Is CDKN2A p.Arg63del (c.184AGA[1]) pathogenic?

CDKN2A p.Arg63del (c.184AGA[1]) is classified Uncertain significance in CDKN2A (ClinVar, Single submitter, 1 submitter; last evaluated 2020-03-25). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Arg63del (c.184AGA[1])?

CDKN2A p.Arg63del (c.184AGA[1]) is associated with hereditary neoplastic syndrome (ClinVar).

How common is CDKN2A p.Arg63del (c.184AGA[1]) in the general population?

CDKN2A p.Arg63del (c.184AGA[1]) is absent from gnomAD (gnomAD).

CDKN2A p.Arg63del

c.184AGA[1] · rs1563902635 · VCV1781676

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.5	GERP -1.3, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CDKN2A
Protein: p.Arg63del
Coding: c.184AGA[1]
MANE Select: NM_000077 · reported on NM_058195
dbSNP: rs1563902635
Type: Microsatellite
Location: chr9:21994143 (GRCh38)
Gene constraint: LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.02 · 5 PDB
Residue 63: 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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CDKN2A p.Arg63Ile Uncertain significance ★★ same residue
CDKN2A p.Arg63Lys Uncertain significance ★★ same residue
CDKN2A p.Arg63= Conflicting classifications of pathogenicity ★ same residue
CDKN2A p.Arg63fs Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN2A p.Leu63Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
CDKN2A p.Leu16fs Pathogenic ★★ same condition
CDKN2A p.Pro11_Ser12insAlaAlaGlySerSerMetGluPro Pathogenic/Likely pathogenic ★★ same condition
CDKN2A p.Leu63fs Likely 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-arg63del (accessed [today's date]).

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