Is CDKN2A p.His66Pro (c.197A>C) pathogenic?

CDKN2A p.His66Pro (c.197A>C) is classified Uncertain significance in CDKN2A (ClinVar, Multiple submitters, 3 submitters; last evaluated 2022-01-26). AlphaMissense: likely pathogenic (0.7036); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.His66Pro (c.197A>C)?

CDKN2A p.His66Pro (c.197A>C) is associated with hereditary neoplastic syndrome, melanoma (ClinVar).

How common is CDKN2A p.His66Pro (c.197A>C) in the general population?

CDKN2A p.His66Pro (c.197A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDKN2A p.His66Pro (c.197A>C)?

AlphaMissense predicts likely pathogenic (score 0.7036) — an in-silico prediction, not a clinical call.

CDKN2A p.His66Pro

c.197A>C · rs756750256 · VCV419802

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely pathogenic

0.7036 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.7036	likely pathogenic
REVEL	0.786	moderately pathogenic-leaning
SaProt	LLR -14.22	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.9	GERP 2.1, phastCons 1
Regional constraint	o/e 1.13	unconstrained · MANE · 6,595 bp · p 0.04 · regional, not allelic
Overall
CADD	23.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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.His66Pro
Coding: c.197A>C
MANE Select: NM_000077
dbSNP: rs756750256
Type: single nucleotide variant
Location: chr9:21971162 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 66: a UniProt-annotated variant site (in non-small cell lung carcinoma); 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

Also linked: melanoma

Similar variants

CDKN2A p.His66Gln Uncertain significance ★★ ⚠ same residue
CDKN2A p.His66= Conflicting classifications of pathogenicity ★ same residue
CDKN2A p.His66Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN2A p.His66Asp Uncertain significance ★ ⚠ same residue
CDKN2A p.His66Tyr 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-his66pro (accessed [today's date]).

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