Is CAV3 p.Ser96Cys (c.287C>G) pathogenic?

CAV3 p.Ser96Cys (c.287C>G) is classified Uncertain significance in CAV3 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-07-28). AlphaMissense: ambiguous (0.4609); Absent from gnomAD v4.1.

How common is CAV3 p.Ser96Cys (c.287C>G) in the general population?

CAV3 p.Ser96Cys (c.287C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CAV3 p.Ser96Cys (c.287C>G)?

AlphaMissense predicts ambiguous (score 0.4609) — an in-silico prediction, not a clinical call.

CAV3 p.Ser96Cys

c.287C>G · rs730880421 · VCV180799

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4609 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.4609	ambiguous
REVEL	0.941	strongly pathogenic-leaning
SaProt	LLR -12.00	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.9, phastCons 1
Regional constraint	o/e 0.83	unconstrained · MANE · 12 kb · p 0.021 · regional, not allelic
Overall
CADD	32.0	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.Ser96Cys
Coding: c.287C>G
MANE Select: NM_033337
dbSNP: rs730880421
Type: single nucleotide variant
Location: chr3:8745698 (GRCh38)
Gene constraint: LOEUF 1.064 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 88.54
Residue 96: the 'required for interaction with dag1' region

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

Similar variants

CAV3 p.Ser96= Likely benign ★ same residue
CAV3 c.114+2T>C Pathogenic ★★ same type
CAV3 p.Ala46Thr Pathogenic/Likely pathogenic ★★ same type
CAV3 p.Arg27Gln Pathogenic ★★ same type
CAV3 p.Trp71Ter Pathogenic/Likely pathogenic ★★ same type
CAV3 c.114+5G>C Uncertain significance ★★ same type
CAV3 c.*134G>A Uncertain significance ★★ same type
CAV3 c.*592G>A Uncertain significance ★★ 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-ser96cys (accessed [today's date]).

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