NM_000232.5(SGCB):c.165_166del (p.Gly56fs) AND Autosomal recessive limb-girdle muscular dystrophy type 2E

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Oct 3, 2023
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:: RCV003466382.3

Allele description [Variation Report for NM_000232.5(SGCB):c.165_166del (p.Gly56fs)]

NM_000232.5(SGCB):c.165_166del (p.Gly56fs)

Gene:

SGCB:sarcoglycan beta [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q12

Genomic location:

Preferred name:

NM_000232.5(SGCB):c.165_166del (p.Gly56fs)

HGVS:

NC_000004.12:g.52033508_52033509del
NG_008891.1:g.9811_9812del
NM_000232.5:c.165_166delMANE SELECT
NP_000223.1:p.Gly56Valfs
NP_000223.1:p.Gly56fs
LRG_204t1:c.165_166del
LRG_204:g.9811_9812del
LRG_204p1:p.Gly56Valfs
NC_000004.11:g.52899674_52899675del
NM_000232.4:c.165_166delAG

Protein change:

G56fs

Molecular consequence:

NM_000232.5:c.165_166del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Autosomal recessive limb-girdle muscular dystrophy type 2E (LGMDR4)
Synonyms:: Limb-girdle muscular dystrophy, type 2E; Muscular dystrophy limb-girdle with beta-sarcoglycan deficiency; Beta-sarcoglycan limb-girdle muscular dystrophy; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0011423; MedGen: C1858593; Orphanet: 119; OMIM: 604286

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PopSet
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Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004208738	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 3, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004549186	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 21, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15938573, 18285821, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004208738

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 3, 2023)

unknown

clinical testing

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

SCV004549186

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 21, 2023)

germline

clinical testing

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

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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

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

See all PubMed Citations (4)

Details of each submission

From Baylor Genetics, SCV004208738.1

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004549186.1

#	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.Gly56Valfs*42) 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 not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SGCB-related conditions. 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

Last Updated: Sep 29, 2024

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