Is CDKN2A p.Pro64Thr (c.190C>A) pathogenic?

CDKN2A p.Pro64Thr (c.190C>A) is classified Uncertain significance in CDKN2A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-04). Absent from gnomAD v4.1.

How common is CDKN2A p.Pro64Thr (c.190C>A) in the general population?

CDKN2A p.Pro64Thr (c.190C>A) is absent from gnomAD v4.1 (gnomAD).

CDKN2A p.Pro64Thr

c.190C>A · rs1427767413 · VCV2663137

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.233	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -1.3, phastCons 1
Overall
CADD	22.4	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.Pro64Thr
Coding: c.190C>A
MANE Select: NM_000077 · reported on NM_058195
dbSNP: rs1427767413
Type: single nucleotide variant
Location: chr9:21994142 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 64: an α-helix; the 'interaction with cdk5rap3 and mdm2' region; the 'disordered' region

Full CDKN2A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CDKN2A p.Leu64Val Uncertain significance ★★ ⚠ same residue
CDKN2A p.Pro64= Uncertain significance ★★ same residue
CDKN2A p.Pro64Arg Uncertain significance ★★ same residue
CDKN2A p.Pro64Gln Uncertain significance ★★ same residue
CDKN2A p.Pro64Leu Uncertain significance ★★ same residue
CDKN2A p.Leu64= Conflicting classifications of pathogenicity ★ same residue
CDKN2A p.Leu64Pro Uncertain significance ★ ⚠ same residue
CDKN2A p.Leu64fs Pathogenic ★★ 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-pro64thr (accessed [today's date]).

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