Is CDKN2A p.Met54Leu (c.160A>T) pathogenic?

CDKN2A p.Met54Leu (c.160A>T) is classified Uncertain significance in CDKN2A (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-06-11). AlphaMissense: likely benign (0.324); Very rare (popmax 0.00017%, nfe); Associated with familial melanoma.

What condition is associated with CDKN2A p.Met54Leu (c.160A>T)?

CDKN2A p.Met54Leu (c.160A>T) is associated with familial melanoma, hereditary neoplastic syndrome (ClinVar).

How common is CDKN2A p.Met54Leu (c.160A>T) in the general population?

CDKN2A p.Met54Leu (c.160A>T) is very rare (popmax 0.00017%, nfe) (gnomAD).

How is Familial melanoma inherited?

Typically Autosomal dominant, Multigenic/multifactorial (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about CDKN2A p.Met54Leu (c.160A>T)?

AlphaMissense predicts likely benign (score 0.324) — an in-silico prediction, not a clinical call.

CDKN2A p.Met54Leu

c.160A>T · rs201314211 · VCV1483043

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.324 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

familial melanoma

Computational evidence

Protein change
AlphaMissense	0.324	likely benign
REVEL	0.682	pathogenic-leaning
SaProt	LLR -5.39	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 2.1, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,595 bp · p 0.04 · regional, not allelic
Overall
CADD	20.9	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 0.00017% European (non-Finnish) · 2/1,179,016 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000138% 2/1,445,492 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: CDKN2A
Protein: p.Met54Leu
Coding: c.160A>T
MANE Select: NM_000077
dbSNP: rs201314211
Type: single nucleotide variant
Location: chr9:21971199 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 54: the 'interaction with cdk5rap3 and mdm2' region

Full CDKN2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

familial melanoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hereditary neoplastic syndrome

For Familial melanoma (Orphanet):

Inheritance: Autosomal dominant, Multigenic/multifactorial
Onset: Adult
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

CDKN2A p.Arg54Cys Uncertain significance ★★ same residue
CDKN2A p.Arg54Ser Uncertain significance ★★ same residue
CDKN2A p.Met54Ile Uncertain significance ★★ ⚠ same residue
CDKN2A p.Arg54His Uncertain significance ★ same residue
CDKN2A p.Met54Arg Uncertain significance ★ ⚠ same residue
CDKN2A p.Met54Thr Uncertain significance ★ ⚠ same residue
CDKN2A p.Met54_Gly55insMet Uncertain significance ★ same residue
CDKN2A p.Met54del Conflicting classifications of pathogenicity ★ same residue

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/cdkn2a-p-met54leu (accessed [today's date]).

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