CAND2 p.Ala680=
c.2040C>T · rs2470942263 · VCV3234324
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 -1.3 | GERP -4 |
| Overall | ||
| CADD | 6.777 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CAND2
- Protein
- p.Ala680=
- Coding
- c.2040C>T
- MANE Select
- NM_001162499
- dbSNP
- rs2470942263
- Type
- single nucleotide variant
- Location
- chr3:12816972 (GRCh38)
- Gene constraint
- LOEUF 0.815 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.14 · 2 PDB
- Residue 680
- an α-helix
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.Ser999= Likely benign ★★ same type
- CAND2 p.Ala1187Val Uncertain significance ★ ⚠ same type
- CAND2 p.Ala1215Thr 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-ala680 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown