Is CDKN2A p.Met54Arg (c.161T>G) pathogenic?

CDKN2A p.Met54Arg (c.161T>G) is classified Uncertain significance in CDKN2A (ClinVar, Single submitter, 1 submitter; last evaluated 2019-02-26). AlphaMissense: likely benign (0.3292); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Met54Arg (c.161T>G)?

CDKN2A p.Met54Arg (c.161T>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CDKN2A p.Met54Arg (c.161T>G) in the general population?

CDKN2A p.Met54Arg (c.161T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDKN2A p.Met54Arg (c.161T>G)?

AlphaMissense predicts likely benign (score 0.3292) — an in-silico prediction, not a clinical call.

CDKN2A p.Met54Arg

c.161T>G · rs1587332544 · VCV819690

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3292 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.3292	likely benign
REVEL	0.668	pathogenic-leaning
SaProt	LLR -5.28	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 11	GERP 2.1, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,595 bp · p 0.04 · regional, not allelic
Overall
CADD	24.7	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

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: CDKN2A
Protein: p.Met54Arg
Coding: c.161T>G
MANE Select: NM_000077
dbSNP: rs1587332544
Type: single nucleotide variant
Location: chr9:21971198 (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

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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.Met54Leu Uncertain significance ★★ ⚠ same residue
CDKN2A p.Arg54His 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-met54arg (accessed [today's date]).

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