The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000070.3(CAPN3):c.327_328dup (p.Arg110fs)

CA347357

210563 (ClinVar)

Gene: CAPN3 (HGNC:825)
Condition: autosomal recessive limb-girdle muscular dystrophy (MONDO:0015152)
Inheritance Mode: Autosomal recessive inheritance
UUID: 479a249a-0ed0-40c2-addc-c723d5e77120
Approved on: 2026-03-12
Published on: 2026-04-09

HGVS expressions

NM_000070.3(CAPN3):c.327_328dup (p.Arg110fs)
NM_000070.3:c.327_328dup
NC_000015.10:g.42384500_42384501dup
CM000677.2:g.42384500_42384501dup
NC_000015.9:g.42676698_42676699dup
CM000677.1:g.42676698_42676699dup
NC_000015.8:g.40463990_40463991dup
NG_008660.1:g.41398_41399dup
ENST00000349748.8:c.327_328dup
ENST00000357568.8:c.327_328dup
ENST00000397163.8:c.327_328dup
ENST00000466369.5:n.558_559dup
ENST00000483208.5:n.558_559dup
ENST00000495723.1:n.558_559dup
ENST00000549793.5:n.558_559dup
ENST00000638141.2:n.342_343dup
ENST00000673705.1:c.18_19dup
ENST00000318023.11:c.327_328dup
ENST00000349748.7:c.327_328dup
ENST00000357568.7:c.327_328dup
ENST00000397163.7:c.327_328dup
NM_000070.2:c.327_328dup
NM_024344.1:c.327_328dup
NM_173087.1:c.327_328dup
NM_024344.2:c.327_328dup
NM_173087.2:c.327_328dup
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Pathogenic

Met criteria codes 4
PM3_Supporting PM2_Supporting PP4_Strong PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Limb Girdle Muscular Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CAPN3 Version 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Limb Girdle Muscular Dystrophy VCEP
The NM_000070.3: c.327_328dup p.(Arg110ProfsTer18) variant is a frameshift variant predicted to cause a premature stop codon in biologically relevant exon 2/24, leading to nonsense-mediated decay in a gene in which loss of function is an established disease mechanism (PVS1). This variant has been identified in at least two patients with features consistent with LGMD (PMID: 30564623, 1805549; LOVD CAPN3_000440), including in unconfirmed phase with a pathogenic variant (c.1993-1G>A, 0.5 pts, PMID: 30564623, LOVD Individual #00220608) (PM3_Supporting). At least one individual with this variant and a second presumed diagnostic CAPN3 variant displayed progressive limb girdle muscle weakness as well as absent CAPN3 expression in skeletal muscle, which is highly specific for CAPN3-related LGMD (PMID: 18055493, LOVD Individual #00214565; PP4_Strong). The upper bound of the 95% confidence interval of the Grpmax variant allele frequency in gnomAD v4.1.0 is 0.000076118 (74/1179616 European (non-Finnish) alleles), which is less than the VCEP threshold of 0.0001 (PM2_Supporting). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive limb-girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen Limb Girdle Muscular Dystrophy Expert Panel (specification version 2.0.0; 03/12/2026): PVS1, PM3_Supporting, PP4_Strong, PM2_Supporting.
Met criteria codes
PM3_Supporting
This variant has been identified in at least two patients with features consistent with LGMD (PMID: 30564623, 1805549; LOVD CAPN3_000440), including in unconfirmed phase with a pathogenic variant (c.1993-1G>A, 0.5 pts, PMID: 30564623, LOVD Individual #00220608) (PM3_Supporting). c.1993-1G>A is independently classified as P; co-occurrence could not be checked since one of the variants is absent from gnomAD v2 exomes
PM2_Supporting
The upper bound of the 95% confidence interval of the Grpmax variant allele frequency in gnomAD v4.1.0 is 0.000076118 (74/1179616 European (non-Finnish) alleles), which is less than the VCEP threshold of 0.0001 (PM2_Supporting).
PP4_Strong
At least one individual with this variant and a second presumed diagnostic CAPN3 variant displayed progressive limb girdle muscle weakness as well as absent CAPN3 expression in skeletal muscle, which is highly specific for CAPN3-related LGMD (PMID: 18055493, LOVD Individual #00214565; PP4_Strong).
PVS1
The NM_000070.3: c.327_328dup p.(Arg110ProfsTer18) variant is a frameshift variant predicted to cause a premature stop codon in biologically relevant exon 2/24, leading to nonsense-mediated decay in a gene in which loss of function is an established disease mechanism (PVS1). Checked SpliceAI (0.010) - no predicted impact
Curation History
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