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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:
Mar 30, 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:
RCV000530736.13

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:
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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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000642377Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 16, 2024)
germlineclinical testing

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

SCV000790743Counsyl
no assertion criteria provided
Likely pathogenic
(Apr 6, 2017)
unknownclinical testing

SCV002783200Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 5, 2021)
unknownclinical testing

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

SCV004201000Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 30, 2024)
unknownclinical testing

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

SCV004238646Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Jul 11, 2023)
germlineclinical testing

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

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

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 Invitae, SCV000642377.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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.

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

From Counsyl, SCV000790743.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002783200.1

#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 Baylor Genetics, SCV004201000.2

#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 Revvity Omics, Revvity, SCV004238646.1

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

Last Updated: Jun 17, 2024