Is CDKN2A p.Ala20Val (c.59C>T) pathogenic?

CDKN2A p.Ala20Val (c.59C>T) is classified Uncertain significance in CDKN2A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-03-25). AlphaMissense: ambiguous (0.4974); No allele count reported in gnomAD v4.1 (AN 1,607,656); Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Ala20Val (c.59C>T)?

CDKN2A p.Ala20Val (c.59C>T) is associated with hereditary neoplastic syndrome, familial melanoma (ClinVar).

How common is CDKN2A p.Ala20Val (c.59C>T) in the general population?

CDKN2A p.Ala20Val (c.59C>T) is no allele count reported in gnomAD v4.1 (AN 1,607,656) (gnomAD).

What do computational predictors say about CDKN2A p.Ala20Val (c.59C>T)?

AlphaMissense predicts ambiguous (score 0.4974) — an in-silico prediction, not a clinical call.

CDKN2A p.Ala20Val

c.59C>T · rs864622484 · VCV1001191

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

ambiguous

0.4974 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,607,656)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.4974	ambiguous
REVEL	0.382	indeterminate
SaProt	LLR -8.48	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,595 bp · p 0.04 · regional, not allelic
Overall
CADD	25.9	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

No allele count reported in gnomAD v4.1 (AN 1,607,656). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CDKN2A
Protein: p.Ala20Val
Coding: c.59C>T
MANE Select: NM_000077
dbSNP: rs864622484
Type: single nucleotide variant
Location: chr9:21974769 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 20: an α-helix; a UniProt-annotated variant site (in a lung tumor and melanoma); a UniProt-annotated variant site (in a biliary tract tumor); 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

Also linked: familial melanoma

Similar variants

CDKN2A p.Ala20Glu Uncertain significance ★★ ⚠ same residue
CDKN2A p.Ala20Gly Uncertain significance ★★ same residue
CDKN2A p.Ala20Ser Uncertain significance ★★ ⚠ same residue
CDKN2A p.Ala20Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN2A p.Ala20Thr Uncertain significance ★ same residue
CDKN2A p.Val20Ala Uncertain significance ★ same residue
CDKN2A p.Ala20= Likely benign ★ same residue
CDKN2A c.150+1G>A Likely pathogenic ★★ 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/cdkn2a-p-ala20val (accessed [today's date]).

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