CDKN2A p.Ser52Arg
c.156C>A · rs2489326972 · VCV2563902
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,604,626)
Conditions
1
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.192 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.59 | GERP -1.5, phastCons 0.1 |
| Overall | ||
| CADD | 15.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,604,626). 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.Ser52Arg
- Coding
- c.156C>A
- MANE Select
- NM_000077 · reported on NM_058195
- dbSNP
- rs2489326972
- Type
- single nucleotide variant
- Location
- chr9:21994176 (GRCh38)
- Gene constraint
- LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.02 · 5 PDB
- Residue 52
- the 'interaction with cdk5rap3 and mdm2' region
Similar variants
- CDKN2A p.Met52Ile Uncertain significance ★★ ⚠ same residue
- CDKN2A p.Met52Thr Uncertain significance ★★ ⚠ same residue
- CDKN2A p.Ser52Asn Uncertain significance ★★ same residue
- CDKN2A p.Ser52Gly Uncertain significance ★★ same residue
- CDKN2A p.Met52Leu 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
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-ser52arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown