CAV3 p.Lys59=
c.177G>A · rs1708131659 · VCV1191338
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 2.1 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 6.261 | 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
- CAV3
- Protein
- p.Lys59=
- Coding
- c.177G>A
- MANE Select
- NM_033337
- dbSNP
- rs1708131659
- Type
- single nucleotide variant
- Location
- chr3:8745588 (GRCh38)
- Gene constraint
- LOEUF 1.064 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 88.54
Similar variants
- CAV3 p.Lys59Asn Uncertain significance ★ ⚠ same residue
- CAV3 c.114+2T>C Pathogenic ★★ same condition
- CAV3 p.Ala46Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
- CAV3 p.Arg27Gln Pathogenic ★★ same condition
- CAV3 p.Trp71Ter Pathogenic/Likely pathogenic ★★ same condition
- CAV3 c.114+5G>C Uncertain significance ★★ same condition
- CAV3 p.Ala102Val Uncertain significance ★★ ⚠ same condition
- CAV3 p.Ala134Glu 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/cav3-p-lys59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown