Is CDK16 p.Ser3= (c.9C>G) pathogenic?

CDK16 p.Ser3= (c.9C>G) is classified Likely benign in CDK16 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-01). Ultra-rare (popmax 0.0724%, amr).

How common is CDK16 p.Ser3= (c.9C>G) in the general population?

CDK16 p.Ser3= (c.9C>G) is ultra-rare (popmax 0.0724%, amr) (gnomAD).

CDK16 p.Ser3=

c.9C>G · rs782533683 · VCV2660412

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0724%, amr)

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 -0.35	GERP -2.1
Overall
CADD	8.379	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0724% Admixed American · 28/38,665 alleles

Filtering AF 0.0514% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0443%

Overall 0.0164% 191/1,166,144 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0724%	1,381
Middle Eastern	0.0465%	2,151
European (non-Finnish)	0.0175%	5,705
Remaining individualsnot grpmax-eligible	0.0152%	6,561
Ashkenazi Jewishnot grpmax-eligible	0.0047%	21,280

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.Ser3=
Coding: c.9C>G
MANE Select: NM_006201 · reported on NM_033018
dbSNP: rs782533683
Type: single nucleotide variant
Location: chrX:47218661 (GRCh38)
Structure: AlphaFold pLDDT 72.92 · 3 PDB
Residue 3: the 'disordered' region

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

Similar variants

CDK16 c.1376-10C>T Benign ★★ same type
CDK16 c.793-5C>T Benign ★★ same type
CDK16 c.-6-279C>T Benign ★★ same type
CDK16 p.Gly347= Likely benign ★★ same type
CDK16 p.Leu15Phe Likely pathogenic ★ ⚠ same type
CDK16 c.-5T>G Uncertain significance ★ same type
CDK16 c.-6-245C>T Uncertain significance ★ same type
CDK16 c.-6-264A>G Uncertain significance ★ 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-ser3 (accessed [today's date]).

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