Is CDKN2A p.Arg10fs (c.28del) pathogenic?

CDKN2A p.Arg10fs (c.28del) is classified Conflicting classifications of pathogenicity in CDKN2A (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-08-12). Absent from gnomAD; Associated with hereditary neoplastic syndrome.

What condition is associated with CDKN2A p.Arg10fs (c.28del)?

CDKN2A p.Arg10fs (c.28del) is associated with hereditary neoplastic syndrome, melanoma-pancreatic cancer syndrome (ClinVar).

How common is CDKN2A p.Arg10fs (c.28del) in the general population?

CDKN2A p.Arg10fs (c.28del) is absent from gnomAD (gnomAD).

CDKN2A p.Arg10fs

c.28del · rs2489328224 · VCV1797424

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

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.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen); NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.3	GERP 1.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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.Arg10fs
Coding: c.28del
MANE Select: NM_000077 · reported on NM_058195
dbSNP: rs2489328224
Type: Deletion
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

Also linked: melanoma-pancreatic cancer syndrome

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.Arg10Trp Uncertain significance ★ same residue
CDKN2A p.Glu10Ala Uncertain significance ★ ⚠ same residue
CDKN2A p.Glu10fs Pathogenic ★ same residue
CDKN2A c.193+1del Likely pathogenic ★★ same condition
CDKN2A c.457+1_457+10del 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-arg10fs (accessed [today's date]).

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