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NM_000232.5(SGCB):c.87_89del (p.Arg30del) AND Autosomal recessive limb-girdle muscular dystrophy type 2E

Germline classification:
Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:
Aug 16, 2022
Review status:
criteria provided, conflicting classifications
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:
RCV001309094.15

Allele description [Variation Report for NM_000232.5(SGCB):c.87_89del (p.Arg30del)]

NM_000232.5(SGCB):c.87_89del (p.Arg30del)

Gene:
SGCB:sarcoglycan beta [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4q12
Genomic location:
Preferred name:
NM_000232.5(SGCB):c.87_89del (p.Arg30del)
HGVS:
  • NC_000004.12:g.52033587_52033589del
  • NG_008891.1:g.9733_9735del
  • NM_000232.5:c.87_89delMANE SELECT
  • NP_000223.1:p.Arg30del
  • LRG_204t1:c.87_89del
  • LRG_204:g.9733_9735del
  • NC_000004.11:g.52899751_52899753del
  • NC_000004.11:g.52899753_52899755del
  • NM_000232.4:c.87_89del
Protein change:
R30del
Links:
dbSNP: rs780654411
NCBI 1000 Genomes Browser:
rs780654411
Molecular consequence:
  • NM_000232.5:c.87_89del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV001498577Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Aug 16, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001976958Laboratory of Medical Genetics, National & Kapodistrian University of Athens
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 1, 2021)
unknownclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV002082993Natera, Inc.
no assertion criteria provided
Uncertain significance
(Mar 11, 2020)
germlineclinical testing

SCV003827610Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(May 21, 2021)
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 providedunknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Phenotype-driven variant filtration strategy in exome sequencing toward a high diagnostic yield and identification of 85 novel variants in 400 patients with rare Mendelian disorders.

Marinakis NM, Svingou M, Veltra D, Kekou K, Sofocleous C, Tilemis FN, Kosma K, Tsoutsou E, Fryssira H, Traeger-Synodinos J.

Am J Med Genet A. 2021 Aug;185(8):2561-2571. doi: 10.1002/ajmg.a.62338. Epub 2021 May 19.

PubMed [citation]
PMID:
34008892
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001498577.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This variant, c.87_89del, results in the deletion of 1 amino acid(s) of the SGCB protein (p.Arg30del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs780654411, gnomAD 0.004%). This variant has been observed in individual(s) with neuromuscular abnormalities (PMID: 34008892). ClinVar contains an entry for this variant (Variation ID: 1011323). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV001976958.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

PM2, PM3, PM4, PP4, PP5

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

From Natera, Inc., SCV002082993.1

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

From Revvity Omics, Revvity, SCV003827610.2

#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: Mar 16, 2024