CCND2 p.Val11=
c.33C>T · rs371641860 · VCV3036591
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.017%, mid)
Conditions
1
CCND2-related disorder
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 0.11 | GERP -3.9, phastCons 0.93 |
| Overall | ||
| CADD | 11.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.017%
Middle Eastern · 1/5,878 alleles
Overall
0.000124%
2/1,612,884 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.017% | 5,878 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,428 |
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.Val11=
- Coding
- c.33C>T
- MANE Select
- NM_001759
- dbSNP
- rs371641860
- Type
- single nucleotide variant
- Location
- chr12:4274073 (GRCh38)
- Gene constraint
- LOEUF 0.385 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.98 · 1 PDB
Disease context
CCND2-related disorder
Similar variants
- CCND2 p.Gln277Ter Pathogenic/Likely pathogenic ★★ same condition
- CCND2 p.Thr280Ala Pathogenic ★★ ⚠ same condition
- CCND2 p.Pro281Arg Conflicting classifications of pathogenicity ★ ⚠ same condition
- CCND2 p.Gln169Arg Uncertain significance ⚠ same condition
- CCND2 c.572-4G>T Likely benign same condition
- CCND2 p.Arg285= Likely benign same condition
- CCND2 p.Pro281Ala Pathogenic ★★ ⚠ same type
- CCND2 p.Pro281Ser 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-val11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown