NM_000070.3(CAPN3):c.1743_1744del (p.Glu582fs) AND Autosomal recessive limb-girdle muscular dystrophy type 2A

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
May 30, 2021
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000283334.8

Allele description [Variation Report for NM_000070.3(CAPN3):c.1743_1744del (p.Glu582fs)]

NM_000070.3(CAPN3):c.1743_1744del (p.Glu582fs)

Gene:
CAPN3:calpain 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
15q15.1
Genomic location:
Preferred name:
NM_000070.3(CAPN3):c.1743_1744del (p.Glu582fs)
HGVS:
  • NC_000015.10:g.42403000_42403001del
  • NG_008660.1:g.59898_59899del
  • NM_000070.3:c.1743_1744delMANE SELECT
  • NM_024344.2:c.1743_1744del
  • NM_173087.2:c.1599_1600del
  • NM_173088.2:c.207_208del
  • NP_000061.1:p.Glu582fs
  • NP_077320.1:p.Glu582fs
  • NP_775110.1:p.Glu534fs
  • NP_775111.1:p.Glu70fs
  • LRG_849t1:c.1743_1744del
  • LRG_849:g.59898_59899del
  • LRG_849p1:p.Glu582fs
  • NC_000015.9:g.42695198_42695199del
  • NM_000070.2:c.1743_1744delTG
Protein change:
E534fs
Links:
dbSNP: rs886042573
NCBI 1000 Genomes Browser:
rs886042573
Molecular consequence:
  • NM_000070.3:c.1743_1744del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_024344.2:c.1743_1744del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_173087.2:c.1599_1600del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_173088.2:c.207_208del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy type 2A (LGMDR1)
Synonyms:
Limb-girdle muscular dystrophy, type 2A; Limb-girdle muscular dystrophy type 2; Muscular dystrophy, pelvofemoral; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009675; MedGen: C1869123; Orphanet: 267; OMIM: 253600

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000792539Counsyl
criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))		Likely pathogenic
(Jun 29, 2017) 		unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link,

SCV002242152Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(May 30, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Calpainopathy-a survey of mutations and polymorphisms.

Richard I, Roudaut C, Saenz A, Pogue R, Grimbergen JE, Anderson LV, Beley C, Cobo AM, de Diego C, Eymard B, Gallano P, Ginjaar HB, Lasa A, Pollitt C, Topaloglu H, Urtizberea JA, de Visser M, van der Kooi A, Bushby K, Bakker E, Lopez de Munain A, Fardeau M, et al.

Am J Hum Genet. 1999 Jun;64(6):1524-40.

PubMed [citation]
PMID:
10330340
PMCID:
PMC1377896

LGMD2A: genotype-phenotype correlations based on a large mutational survey on the calpain 3 gene.

Sáenz A, Leturcq F, Cobo AM, Poza JJ, Ferrer X, Otaegui D, Camaño P, Urtasun M, Vílchez J, Gutiérrez-Rivas E, Emparanza J, Merlini L, Paisán C, Goicoechea M, Blázquez L, Eymard B, Lochmuller H, Walter M, Bonnemann C, Figarella-Branger D, Kaplan JC, Urtizberea JA, et al.

Brain. 2005 Apr;128(Pt 4):732-42. Epub 2005 Feb 2.

PubMed [citation]
PMID:
15689361
See all PubMed Citations (3)

Details of each submission

From Counsyl, SCV000792539.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002242152.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has been observed in individual(s) with limb-girdle muscular dystrophy (PMID: 10330340). ClinVar contains an entry for this variant (Variation ID: 283179). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Glu582Glyfs*3) in the CAPN3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CAPN3 are known to be pathogenic (PMID: 10330340, 15689361).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024