CDKN2A p.Phe90fs
c.267del · VCV3903663
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
melanoma-pancreatic cancer 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 | predicted | premature termination codon in exon 2 of 3 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDKN2A
- Protein
- p.Phe90fs
- Coding
- c.267del
- MANE Select
- NM_000077
- Type
- Deletion
- Location
- chr9:21971092 (GRCh38)
- Gene constraint
- LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.02 · 5 PDB
- Residue 90
- the 'disordered' region
Disease context
melanoma-pancreatic cancer syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Familial atypical multiple mole melanoma syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- All ages
Similar variants
- CDKN2A p.Ala36fs Pathogenic ★★ same condition
- CDKN2A p.Ala76fs Pathogenic/Likely pathogenic ★★ same condition
- CDKN2A p.Pro81fs Pathogenic ★★ same condition
- CDKN2A p.Ser43_Tyr44insTer Pathogenic ★★ same condition
- CDKN2A c.194-3646_194-3624del Uncertain significance ★★ same condition
- CDKN2A p.Phe90Leu Uncertain significance ★★ ⚠ same residue
- CDKN2A c.193+10del Likely benign ★★ same condition
- CDKN2A p.Phe90= 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-phe90fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown