Is CDK4 p.Lys88= (c.264G>A) pathogenic?

CDK4 p.Lys88= (c.264G>A) is classified Benign/Likely benign in CDK4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-09-25). Absent from gnomAD v4.1; Associated with melanoma, cutaneous malignant, susceptibility to, 3.

What condition is associated with CDK4 p.Lys88= (c.264G>A)?

CDK4 p.Lys88= (c.264G>A) is associated with melanoma, cutaneous malignant, susceptibility to, 3, familial melanoma (ClinVar).

How common is CDK4 p.Lys88= (c.264G>A) in the general population?

CDK4 p.Lys88= (c.264G>A) is absent from gnomAD v4.1 (gnomAD).

CDK4 p.Lys88=

c.264G>A · rs2140387452 · VCV1160538

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

melanoma, cutaneous malignant, susceptibility to, 3

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 1.1	GERP -0.16, phastCons 1
Overall
CADD	17.72	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CDK4
Protein: p.Lys88=
Coding: c.264G>A
MANE Select: NM_000075
dbSNP: rs2140387452
Type: single nucleotide variant
Location: chr12:57751297 (GRCh38)
Gene constraint: LOEUF 0.61 · pLI 0.57 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 87.56 · 15 PDB
Residue 88: the protein kinase domain; a β-strand

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

Disease context

melanoma, cutaneous malignant, susceptibility to, 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial melanoma

Similar variants

CDK4 p.Lys88Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
CDK4 p.Lys88Gln Uncertain significance ★ ⚠ same residue
CDK4 p.Lys88Glu 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-lys88 (accessed [today's date]).

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