Is CAV3 p.Ile13Phe (c.37A>T) pathogenic?

CAV3 p.Ile13Phe (c.37A>T) is classified Likely pathogenic in CAV3 (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely benign (0.0969); Absent from gnomAD v4.1; Associated with long QT syndrome.

What condition is associated with CAV3 p.Ile13Phe (c.37A>T)?

CAV3 p.Ile13Phe (c.37A>T) is associated with long QT syndrome (ClinVar).

How common is CAV3 p.Ile13Phe (c.37A>T) in the general population?

CAV3 p.Ile13Phe (c.37A>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CAV3 p.Ile13Phe (c.37A>T)?

AlphaMissense predicts likely benign (score 0.0969) — an in-silico prediction, not a clinical call.

CAV3 p.Ile13Phe

c.37A>T · rs796052171 · VCV207882

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0969 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

long QT syndrome

Computational evidence

Protein change
AlphaMissense	0.0969	likely benign ⚠ discordant with ClinVar
REVEL	0.47	indeterminate
SaProt	LLR -8.17	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.3	GERP 2.1, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 12 kb · p 0.021 · regional, not allelic
Overall
CADD	21.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Ile13Phe
Coding: c.37A>T
MANE Select: NM_033337
dbSNP: rs796052171
Type: single nucleotide variant
Location: chr3:8733913 (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

long QT syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAV3 p.Ile13= Benign/Likely benign ★★ same residue
CAV3 p.Ile13Val 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

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-ile13phe (accessed [today's date]).

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