Is CAV3 p.Asp43= (c.129C>T) pathogenic?

CAV3 p.Asp43= (c.129C>T) is classified Likely benign in CAV3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-24). Ultra-rare (popmax 0.0446%, eas); Associated with Cardiovascular phenotype.

What condition is associated with CAV3 p.Asp43= (c.129C>T)?

CAV3 p.Asp43= (c.129C>T) is associated with Cardiovascular phenotype, long QT syndrome (ClinVar).

How common is CAV3 p.Asp43= (c.129C>T) in the general population?

CAV3 p.Asp43= (c.129C>T) is ultra-rare (popmax 0.0446%, eas) (gnomAD).

CAV3 p.Asp43=

c.129C>T · rs374584030 · VCV506389

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0446%, eas)

Conditions

Cardiovascular phenotype

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 -9	GERP -5.3
Overall
CADD	5.374	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0446% East Asian · 20/44,870 alleles

Filtering AF 0.0295% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0246%

Overall 0.00756% 122/1,614,036 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0446%	2,244
Remaining individualsnot grpmax-eligible	0.0096%	10,418
European (non-Finnish)	0.00763%	13,110
Admixed American	0.00333%	30,012
Finnishnot grpmax-eligible	0.00312%	32,006
South Asian	0.0022%	45,528

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.Asp43=
Coding: c.129C>T
MANE Select: NM_033337
dbSNP: rs374584030
Type: single nucleotide variant
Location: chr3:8745540 (GRCh38)
Gene constraint: LOEUF 1.064 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 88.54

Full CAV3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: long QT syndrome

Similar variants

CAV3 p.Asp43Val Uncertain significance ★★ ⚠ same residue
CAV3 p.Asp43Gly Likely 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

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-asp43 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown