CACNA1C p.Pro613=
c.1839A>C · rs1060504922 · VCV416862
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 6.2e-05%)
Conditions
1
long QT syndrome
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 -3 | GERP -4.9 |
| Overall | ||
| CADD | 5.507 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.2e-05%
Overall
6.2e-05%
1/1,613,512 alleles · very rare
exomes 1/1,461,404 · genomes 0/152,108 · joint denominator
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
- CACNA1C
- Protein
- p.Pro613=
- Coding
- c.1839A>C
- MANE Select
- NM_000719
- dbSNP
- rs1060504922
- Type
- single nucleotide variant
- Location
- chr12:2567738 (GRCh38)
- Gene constraint
- LOEUF 0.186 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.73 · 33 PDB
- Residue 613
- a UniProt-annotated variant site (in nedhlss); an α-helix
Similar variants
- CACNA1C p.Pro613Arg Likely pathogenic ★ same residue
- CACNA1C p.Arg518Cys Pathogenic/Likely pathogenic ★★ same condition
- CACNA1C p.Arg518His Pathogenic/Likely pathogenic ★★ same condition
- CACNA1C p.Arg858His Pathogenic/Likely pathogenic ★★ same condition
- CACNA1C p.Arg860Gly Likely pathogenic ★★ same condition
- CACNA1C p.Arg860Ter Pathogenic ★★ same condition
- CACNA1C p.Glu1115Lys Pathogenic/Likely pathogenic ★★ same condition
- CACNA1C p.Gly1378Arg Pathogenic/Likely pathogenic ★★ 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/cacna1c-p-pro613 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown