Is CDKN2A p.Ala102= (c.306G>A) pathogenic?

CDKN2A p.Ala102= (c.306G>A) is classified Uncertain significance in CDKN2A (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-01). Very rare (popmax 0.00017%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Ala102= (c.306G>A)?

CDKN2A p.Ala102= (c.306G>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CDKN2A p.Ala102= (c.306G>A) in the general population?

CDKN2A p.Ala102= (c.306G>A) is very rare (popmax 0.00017%, nfe) (gnomAD).

CDKN2A p.Ala102=

c.306G>A · rs1064794863 · VCV1732029

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.274	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.34	GERP -3.4, phastCons 0.008
Overall
CADD	7.209	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00017% European (non-Finnish) · 2/1,179,312 alleles

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

Overall 0.000138% 2/1,452,984 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.Ala102=
Coding: c.306G>A
MANE Select: NM_000077
dbSNP: rs1064794863
Type: single nucleotide variant
Location: chr9:21971053 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 102: a UniProt-annotated variant site (found in seminoma and medulloblastoma tissues from li-fraumeni syndrome patients carrying a mutation in tp53; somatic mutation); a UniProt-annotated variant site (in); the 'disordered' 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.Ala102Thr Uncertain significance ★★ ⚠ same residue
CDKN2A p.Ala102Val Uncertain significance ★★ ⚠ same residue
CDKN2A p.Ala102Glu Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN2A p.Ala102Leu Uncertain significance ★ same residue
CDKN2A p.Ala102Ser Uncertain significance ★ ⚠ same residue
CDKN2A c.150+2T>G Likely pathogenic ★★ same condition
CDKN2A c.151-1G>C Pathogenic ★★ same condition
CDKN2A c.151-1G>T Pathogenic/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-ala102 (accessed [today's date]).

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