CAND2 p.Ser999=
c.2997G>A · rs145134860 · VCV3136965
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0825%, mid)
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 -7.8 | GERP -4.1 |
| Overall | ||
| CADD | 0.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0825%
Middle Eastern · 5/6,060 alleles
Filtering AF
0.0324%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.0152%
246/1,614,112 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0825% | 1,212 |
| European (non-Finnish) | 0.0177% | 5,646 |
| African / African-American | 0.0147% | 6,821 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,417 |
| Admixed American | 0.00833% | 12,002 |
| South Asian | 0.00769% | 13,011 |
| East Asian | 0.00669% | 14,959 |
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
- CAND2
- Protein
- p.Ser999=
- Coding
- c.2997G>A
- MANE Select
- NM_001162499
- dbSNP
- rs145134860
- Type
- single nucleotide variant
- Location
- chr3:12820138 (GRCh38)
- Gene constraint
- LOEUF 0.815 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.14 · 2 PDB
Similar variants
- CAND2 p.Arg768Cys Uncertain significance ★★ ⚠ same type
- CAND2 p.Arg1028Cys Benign ★★ same type
- CAND2 p.Arg987Gln Benign ★★ ⚠ same type
- CAND2 p.His709Arg Benign ★★ same type
- CAND2 p.Ser491= Benign ★★ same type
- CAND2 p.Ala1187Val Uncertain significance ★ ⚠ same type
- CAND2 p.Ala1215Thr Uncertain significance ★ ⚠ same type
- CAND2 p.Ala171Thr Uncertain significance ★ ⚠ 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/cand2-p-ser999 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown