CACNA2D2 p.Gly89=
c.267A>C · rs781051837 · VCV1583330
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
early-infantile DEE
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 0.26 | GERP 0.061, phastCons 0.99 |
| Overall | ||
| CADD | 9.221 | 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
- CACNA2D2
- Protein
- p.Gly89=
- Coding
- c.267A>C
- MANE Select
- NM_006030
- dbSNP
- rs781051837
- Type
- single nucleotide variant
- Location
- chr3:50476139 (GRCh38)
- Gene constraint
- LOEUF 0.396 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 81.48
Similar variants
- CACNA2D2 c.2234+1G>A Likely pathogenic ★★ same condition
- CACNA2D2 p.Gln519Ter Pathogenic/Likely pathogenic ★★ same condition
- CACNA2D2 c.1907+3A>C Uncertain significance ★★ same condition
- CACNA2D2 c.785-3C>T Uncertain significance ★★ same condition
- CACNA2D2 p.Ala1096Thr Uncertain significance ★★ ⚠ same condition
- CACNA2D2 p.Ala253Thr Uncertain significance ★★ ⚠ same condition
- CACNA2D2 p.Arg188Ser Uncertain significance ★★ ⚠ same condition
- CACNA2D2 p.Arg422Cys Uncertain significance ★★ ⚠ same condition
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/cacna2d2-p-gly89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown