NM_000070.3(CAPN3):c.2380+12del AND Autosomal recessive limb-girdle muscular dystrophy type 2A

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Feb 1, 2024
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:: RCV000283123.18

Allele description [Variation Report for NM_000070.3(CAPN3):c.2380+12del]

NM_000070.3(CAPN3):c.2380+12del

Gene:

CAPN3:calpain 3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

15q15.1

Genomic location:

Preferred name:

NM_000070.3(CAPN3):c.2380+12del

HGVS:

NC_000015.10:g.42411012del
NG_008660.1:g.67910del
NM_000070.3:c.2380+12delMANE SELECT
NM_024344.2:c.2362+12del
NM_173087.2:c.2104+12del
NM_173088.2:c.844+12del
NM_173089.2:c.385+12del
NM_173090.2:c.385+12del
LRG_849t1:c.2380+12del
LRG_849:g.67910del
NC_000015.9:g.42703210del
NM_000070.2:c.2380+12del
NM_000070.2:c.2380+12delA

Links:

dbSNP: rs28364538

NCBI 1000 Genomes Browser:

rs28364538

Molecular consequence:

NM_000070.3:c.2380+12del - intron variant - [Sequence Ontology: SO:0001627]
NM_024344.2:c.2362+12del - intron variant - [Sequence Ontology: SO:0001627]
NM_173087.2:c.2104+12del - intron variant - [Sequence Ontology: SO:0001627]
NM_173088.2:c.844+12del - intron variant - [Sequence Ontology: SO:0001627]
NM_173089.2:c.385+12del - intron variant - [Sequence Ontology: SO:0001627]
NM_173090.2:c.385+12del - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000391037	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification 20161018)	Likely benign (Jun 14, 2016)	germline	clinical testing	ICSL_Variant_Classification_20161018.pdf, Citation Link,
SCV000677225	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (May 15, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 12461690, 26467025
SCV000743940	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Oct 9, 2014)	germline	clinical testing	Citation Link,
SCV002481948	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

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

Citations

PubMed

Clinical variability in calpainopathy: what makes the difference?

de Paula F, Vainzof M, Passos-Bueno MR, de Cássia M Pavanello R, Matioli SR, V B Anderson L, Nigro V, Zatz M.

Eur J Hum Genet. 2002 Dec;10(12):825-32.

PubMed [citation]

PMID:: 12461690

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000391037.2

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

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

From Athena Diagnostics, SCV000677225.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743940.1

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

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002481948.3

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

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

Last Updated: Jan 13, 2025

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