CAV3 p.Thr66=
c.198T>C · VCV4754962
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.84e-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 -15 | GERP -5.9 |
| Overall | ||
| CADD | 0.077 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.84e-05%
Overall
6.84e-05%
1/1,461,826 alleles · very rare
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
- CAV3
- Protein
- p.Thr66=
- Coding
- c.198T>C
- MANE Select
- NM_033337
- Type
- single nucleotide variant
- Location
- chr3:8745609 (GRCh38)
- Gene constraint
- LOEUF 1.064 · pLI 0.04 (gnomAD)
- Structure
- AlphaFold pLDDT 88.54
- Residue 66
- a UniProt-annotated variant site (in rmd2); the 'required for interaction with dag1' region
Similar variants
- CAV3 p.Thr66fs Pathogenic ★ 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-thr66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown