Is CAV3 p.Val49= (c.147G>A) pathogenic?

CAV3 p.Val49= (c.147G>A) is classified Likely benign in CAV3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-17). Very rare (popmax 0.00559%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with CAV3 p.Val49= (c.147G>A)?

CAV3 p.Val49= (c.147G>A) is associated with Cardiovascular phenotype, long QT syndrome (ClinVar).

How common is CAV3 p.Val49= (c.147G>A) in the general population?

CAV3 p.Val49= (c.147G>A) is very rare (popmax 0.00559%, nfe) (gnomAD).

CAV3 p.Val49=

c.147G>A · rs777363173 · VCV1153870

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00559%, nfe)

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 1.4	GERP -0.26, phastCons 1
Overall
CADD	6.091	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00559% European (non-Finnish) · 66/1,180,006 alleles

Filtering AF 0.00451% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00411%

Overall 0.00465% 68/1,461,844 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00559%	17,879
Remaining individualsnot grpmax-eligible	0.0032%	31,255

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.Val49=
Coding: c.147G>A
MANE Select: NM_000916 · reported on NM_033337
dbSNP: rs777363173
Type: single nucleotide variant
Location: chr3:8745558 (GRCh38)

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

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-val49 (accessed [today's date]).

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