CACNA2D3 p.Leu768=
c.2304C>G · rs1469169292 · VCV2653905
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.033%, 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 0.025 | GERP -1.2, phastCons 0.81 |
| Overall | ||
| CADD | 13.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.033%
Middle Eastern · 2/6,062 alleles
Filtering AF
0.00582%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00242%
Overall
0.000205%
3/1,461,696 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.033% | 3,031 |
| African / African-American | 0.00133% | 75,072 |
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
- CACNA2D3
- Protein
- p.Leu768=
- Coding
- c.2304C>G
- MANE Select
- NM_018398
- dbSNP
- rs1469169292
- Type
- single nucleotide variant
- Location
- chr3:54896806 (GRCh38)
- Gene constraint
- LOEUF 0.454 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 83.30
- Residue 768
- a disulfide bond
Similar variants
- CACNA2D3 c.676+9A>C Benign ★★ same type
- CACNA2D3 p.Ala1064= Benign ★★ same type
- LRTM1 p.Glu265Gln Benign ★★ same type
- LRTM1 p.Val294Ile Benign ★★ same type
- CACNA2D3 c.2620-4A>G Uncertain significance ★ same type
- CACNA2D3 p.Ala1070Thr Uncertain significance ★ ⚠ same type
- CACNA2D3 p.Ala14Thr Uncertain significance ★ ⚠ same type
- CACNA2D3 p.Ala217Gly 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/cacna2d3-p-leu768 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown