NM_000232.5(SGCB):c.656_657del (p.Lys219fs) AND Autosomal recessive limb-girdle muscular dystrophy type 2E

Germline classification:: Pathogenic/Likely pathogenic (5 submissions)
Last evaluated:: Aug 14, 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:: RCV000530736.16

Allele description [Variation Report for NM_000232.5(SGCB):c.656_657del (p.Lys219fs)]

NM_000232.5(SGCB):c.656_657del (p.Lys219fs)

Gene:

SGCB:sarcoglycan beta [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q12

Genomic location:

Preferred name:

NM_000232.5(SGCB):c.656_657del (p.Lys219fs)

HGVS:

NC_000004.12:g.52028066_52028067del
NG_008891.1:g.15255_15256del
NM_000232.5:c.656_657delMANE SELECT
NP_000223.1:p.Lys219fs
NP_000223.1:p.Lys219fs
LRG_204t1:c.656_657del
LRG_204:g.15255_15256del
LRG_204p1:p.Lys219fs
NC_000004.11:g.52894230_52894231del
NC_000004.11:g.52894232_52894233del
NM_000232.4:c.656_657del
NM_000232.4:c.656_657delAA

Protein change:

K219fs

Links:

dbSNP: rs775458201

NCBI 1000 Genomes Browser:

rs775458201

Molecular consequence:

NM_000232.5:c.656_657del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Autosomal recessive limb-girdle muscular dystrophy type 2E (LGMDR4)
Synonyms:: MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 4
Identifiers:: MONDO: MONDO:0011423; MedGen: C1858593; Orphanet: 119; OMIM: 604286

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000642377	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 14, 2024)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15938573, 18285821, 28492532
SCV000790743	Counsyl	no assertion criteria provided	Likely pathogenic (Apr 6, 2017)	unknown	clinical testing
SCV002783200	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 5, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004201000	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 30, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004238646	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jul 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Help

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Beta-sarcoglycan gene mutations in Turkey.

Balci B, Wilichowski E, Haliloğlu G, Talim B, Aurino S, Kremer E, Ebinger F, Senbil N, Anlar B, Kale G, Nigro V, Topaloğlu H, Bonnemann C, Dinçer P.

Acta Myol. 2004 Dec;23(3):154-8.

PubMed [citation]

PMID:: 15938573

Revised spectrum of mutations in sarcoglycanopathies.

Trabelsi M, Kavian N, Daoud F, Commere V, Deburgrave N, Beugnet C, Llense S, Barbot JC, Vasson A, Kaplan JC, Leturcq F, Chelly J.

Eur J Hum Genet. 2008 Jul;16(7):793-803. doi: 10.1038/ejhg.2008.9. Epub 2008 Feb 20.

PubMed [citation]

PMID:: 18285821

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000642377.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Lys219Serfs*2) in the SGCB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SGCB are known to be pathogenic (PMID: 15938573, 18285821). This variant is present in population databases (no rsID available, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with SGCB-related conditions. ClinVar contains an entry for this variant (Variation ID: 466603). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#	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 Counsyl, SCV000790743.2

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Fulgent Genetics, Fulgent Genetics, SCV002783200.2

#	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

From Baylor Genetics, SCV004201000.2

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV004238646.1

#	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: May 16, 2025

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