15-42396883-T-A

Variant names:

• chr15-42396883-T-A
• rs1555421532
• NM_000070.3:c.1193+6T>A

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_000070.3(CAPN3):​c.1193+6T>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: CAPN3 NM_000070.3 splice_region, intron
• Scores: Splicing: ADA: 0.6594
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:4 O:1
• Conservation: PhyloP100: 0.580
• Publications: 2 publications found

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]

CAPN3 Gene-Disease associations (from GenCC):

• autosomal recessive limb-girdle muscular dystrophy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• autosomal recessive limb-girdle muscular dystrophy type 2A

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Myriad Women’s Health, Labcorp Genetics (formerly Invitae)
• muscular dystrophy, limb-girdle, autosomal dominant 4

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• muscular dystrophy, limb-girdle, autosomal dominant

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ENSG00000258461 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. Scorers claiming Benign: dbscSNV1_ADA.
• PP5: Variant 15-42396883-T-A is Pathogenic according to our data. Variant chr15-42396883-T-A is described in ClinVar as Pathogenic. ClinVar VariationId is 813980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CAPN3	NM_000070.3	c.1193+6T>A		splice_region_variant, intron_variant	Intron 9 of 23	ENST00000397163.8	NP_000061.1
CAPN3	NM_024344.2	c.1193+6T>A		splice_region_variant, intron_variant	Intron 9 of 22		NP_077320.1
CAPN3	NM_173087.2	c.1049+6T>A		splice_region_variant, 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.1193+6T>A		splice_region_variant, intron_variant	Intron 9 of 23	1	NM_000070.3	ENSP00000380349.3
ENSG00000258461	ENST00000495723.1	n.*989+6T>A		splice_region_variant, intron_variant	Intron 13 of 25	2		ENSP00000492063.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2A Pathogenic:2 Other:1

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

Pathogenic variant most likely the result of a founder effect followed by the Mocheni community in the Fersina River valley in the Italian Alps [Fanin et al 2012]. -

Apr 11, 2024

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

The homozygous c.1193+6T>A variant in CAPN3 was identified by our study in one individual with Limb-Girdle Muscular Dystrophy (LGMD). The c.1193+6T>A variant has been reported in >10 individuals with limb-girdle muscular dystrophy (PMID: 22486197, 17994539, 20635405, 30028523), segregated with disease in 5 affected relatives from 1 family (22486197), and absent from large population studies. This variant has also been reported in ClinVar (Variation ID: 813980) and has been interpreted as pathogenic by Women's Health and Genetics/Laboratory Corporation of America (LabCorp), Invitae, and CeGaT Center for Human Genetics Tuebingen. Of the 12 affected individuals, five of those were homozygotes and 5 were compound heterozygotes that carried a reported pathogenic variant in trans or with unknown phase, which increases the likelihood that the c.1193+6T>A variant is pathogenic (Variation ID: 17622, 282173, 217154, 166790; PMID: 22486197, 17994539, 20635405, 30028523). 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. RT-PCR analysis performed on affected tissue shows possible evidence of intron retention after exon 9 (PMID: 20635405). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Limb-Girdle Muscular Dystrophy. ACMG/AMP Criteria applied: PP1_strong, PM3_strong, PVS1_strong, PM2_supporting (Richards 2015). -

Oct 13, 2023

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 disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with autosomal recessive limb-girdle muscular dystrophy 2A (LGMD2A) (PMID: 17994539, 20635405). ClinVar contains an entry for this variant (Variation ID: 813980). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in a 31 base pair insertion in intron 9 leading to alternate splicing and introduces a premature termination codon (PMID: 20635405). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

Autosomal recessive limb-girdle muscular dystrophy Pathogenic:1

May 04, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CAPN3 c.1193+6T>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant weakens the canonical 5' donor site. At least one publication reports experimental evidence that this variant affects splicing by inserting 31 base pair in the intron 9 which introduces a premature termination codon (example: Nascimbeni_2010). The variant was absent in 251312 control chromosomes (gnomAD). c.1193+6T>A has been reported in the literature in multiple bi-allelic individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive (example: Guglieri_2008, Nascimbeni_2010, and Fanin_2012). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 17994539, 20635405, 22486197). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic (n=2) and VUS (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:1

Jan 01, 2021

CeGaT Center for Human Genetics Tuebingen

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	-0.20
CADD	Benign	17
DANN	Benign	0.93
PhyloP100		0.58
Mutation Taster		=1/99	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.66
dbscSNV1_RF	Pathogenic	0.73
Splicevardb		3.0
SpliceAI score (max)		0.68		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.68		Position offset: 25
DS_DL_spliceai		0.21		Position offset: -6

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

Other links and lift over

dbSNP: rs1555421532; hg19: chr15-42689081;