CCND2 p.Leu38=
c.114T>G · rs146122734 · VCV1280861
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.253%, afr)
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 -4.4 | GERP -4.2 |
| Overall | ||
| CADD | 5.242 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.253%
African / African-American · 190/75,024 alleles
Filtering AF
0.224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.212%
Overall
0.0143%
230/1,613,990 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.253% | 395 |
| Remaining individualsnot grpmax-eligible | 0.0352% | 2,841 |
| Middle Eastern | 0.033% | 3,030 |
| Admixed American | 0.0183% | 5,457 |
| East Asian | 0.00223% | 44,844 |
| South Asian | 0.0022% | 45,532 |
| European (non-Finnish) | 0.00017% | 589,971 |
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.Leu38=
- Coding
- c.114T>G
- MANE Select
- NM_001759
- dbSNP
- rs146122734
- Type
- single nucleotide variant
- Location
- chr12:4274154 (GRCh38)
- Gene constraint
- LOEUF 0.385 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 87.98 · 1 PDB
- Residue 38
- the cyclin n-terminal domain
Similar variants
- CCND2 p.Leu38Arg Uncertain significance ★ ⚠ same residue
- 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
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-leu38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown