CCND2 c.*36A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.05%, 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 -3.1 | GERP -3.2 |
| Non-coding constraint | Z 3.34 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 0.083 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.05%
South Asian · 933/88,792 alleles
Filtering AF
0.995%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.972%
Overall
0.0617%
982/1,592,472 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.05% | 95 |
| Middle Eastern | 0.12% | 836 |
| Remaining individualsnot grpmax-eligible | 0.0552% | 1,812 |
| African / African-American | 0.00134% | 74,626 |
| European (non-Finnish) | 0.0006% | 166,765 |
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
- Coding
- c.*36A>C
- MANE Select
- NM_001759
- dbSNP
- rs369380641
- Type
- single nucleotide variant
- Location
- chr12:4300045 (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-c-star-36a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown