Is CAV3 p.Ser141= (c.423C>T) pathogenic?

CAV3 p.Ser141= (c.423C>T) is classified Likely benign in CAV3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-17). Absent from gnomAD v4.1; Associated with long QT syndrome.

What condition is associated with CAV3 p.Ser141= (c.423C>T)?

CAV3 p.Ser141= (c.423C>T) is associated with long QT syndrome (ClinVar).

How common is CAV3 p.Ser141= (c.423C>T) in the general population?

CAV3 p.Ser141= (c.423C>T) is absent from gnomAD v4.1 (gnomAD).

CAV3 p.Ser141=

c.423C>T · rs104893713 · VCV1617877

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

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 4.8	GERP 1.9, phastCons 1
Overall
CADD	11.14	PHRED · no single calibrated threshold — expert panels disagree

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.Ser141=
Coding: c.423C>T
MANE Select: NM_033337
dbSNP: rs104893713
Type: single nucleotide variant
Location: chr3:8745834 (GRCh38)
Gene constraint: LOEUF 1.064 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 88.54
Residue 141: a UniProt-annotated variant site (in lqt9; increase in late sodium current)

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.Ser141Asn Uncertain significance ★ ⚠ same residue
CAV3 p.Ser141Arg 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-ser141 (accessed [today's date]).

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