Is CDKN2A p.Val20Ala (c.59T>C) pathogenic?

CDKN2A p.Val20Ala (c.59T>C) is classified Uncertain significance in CDKN2A (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-18). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Val20Ala (c.59T>C)?

CDKN2A p.Val20Ala (c.59T>C) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CDKN2A p.Val20Ala (c.59T>C) in the general population?

CDKN2A p.Val20Ala (c.59T>C) is absent from gnomAD v4.1 (gnomAD).

CDKN2A p.Val20Ala

c.59T>C · VCV4224767

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.094	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3	GERP -2.6, phastCons 1
Overall
CADD	17.99	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: CDKN2A
Protein: p.Val20Ala
Coding: c.59T>C
MANE Select: NM_000077 · reported on NM_058195
Type: single nucleotide variant
Location: chr9:21994273 (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

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.Ala20Val Uncertain significance ★★ ⚠ same residue
CDKN2A p.Ala20Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN2A p.Ala20Thr Uncertain significance ★ ⚠ same residue
CDKN2A p.Ala20= Likely benign ★ same residue
CDKN2A c.150+2T>G 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-val20ala (accessed [today's date]).

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