NM_000070.3(CAPN3):c.742_743del (p.Met248fs) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 20, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000482838.1

Allele description [Variation Report for NM_000070.3(CAPN3):c.742_743del (p.Met248fs)]

NM_000070.3(CAPN3):c.742_743del (p.Met248fs)

Gene:

CAPN3:calpain 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

15q15.1

Genomic location:

Preferred name:

NM_000070.3(CAPN3):c.742_743del (p.Met248fs)

HGVS:

NC_000015.10:g.42389037_42389038del
NG_008660.1:g.45935_45936del
NM_000070.3:c.742_743delMANE SELECT
NM_024344.2:c.742_743del
NM_173087.2:c.742_743del
NP_000061.1:p.Met248fs
NP_077320.1:p.Met248fs
NP_775110.1:p.Met248fs
LRG_849t1:c.742_743del
LRG_849:g.45935_45936del
LRG_849p1:p.Met248fs
NC_000015.9:g.42681235_42681236del
NC_000015.9:g.42681235_42681236delAT
NM_000070.2:c.742_743delAT

Protein change:

M248fs

Links:

dbSNP: rs1064793620

NCBI 1000 Genomes Browser:

rs1064793620

Molecular consequence:

NM_000070.3:c.742_743del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024344.2:c.742_743del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_173087.2:c.742_743del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566616	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Likely pathogenic (Jun 20, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000566616

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Likely pathogenic
(Jun 20, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000566616.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.742_743delAT variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The c.742_743delAT variant causes a frameshift starting with codon Methionine 248, changes this amino acid to a Valine residue and creates a premature Stop codon at position 19 of the new reading frame, denoted p.Met248ValfsX19. This variant is predicted to cause loss of normal protein function through protein truncation or nonsense-mediated mRNA decay. Although this variant has not been reported previously to our knowledge, other loss-of-function variants in the CAPN3 gene have been reported in the Human Gene Mutation Database in association with LGMD2A (Stenson et al., 2014).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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