Is CAV3 p.Ser61Arg (c.183C>A) pathogenic?

CAV3 p.Ser61Arg (c.183C>A) is classified Likely pathogenic in CAV3 (ClinVar, Single submitter, 2 submitters; last evaluated 2022-11-04). AlphaMissense: likely pathogenic (0.9985); Absent from gnomAD v4.1; Associated with CAV3-related disorder.

What condition is associated with CAV3 p.Ser61Arg (c.183C>A)?

CAV3 p.Ser61Arg (c.183C>A) is associated with CAV3-related disorder (ClinVar).

How common is CAV3 p.Ser61Arg (c.183C>A) in the general population?

CAV3 p.Ser61Arg (c.183C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CAV3 p.Ser61Arg (c.183C>A)?

AlphaMissense predicts likely pathogenic (score 0.9985) — an in-silico prediction, not a clinical call.

CAV3 p.Ser61Arg

c.183C>A · rs116840796 · VCV31729

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.9985 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CAV3-related disorder

Computational evidence

Protein change
AlphaMissense	0.9985	likely pathogenic ✓ concordant with ClinVar · top 1% in CAV3
REVEL	0.91	moderately pathogenic-leaning
SaProt	LLR -12.46	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>T here scores Δ0.30 · evaluated, not missing
Constraint at this position
Conservation	phyloP 4.8	GERP 2.9, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 12 kb · p 0.021 · regional, not allelic
Overall
CADD	29.1	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.Ser61Arg
Coding: c.183C>A
MANE Select: NM_033337
dbSNP: rs116840796
Type: single nucleotide variant
Location: chr3:8745594 (GRCh38)
Gene constraint: LOEUF 1.064 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 88.54
Residue 61: a UniProt-annotated variant site (in a patient with mild proximal myopathy)

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

Disease context

CAV3-related disorder

Similar variants

CAV3 p.Ser61Asn Uncertain significance ★★ ⚠ same residue
CAV3 p.Ser61Thr Uncertain significance ★ ⚠ same residue
CAV3 p.Ser61= Likely benign ★ same residue
CAV3 p.Arg126His Uncertain significance ★★ ⚠ same condition
CAV3 p.Arg27Pro Conflicting classifications of pathogenicity ★ ⚠ same condition
CAV3 p.Ile32Phe Uncertain significance ★ ⚠ same condition
CAV3 c.114+2T>C Pathogenic ★★ same type
CAV3 p.Ala46Thr Pathogenic/Likely pathogenic ★★ same type

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-ser61arg (accessed [today's date]).

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