CCND2 p.Pro199=
c.597G>A · rs747054950 · VCV391416
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00894%, eas)
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 -8.3 | GERP -4.7 |
| Overall | ||
| CADD | 3.22 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00894%
East Asian · 4/44,762 alleles
Filtering AF
0.00324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00254%
41/1,613,214 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00894% | 11,191 |
| Admixed American | 0.00835% | 11,974 |
| African / African-American | 0.00401% | 24,949 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,564 |
| South Asian | 0.0033% | 30,342 |
| European (non-Finnish) | 0.00212% | 47,189 |
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
- CCND2
- Protein
- p.Pro199=
- Coding
- c.597G>A
- MANE Select
- NM_001759
- dbSNP
- rs747054950
- Type
- single nucleotide variant
- Location
- chr12:4288867 (GRCh38)
- Gene constraint
- LOEUF 0.385 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.98 · 1 PDB
Similar variants
- CCND2 p.Gln277Ter Pathogenic/Likely pathogenic ★★ same type
- CCND2 p.Pro281Ala Pathogenic ★★ ⚠ same type
- CCND2 p.Pro281Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- CCND2 p.Ser271Ter Likely pathogenic ★★ same type
- CCND2 p.Thr280Ala Pathogenic ★★ ⚠ same type
- CCND2 p.Thr280Asn Pathogenic/Likely pathogenic ★★ ⚠ same type
- CCND2 p.Thr280Ile Pathogenic/Likely pathogenic ★★ ⚠ same type
- CCND2 p.Thr280Pro Pathogenic/Likely pathogenic ★★ ⚠ 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/ccnd2-p-pro199 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown