Variant: NM_000070.3(CAPN3):c.1746-20C>G

CA220343

92408 (ClinVar)

Gene: CAPN3

Condition: autosomal recessive limb-girdle muscular dystrophy

Inheritance Mode: Autosomal recessive inheritance

UUID: a1ce02f1-f49e-4baf-aea0-8c98459736de

Approved on: 2025-01-09

Published on: 2025-01-09

HGVS expressions

NM_000070.3:c.1746-20C>G
NM_000070.3(CAPN3):c.1746-20C>G
NC_000015.10:g.42403721C>G
CM000677.2:g.42403721C>G
NC_000015.9:g.42695919C>G
CM000677.1:g.42695919C>G
NC_000015.8:g.40483211C>G
NG_008660.1:g.60619C>G
ENST00000349748.8:c.1602-20C>G
ENST00000357568.8:c.1746-20C>G
ENST00000397163.8:c.1746-20C>G
ENST00000466369.5:n.2255-20C>G
ENST00000483208.5:n.2635-20C>G
ENST00000495723.1:n.2635-20C>G
ENST00000549793.5:n.1977-20C>G
ENST00000638141.2:n.1617-20C>G
ENST00000673646.1:c.210-20C>G
ENST00000673705.1:c.309+4069C>G
ENST00000673813.1:n.581-20C>G
ENST00000318023.11:c.1602-20C>G
ENST00000349748.7:c.1602-20C>G
ENST00000357568.7:c.1746-20C>G
ENST00000397163.7:c.1746-20C>G
ENST00000397200.8:c.210-20C>G
ENST00000567071.5:c.205-20C>G
ENST00000569827.5:c.210-20C>G
NM_000070.2:c.1746-20C>G
NM_024344.1:c.1746-20C>G
NM_173087.1:c.1602-20C>G
NM_173088.1:c.210-20C>G
NM_024344.2:c.1746-20C>G
NM_173087.2:c.1602-20C>G
NM_173088.2:c.210-20C>G

Pathogenic

• Met criteria codes: PM3_Very Strong PVS1_Moderate PP4_Moderate PP1_Moderate

• Not Met criteria codes: BS1 PP3

Expert Panel

Limb Girdle Muscular Dystrophy VCEP

Criteria Specification Information

Criteria Specification: ClinGen Limb Girdle Muscular Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CAPN3 Version 1.0.0

Evidence submitted by expert panel

Limb Girdle Muscular Dystrophy VCEP

The NM_000070.3: c.1746-20C>G variant occurs in intron 13 of the CAPN3 gene. The filtering allele frequency for this variant is 0.006051 in gnomAD v2.1.1 European (non-Finnish) genomes (the lower threshold of the 95% CI of 172/31388), which is higher than the LGMD VCEP threshold of 0.001 for BS1; in total, three homozygous individuals are also observed. However, this variant may act as a hypomorphic allele, and the VCEP opted not to apply this code (BS1 exception). RNAseq/cDNA analysis of muscle from patients carrying one copy of the variant suggests that it results in aberrant splicing, the inclusion of various portions of intron 13, and premature truncation (PMID: 20635405, 35731190). An earlier study concluded the variant does not affect splicing (PMID: 17979987); however, later investigations showed that the aberrantly spliced transcripts are variably expressed and not always detectable even when splicing-specific PCR is used, possibly due to nonsense-mediated mRNA decay (PMID: 20635405) (PVS1_RNA_Moderate). The c.1746-20C>G variant has been detected with a second CAPN3 variant in at least 34 individuals with LGMD (PMID: 37589857, 20635405, 17979987, 17157502, 35731190), including confirmed in trans with a pathogenic variant in five cases (c.550delA p.(Thr184ArgfsTer36), 4.0 pts, PMID: 20635405, 35731190; c.643_663del p.(Ser215_Gly221del): 1.0 pt, PMID: 35731190) (PM3_Very Strong). The variant was also reported to co-segregate with autosomal recessive disease in four affected family members from three families (PP1_Moderate; PMID: 37589857, 20635405, 35731190). Several patients with the c.1746-20C>G variant and a second CAPN3 variant displayed progressive limb girdle muscle weakness or clinical suspicion of limb-girdle muscular dystrophy as well as significantly reduced or absent expression of calpain-3, which is specific for CAPN3-related LGMD (PP4_Moderate; PMID: 20635405). While two homozygous patients with a mild phenotype have been reported (PMID: 35731190), the number of apparently unaffected homozygous individuals described and present in population databases suggests this variant may show reduced penetrance in the homozygous state. 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 LGMD VCEP (LGMD VCEP specifications version 1.0.0; 01/09/2025): PVS1_RNA_Moderate, PM3_Very Strong, PP1_Moderate, PP4_Moderate. The LGMD VCEP recommends careful correlation with patient phenotype and family history as well as consideration of the combined functional impact of both CAPN3 alleles when the c.1746-20C>G variant is detected in an individual with signs of limb girdle muscular dystrophy.

Met criteria codes

• PM3_Very Strong: This variant has been detected in at least 34 unrelated individuals with LGMD (PMID: 37589857, 20635405, 17979987, 17157502, 35731190), including confirmed in trans with a pathogenic variant in five cases (c.550delA p.(Thr184ArgfsTer36), 4.0 pts, PMID: 20635405, 35731190; c.643_663del p.(Ser215_Gly221del): 1.0 pt, PMID: 35731190) (PM3_Very Strong).
• PVS1_Moderate: The NM_000070.3: c.1746-20C>G occurs in intron 13 of the CAPN3 gene. RNAseq/cDNA analysis of muscle from patients carrying one copy of the variant suggests that it results in aberrant splicing, the inclusion of various portions of intron 13, and premature truncation (PMID: 20635405, 35731190). An earlier study concluded the variant does not affect splicing (PMID: 17979987); however, later investigations showed that the aberrantly spliced transcripts are variably expressed and not always detectable even when splicing-specific PCR is used (PMID: 20635405), possibly due to nonsense-mediated decay. SpliceAI gives a delta score of 0.31 for an acceptor gain at -102 bp (ref score 0.15, alt score 0.46). (PVS1_RNA_Moderate).
• PP4_Moderate: At least one patient with this variant displayed progressive limb girdle muscle weakness or clinical suspicion of limb-girdle muscular dystrophy as well as significantly reduced or absent expression of calpain-3, which is specific for CAPN3-related LGMD (PP4_Moderate; PMID: 20635405). (capped at two Moderates in combination with PP1).
• PP1_Moderate: The variant was also reported to co-segregate with autosomal recessive disease in four affected family members from three families (PP1_Moderate; PMID: 37589857, 20635405, 35731190). (capped at two Moderates in combination with PP4).

Not Met criteria codes

• BS1: The filtering allele frequency for this variant is 0.006051 in gnomAD v2.1.1 European (non-Finnish) genomes (the lower threshold of the 95% CI of 172/31388), which is higher than the LGMD VCEP threshold of 0.001; in total, three homozygous individuals are also observed. However, this variant appears to act as a hypomorphic allele, and the VCEP opted not to apply this code (BS1 exception).
• PP3: Splice AI 0.31 acceptor gain at -102 bp; ref score 0.15, alt score 0.46. Not scoring because RNA evidence available - PVS1_RNA.