CDKN1B p.Arg15=
c.45G>C · rs775058606 · VCV1117692
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000254%, nfe)
Conditions
2
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 10.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,180,042 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000205%
3/1,461,668 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CDKN1B
- Protein
- p.Arg15=
- Coding
- c.45G>C
- MANE Select
- NM_004064
- dbSNP
- rs775058606
- Type
- single nucleotide variant
- Location
- chr12:12717884 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI 0.24 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.08 · 19 PDB
- Residue 15
- the 'disordered' region; a UniProt-annotated variant site (in)
Similar variants
- CDKN1B p.Arg15Trp Uncertain significance ★★ ⚠ same residue
- CDKN1B p.Arg15delinsProTer Pathogenic ★ same residue
- CDKN1B p.Arg154Ter Pathogenic ★★ same condition
- CDKN1B p.Arg5Ter Pathogenic/Likely pathogenic ★★ same condition
- CDKN1B p.Gln104Ter Pathogenic ★★ same condition
- CDKN1B p.Gln107Ter Pathogenic ★★ same condition
- CDKN1B p.Gln141Ter Pathogenic ★★ same condition
- CDKN1B p.Gln163Ter 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/cdkn1b-p-arg15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown