Is CDK16 p.Asn103Asp (c.307A>G) pathogenic?

CDK16 p.Asn103Asp (c.307A>G) is classified Uncertain significance in CDK16 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-21). AlphaMissense: ambiguous (0.512); Ultra-rare (popmax 0.0218%, sas).

How common is CDK16 p.Asn103Asp (c.307A>G) in the general population?

CDK16 p.Asn103Asp (c.307A>G) is ultra-rare (popmax 0.0218%, sas) (gnomAD).

What do computational predictors say about CDK16 p.Asn103Asp (c.307A>G)?

AlphaMissense predicts ambiguous (score 0.512) — an in-silico prediction, not a clinical call.

CDK16 p.Asn103Asp

c.307A>G · rs779886300 · VCV2620351

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.512 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0218%, sas)

Missense predictors

0/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.512	ambiguous
REVEL	0.168	moderately benign-leaning
SaProt	LLR -6.12	tolerated
⇒ REVEL and SaProt both call this tolerated; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.4	GERP 1.8, phastCons 1
Regional constraint	o/e 0.69	unconstrained · MANE · 954 bp · p 0.002 · regional, not allelic
Overall
CADD	22.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0218% South Asian · 12/55,106 alleles

Filtering AF 0.0125% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00982%

Overall 0.00225% 27/1,199,571 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0218%	4,592
Admixed American	0.00887%	11,269
Remaining individualsnot grpmax-eligible	0.00424%	23,603
African / African-American	0.00356%	28,106
European (non-Finnish)	0.000787%	127,121

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.Asn103Asp
Coding: c.307A>G
MANE Select: NM_006201
dbSNP: rs779886300
Type: single nucleotide variant
Location: chrX:47224489 (GRCh38)
Structure: AlphaFold pLDDT 72.92 · 3 PDB

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-asn103asp (accessed [today's date]).

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