CCND1 p.Phe223=
c.669C>T · rs3862792 · VCV1250573
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 13.7%, afr) — 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 0.76, phastCons 1 |
| Overall | ||
| CADD | 12.78 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
13.7%
African / African-American · 10,304/75,010 alleles
Filtering AF
13.5%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 13.4%
Overall
3.56%
57,462/1,613,888 alleles · common
exomes 48,352/1,461,586 · genomes 9,110/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 13.7% | 7 |
| South Asian | 9.15% | 11 |
| Middle Eastern | 7.39% | 14 |
| Remaining individualsnot grpmax-eligible | 4.29% | 23 |
| Admixed American | 3.08% | 32 |
| European (non-Finnish) | 2.72% | 37 |
| Ashkenazi Jewishnot grpmax-eligible | 2.57% | 39 |
| East Asian | 1.47% | 68 |
| Amishnot grpmax-eligible | 1.21% | 83 |
| Finnishnot grpmax-eligible | 0.514% | 195 |
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.Phe223=
- Coding
- c.669C>T
- MANE Select
- NM_053056
- dbSNP
- rs3862792
- Type
- single nucleotide variant
- Location
- chr11:69648088 (GRCh38)
- Gene constraint
- LOEUF 0.609 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 87.31 · 11 PDB
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.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-phe223 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown