Is CAPN3 p.Asp230fs (c.689del) pathogenic?

CAPN3 p.Asp230fs (c.689del) is classified Likely pathogenic in CAPN3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-10). Absent from gnomAD; Associated with Abnormality of the musculature.

What condition is associated with CAPN3 p.Asp230fs (c.689del)?

CAPN3 p.Asp230fs (c.689del) is associated with Abnormality of the musculature (ClinVar).

How common is CAPN3 p.Asp230fs (c.689del) in the general population?

CAPN3 p.Asp230fs (c.689del) is absent from gnomAD (gnomAD).

CAPN3 p.Asp230fs

c.689del · rs2141167797 · VCV1180794

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	predicted	premature termination codon in exon 5 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.8, 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: CAPN3
Protein: p.Asp230fs
Coding: c.689del
MANE Select: NM_000070
dbSNP: rs2141167797
Type: Deletion
Location: chr15:42388984 (GRCh38)
Gene constraint: LOEUF 0.896 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 79.18 · 5 PDB
Residue 230: the calpain catalytic domain; an α-helix

Full CAPN3 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

CAPN3 p.Gln545fs Likely pathogenic ★ same condition
CAPN3 p.Asp230Gly Uncertain significance ★ ⚠ same residue
CAPN3 p.Asp230His Uncertain significance ★ ⚠ same residue
CAPN3 p.Asp230= Likely benign ★ same residue
CAPN3 p.Gly221Cys Pathogenic/Likely pathogenic ★★ same condition
CAPN3 p.Ala483Thr Likely pathogenic ★ same condition
CAPN3 p.Ser337Pro Likely pathogenic ★ same condition
CAPN3 p.Ser432fs Pathogenic ★ 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/capn3-p-asp230fs (accessed [today's date]).

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