Is CDK16 p.Ala474Thr (c.1420G>A) pathogenic?

CDK16 p.Ala474Thr (c.1420G>A) is classified Uncertain significance in CDK16 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-10). AlphaMissense: likely benign (0.0674); Very rare (popmax 0.00101%, nfe).

How common is CDK16 p.Ala474Thr (c.1420G>A) in the general population?

CDK16 p.Ala474Thr (c.1420G>A) is very rare (popmax 0.00101%, nfe) (gnomAD).

What do computational predictors say about CDK16 p.Ala474Thr (c.1420G>A)?

AlphaMissense predicts likely benign (score 0.0674) — an in-silico prediction, not a clinical call.

CDK16 p.Ala474Thr

c.1420G>A · VCV3489451

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0674 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00101%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0674	likely benign
REVEL	0.13	moderately benign-leaning
SaProt	LLR -2.94	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.8	GERP 1.8, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 1,939 bp · p 0.00071 · regional, not allelic
Overall
CADD	21.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00101% European (non-Finnish) · 9/894,735 alleles

Filtering AF 0.000473% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000343%

Overall 0.000744% 9/1,209,494 alleles · very rare

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.Ala474Thr
Coding: c.1420G>A
MANE Select: NM_006201
Type: single nucleotide variant
Location: chrX:47228611 (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-ala474thr (accessed [today's date]).

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