CCND1 p.Arg245=
c.735G>A · rs201299704 · VCV736722
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.535%, sas)
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 -5.4 | GERP -4.4 |
| Overall | ||
| CADD | 2.749 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.535%
South Asian · 487/90,964 alleles
Filtering AF
0.496%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.481%
Overall
0.0503%
811/1,612,858 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.535% | 187 |
| Middle Eastern | 0.363% | 275 |
| Ashkenazi Jewishnot grpmax-eligible | 0.166% | 603 |
| Admixed American | 0.113% | 882 |
| Remaining individualsnot grpmax-eligible | 0.0721% | 1,387 |
| European (non-Finnish) | 0.0112% | 8,935 |
| African / African-American | 0.00801% | 12,491 |
| East Asian | 0.00223% | 44,746 |
| Finnishnot grpmax-eligible | 0.00157% | 63,860 |
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
- CCND1
- Protein
- p.Arg245=
- Coding
- c.735G>A
- MANE Select
- NM_053056
- dbSNP
- rs201299704
- Type
- single nucleotide variant
- Location
- chr11:69651129 (GRCh38)
- Gene constraint
- LOEUF 0.609 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 87.31 · 11 PDB
- Residue 245
- an α-helix
Similar variants
- CCND1 p.Ile251Met Uncertain significance ★★ ⚠ same type
- CCND1 c.415-170G>C Benign ★★ same type
- CCND1 c.575-120G>A Benign ★★ same type
- CCND1 c.724-205A>G Benign ★★ same type
- CCND1 c.724-26A>G Benign ★★ same type
- CCND1 c.*65C>A Benign ★★ same type
- CCND1 p.Phe223= Benign ★★ same type
- CCND1 p.Pro241= Benign ★★ same type
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/ccnd1-p-arg245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown