Is CAV3 p.Ser53fs (c.154_155dup) pathogenic?

CAV3 p.Ser53fs (c.154155dup) is classified Likely pathogenic in CAV3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-10). Absent from gnomAD; Associated with Abnormality of the musculature.

What condition is associated with CAV3 p.Ser53fs (c.154_155dup)?

CAV3 p.Ser53fs (c.154_155dup) is associated with Abnormality of the musculature (ClinVar).

How common is CAV3 p.Ser53fs (c.154_155dup) in the general population?

CAV3 p.Ser53fs (c.154_155dup) is absent from gnomAD (gnomAD).

CAV3 p.Ser53fs

c.154_155dup · rs2124988278 · VCV1180807

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Abnormality of the musculature

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (2 of 2) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP -0.66, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CAV3
Protein: p.Ser53fs
Coding: c.154_155dup
MANE Select: NM_033337
dbSNP: rs2124988278
Type: Duplication
Location: chr3:8745564 (GRCh38)
Gene constraint: LOEUF 1.064 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 88.54
Residue 53: a UniProt-annotated variant site (in rmd2)

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

Disease context

Abnormality of the musculature — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CAV3 p.Ser53Arg Uncertain significance ★★ ⚠ same residue
CAV3 p.Glu113_Gln115dup 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-ser53fs (accessed [today's date]).

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