Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 52.6%, eas) — too common for a highly-penetrant pathogenic allele
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 2.2 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 17.79 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
52.6%
East Asian · 23,571/44,848 alleles
Filtering AF
52%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 51.8%
Overall
44.4%
716,284/1,613,168 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 52.6% | 2 |
| South Asian | 52.3% | 2 |
| Middle Eastern | 51.3% | 2 |
| Finnishnot grpmax-eligible | 47.9% | 2 |
| Remaining individualsnot grpmax-eligible | 45.4% | 2 |
| European (non-Finnish) | 44.9% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 44.4% | 2 |
| Amishnot grpmax-eligible | 39.5% | 3 |
| Admixed American | 38.5% | 3 |
| African / African-American | 21.7% | 5 |
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.Pro241=
- Coding
- c.723G>A
- MANE Select
- NM_053056
- dbSNP
- rs9344
- Type
- single nucleotide variant
- Location
- chr11:69648142 (GRCh38)
- Gene constraint
- LOEUF 0.609 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 87.31 · 11 PDB
- Residue 241
- 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.Arg245= Benign/Likely benign ★★ same type
- CCND1 p.Phe223= 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-pro241 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown