Is CAV3 p.Phe92= (c.276C>T) pathogenic?

CAV3 p.Phe92= (c.276C>T) is classified Conflicting classifications of pathogenicity in CAV3 (ClinVar, Conflicting submitters, 17 submitters; last evaluated 2026-01-17). Ultra-rare (popmax 0.0875%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with CAV3 p.Phe92= (c.276C>T)?

CAV3 p.Phe92= (c.276C>T) is associated with Cardiovascular phenotype, long QT syndrome, cardiomyopathy (ClinVar).

How common is CAV3 p.Phe92= (c.276C>T) in the general population?

CAV3 p.Phe92= (c.276C>T) is ultra-rare (popmax 0.0875%, nfe) (gnomAD).

CAV3 p.Phe92=

c.276C>T · rs72546669 · VCV46534

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 17 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0875%, 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 -5	GERP -5.9
Overall
CADD	12.02	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0875% European (non-Finnish) · 1,033/1,180,034 alleles

Filtering AF 0.0831% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0813%

Overall 0.0711% 1,147/1,614,168 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0875%	1,142
East Asian	0.0825%	1,213
Remaining individualsnot grpmax-eligible	0.0624%	1,603
Finnishnot grpmax-eligible	0.0281%	3,557
Ashkenazi Jewishnot grpmax-eligible	0.0203%	4,934
Admixed American	0.00833%	12,006
African / African-American	0.00799%	12,509
South Asian	0.00329%	30,357

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.Phe92=
Coding: c.276C>T
MANE Select: NM_000916 · reported on NM_033337
dbSNP: rs72546669
Type: single nucleotide variant
Location: chr3:8745687 (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 cardiomyopathy caveolinopathy

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-phe92 (accessed [today's date]).

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