Is CDK4 p.Thr116Met (c.347C>T) pathogenic?

CDK4 p.Thr116Met (c.347C>T) is classified Uncertain significance in CDK4 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-11-10). AlphaMissense: likely benign (0.1049); Very rare (popmax 0.00133%, afr); Associated with CDK4-related disorder.

What condition is associated with CDK4 p.Thr116Met (c.347C>T)?

CDK4 p.Thr116Met (c.347C>T) is associated with CDK4-related disorder, hereditary neoplastic syndrome, familial melanoma (ClinVar).

How common is CDK4 p.Thr116Met (c.347C>T) in the general population?

CDK4 p.Thr116Met (c.347C>T) is very rare (popmax 0.00133%, afr) (gnomAD).

What do computational predictors say about CDK4 p.Thr116Met (c.347C>T)?

AlphaMissense predicts likely benign (score 0.1049) — an in-silico prediction, not a clinical call.

CDK4 p.Thr116Met

c.347C>T · rs1060501931 · VCV408339

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.1049 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CDK4-related disorder

Computational evidence

Protein change
AlphaMissense	0.1049	likely benign
REVEL	0.104	moderately benign-leaning
SaProt	LLR -10.13	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 0.74	unconstrained · MANE · 3,189 bp · p 2e-07 · regional, not allelic
Overall
CADD	23.4	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 0.00133% African / African-American · 1/74,926 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000558% 9/1,614,040 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00133%	74,926
European (non-Finnish)	0.000678%	147,505

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: CDK4
Protein: p.Thr116Met
Coding: c.347C>T
MANE Select: NM_000075
dbSNP: rs1060501931
Type: single nucleotide variant
Location: chr12:57751214 (GRCh38)
Gene constraint: LOEUF 0.61 · pLI 0.57 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 87.56 · 15 PDB
Residue 116: the protein kinase domain; an α-helix

Full CDK4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CDK4-related disorder

Also linked: hereditary neoplastic syndrome familial melanoma

Similar variants

CDK4 p.Thr116= Benign/Likely benign ★★ same residue
CDK4 p.Thr116Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
CDK4 p.Thr116Arg Uncertain significance ★ same residue
CDK4 p.Arg24Cys Pathogenic ★★ same condition
CDK4 p.Arg24His Pathogenic ★★ same condition
CDK4 c.354+3G>C Uncertain significance ★★ same condition
CDK4 c.354+5G>T Uncertain significance ★★ same condition
CDK4 c.355-4C>G Uncertain significance ★★ 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/cdk4-p-thr116met (accessed [today's date]).

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