15-42399483-A-G

Variant names:

• chr15-42399483-A-G
• rs374665929
• NM_000070.3:c.1194-9A>G

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PP4 PM2_Supporting PM3

This summary comes from the ClinGen Evidence Repository: The NM_000070.3:c.1194-9A>G variant in CAPN3 is located in intron 9 of 23 and is expected to disrupt the canonical splice acceptor site (SpliceAI score 0.97 for acceptor loss) and create an alternative acceptor site (SpliceAI score 1.0 for acceptor gain). RNA analysis has demonstrated a splice effect of this variant, resulting in inclusion of the last eight nucleotides of intron 9, which is expected to lead to a frameshift, premature truncation, and subsequent nonsense mediated decay (PVS1_RNA). This variant has been detected in at least 9 unrelated individuals with clinical features of limb girdle muscular dystrophy (PMID:30564623, 22158424, 12461690, 18055493, 25135358, 10330340, 11525884; LOVD CAPN3_000088; ClinVar SCV003922313.1), including in a homozygous state (0.75 pts) (PMID:12461690, 11525884) and in unknown phase with a pathogenic variant (c.1469G>A p.(Arg490Gln), 0.5 pts, ClinVar SCV003922313.1 (PM3). At least one individual with this variant displayed progressive limb girdle muscle weakness or had a clinical suspicion of LGMD (PP4). The minor allele frequency of this variant is 0.00001758 in the European (non-Finnish) population in gnomAD v2.1.1 (2/113748 chromosomes), which is lower than the LGMD VCEP threshold (<0.0001) for PM2_Supporting, meeting this criterion (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 LGMD VCEP (LGMD VCEP specifications version 1.0.0; 03/18/2025): PVS1_RNA, PM3, PP4, PM2_Supporting. LINK:https://erepo.genome.network/evrepo/ui/classification/CA347487/MONDO:0015152/187

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000021 (0 hom.)
• Consequence: CAPN3 NM_000070.3 intron
• Scores: Splicing: ADA: 0.9900
• Clinical Significance: Pathogenic reviewed by expert panel P:12
• Conservation: PhyloP100: -0.0700

Genes affected

CAPN3 (HGNC:1480): (calpain 3) Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit family that specifically binds to titin. Mutations in this gene are associated with limb-girdle muscular dystrophies type 2A. Alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms and some variants are ubiquitously expressed. [provided by RefSeq, Jul 2008]

ENSG00000258461 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAPN3	NM_000070.3	c.1194-9A>G		intron_variant	Intron 9 of 23	ENST00000397163.8	NP_000061.1
CAPN3	NM_024344.2	c.1194-9A>G		intron_variant	Intron 9 of 22		NP_077320.1
CAPN3	NM_173087.2	c.1050-9A>G		intron_variant	Intron 8 of 20		NP_775110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CAPN3	ENST00000397163.8	c.1194-9A>G		intron_variant	Intron 9 of 23	1	NM_000070.3	ENSP00000380349.3
ENSG00000258461	ENST00000495723.1	n.*990-9A>G		intron_variant	Intron 13 of 25	2		ENSP00000492063.1

Frequencies

GnomAD3 genomes AF: 0.0000132 AC: 2 AN: 151774 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000119 AC: 3 AN: 251462 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135904

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000176

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000212 AC: 31 AN: 1459346 Hom.: 0 Cov.: 29 AF XY: 0.0000165 AC XY: 12 AN XY: 726242

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.0000504

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000243

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000132 AC: 2 AN: 151774 Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1 AN XY: 74106

Gnomad4 AFR AF: 0.0000242

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00

Alfa AF: 0.00000961 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:4

Oct 10, 2017

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 24, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate a damaging effect by impairing splicing causing at least a partial intron 9 retention (Salem et al., 2012); This variant is associated with the following publications: (PMID: 25525159, 10330340, 22158424, 33335567, 34720847, 32528171, 31788660, 25135358, 27500519, 30919934, 28403181, 11525884, 26404900) -

Apr 28, 2017

Athena Diagnostics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 22, 2020

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Autosomal recessive limb-girdle muscular dystrophy type 2A Pathogenic:3

Nov 25, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 9 of the CAPN3 gene. It does not directly change the encoded amino acid sequence of the CAPN3 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or altered protein product. This variant is present in population databases (rs374665929, gnomAD 0.007%). This variant has been observed in individuals with autosomal recessive limb-girdle muscular dystrophy (PMID: 10330340, 11525884, 12461690, 18055493, 22158424, 25135358). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 217146). Studies have shown that this variant results in the retention of 8 nucleotides of intron 9, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 22158424). For these reasons, this variant has been classified as Pathogenic. -

Sep 16, 2020

Natera, Inc.

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Sep 11, 2017

Counsyl

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Autosomal recessive limb-girdle muscular dystrophy Pathogenic:2

May 02, 2023

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

The heterozygous c.1194-9A>G variant in CAPN3 was identified by our study, in the compound heterozygous state with a pathogenic variant (ClinVar Variation ID: 17622), in one individual with limb-girdle muscular dystrophy. This individual also carried a pathogenic variant (ClinVar Variation ID: 17622), however the phase of these variants are unknown at this time. The c.1194-9A>G variant in CAPN3 has been previously reported in twelve individuals with autosomal recessive limb-girdle muscular dystrophy 1 (PMID: 25135358, PMID: 27066573, PMID: 10330340, PMID: 10330340, PMID: 31788660, PMID: 32528171, PMID: 30919934, PMID: 34720847, PMID: 33335567, PMID: 18055493, PMID: 11525884, PMID: 22158424, PMID: 12461690), segregated with disease in 3 affected relatives from one family (PMID: 22158424), but has been identified in 0.006% (1/16256) of African/African American chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs374665929). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID: 217146) and has been interpreted as pathogenic by PerkinElmer Genomics, Natera, Inc, Athena Diagnostics, Invitae, and Eurofins NTD LLC, and as likely pathogenic by Counsyl and GeneDx. Of these twelve affected individuals previously reported (PMID: 25135358, PMID: 27066573, PMID: 10330340, PMID: 10330340, PMID: 31788660, PMID: 32528171, PMID: 30919934, PMID: 34720847, PMID: 33335567, PMID: 18055493, PMID: 11525884, PMID: 22158424, PMID: 12461690), 6 were homozygotes (PMID: 10330340, PMID: 30919934, PMID: 22158424, PMID: 12461690, PMID: 11525884, PMID: 30919934) , two were compound heterozygotes who carried pathogenic variants in trans (PMID: 25135358, PMID: 31788660), one was a compound heterozygote who carried a likely pathogenic variant in unknown phase (PMID: 18055493), and four were compound heterozygotes who carried variants of uncertain significance in trans (PMID: 25135358, PMID: 27066573, PMID: 34720847), and, in addition, the individual identified by our study was a compound heterozygote who carried a pathogenic variant (ClinVar Variation ID: 17622) in unknown phase, which increases the likelihood that the c.1194-9A>G variant is pathogenic. RT-PCR analysis performed on RNA from an affected individual’s muscle biopsy showed altered splicing, with incorporation of eight nucleotides from intron 9 in a transcript lacking the seven first exons, versus the wild-type transcript seen in RNA from a muscle biopsy of a unaffected control individual (PMID: 22158424). This variant is located in the 3’ splice region. Computational tools do suggest an impact to splicing. However, this information is not predictive enough to determine pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive limb-girdle muscular dystrophy 1. ACMG/AMP Criteria applied: PM3_VeryStrong, PS3_Moderate, PM2_Supporting, PP1 (Richards 2015). -

Mar 18, 2025

ClinGen Limb Girdle Muscular Dystrophy Variant Curation Expert Panel, ClinGen

Significance: Pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

The NM_000070.3:c.1194-9A>G variant in CAPN3 is located in intron 9 of 23 and is expected to disrupt the canonical splice acceptor site (SpliceAI score 0.97 for acceptor loss) and create an alternative acceptor site (SpliceAI score 1.0 for acceptor gain). RNA analysis has demonstrated a splice effect of this variant, resulting in inclusion of the last eight nucleotides of intron 9, which is expected to lead to a frameshift, premature truncation, and subsequent nonsense mediated decay (PVS1_RNA). This variant has been detected in at least 9 unrelated individuals with clinical features of limb girdle muscular dystrophy (PMID: 30564623, 22158424, 12461690, 18055493, 25135358, 10330340, 11525884; LOVD CAPN3_000088; ClinVar SCV003922313.1), including in a homozygous state (0.75 pts) (PMID: 12461690, 11525884) and in unknown phase with a pathogenic variant (c.1469G>A p.(Arg490Gln), 0.5 pts, ClinVar SCV003922313.1 (PM3). At least one individual with this variant displayed progressive limb girdle muscle weakness or had a clinical suspicion of LGMD (PP4). The minor allele frequency of this variant is 0.00001758 in the European (non-Finnish) population in gnomAD v2.1.1 (2/113748 chromosomes), which is lower than the LGMD VCEP threshold (<0.0001) for PM2_Supporting, meeting this criterion (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 LGMD VCEP (LGMD VCEP specifications version 1.0.0; 03/18/2025): PVS1_RNA, PM3, PP4, PM2_Supporting. -

Autosomal recessive limb-girdle muscular dystrophy type 2A;C4748295:Muscular dystrophy, limb-girdle, autosomal dominant 4 Pathogenic:2

-

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PM2_Supporting+PP3+PM3_Strong+PP1_Strong -

Apr 08, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Muscular dystrophy, limb-girdle, autosomal dominant 4 Pathogenic:1

Mar 19, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	23
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.99
dbscSNV1_RF	Pathogenic	0.97
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_AG_spliceai		1.0		Position offset: 1
DS_AL_spliceai		0.97		Position offset: 9

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs374665929; hg19: chr15-42691681;