligible	2.09%	48
Admixed American	1.76%	57
Middle Eastern	1.68%	60
Ashkenazi Jewishnot grpmax-eligible	0.191%	524
South Asian	0.0915%	1,092
European (non-Finnish)	0.0366%	2,729
Finnishnot grpmax-eligible	0.00215%	46,539

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: CDK16
Protein: p.Ser119=
Coding: c.357A>G
MANE Select: NM_006201
dbSNP: rs5952422
Type: single nucleotide variant
Location: chrX:47224638 (GRCh38)
Structure: AlphaFold pLDDT 72.92 · 3 PDB
Residue 119: a modified residue (phosphoserine)

Full CDK16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CDK16-related disorder

Similar variants

CDK16 c.-6-416C>T Uncertain significance ★ same condition
CDK16 p.Asn392Ile Uncertain significance ⚠ same condition
CDK16 p.Ser65Pro Uncertain significance ⚠ same condition
CDK16 c.-6-431A>G Benign same condition
CDK16 p.His261Tyr Benign ⚠ same condition
CDK16 p.Leu118= Likely benign same condition
CDK16 c.12+1del Uncertain significance ★ same condition
CDK16 c.1376-10C>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/cdk16-p-ser119 (accessed [today's date]).

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