CDKN2A p.Leu104=
c.312G>A · rs2131093926 · VCV1727943
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.476 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.017 | GERP -0.82, phastCons 0.72 |
| Overall | ||
| CADD | 9.567 | 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.Leu104=
- Coding
- c.312G>A
- MANE Select
- NM_000077
- dbSNP
- rs2131093926
- Type
- single nucleotide variant
- Location
- chr9:21971047 (GRCh38)
- Gene constraint
- LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.02 · 5 PDB
- Residue 104
- a UniProt-annotated variant site (sequence variant); the 'disordered' region
Similar variants
- CDKN2A p.Leu104Pro Uncertain significance ★ ⚠ same residue
- CDKN2A c.150+2T>G Likely pathogenic ★★ same condition
- CDKN2A c.151-1G>C Pathogenic ★★ same condition
- CDKN2A c.151-1G>T Pathogenic/Likely pathogenic ★★ same condition
- CDKN2A c.151-2A>G Pathogenic/Likely pathogenic ★★ same condition
- CDKN2A c.193+2T>C Likely pathogenic ★★ same condition
- CDKN2A c.193+5G>A Pathogenic/Likely pathogenic ★★ same condition
- CDKN2A c.194-3653G>T 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-leu104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown