Is CDKN2A p.Arg10Trp (c.28C>T) pathogenic?

CDKN2A p.Arg10Trp (c.28C>T) is classified Uncertain significance in CDKN2A (ClinVar, Single submitter, 1 submitter; last evaluated 2021-04-19). Ultra-rare (popmax 0.0166%, mid); Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Arg10Trp (c.28C>T)?

CDKN2A p.Arg10Trp (c.28C>T) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CDKN2A p.Arg10Trp (c.28C>T) in the general population?

CDKN2A p.Arg10Trp (c.28C>T) is ultra-rare (popmax 0.0166%, mid) (gnomAD).

CDKN2A p.Arg10Trp

c.28C>T · rs1554659242 · VCV1797416

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0166%, mid)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.578	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.5	GERP -1.5, phastCons 1
Overall
CADD	24.0	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0166% Middle Eastern · 1/6,038 alleles

Overall 6.88e-05% 1/1,452,616 alleles · ultra-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.Arg10Trp
Coding: c.28C>T
MANE Select: NM_000077 · reported on NM_058195
dbSNP: rs1554659242
Type: single nucleotide variant
Location: chr9:21994304 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 10: 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.Arg10Gly Uncertain significance ★★ same residue
CDKN2A p.Glu10Lys Uncertain significance ★★ ⚠ same residue
CDKN2A p.Arg10= Benign/Likely benign ★★ same residue
CDKN2A p.Glu10Ala Uncertain significance ★ ⚠ same residue
CDKN2A p.Arg10fs Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN2A p.Glu10Ter Pathogenic ★ same residue
CDKN2A p.Arg10Gln Uncertain significance ★ same residue
CDKN2A p.Glu10= Likely benign ★ 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-arg10trp (accessed [today's date]).

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