NM_000232.5(SGCB):c.943G>A (p.Gly315Arg) AND Autosomal recessive limb-girdle muscular dystrophy type 2E

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Oct 2, 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:: RCV000815228.9

Allele description [Variation Report for NM_000232.5(SGCB):c.943G>A (p.Gly315Arg)]

NM_000232.5(SGCB):c.943G>A (p.Gly315Arg)

Gene:

SGCB:sarcoglycan beta [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4q12

Genomic location:

Preferred name:

NM_000232.5(SGCB):c.943G>A (p.Gly315Arg)

HGVS:

NC_000004.12:g.52023971C>T
NG_008891.1:g.19349G>A
NG_053164.1:g.1341G>A
NM_000232.5:c.943G>AMANE SELECT
NP_000223.1:p.Gly315Arg
NP_000223.1:p.Gly315Arg
LRG_204t1:c.943G>A
LRG_204:g.19349G>A
LRG_204p1:p.Gly315Arg
NC_000004.11:g.52890137C>T
NM_000232.4:c.943G>A

Protein change:

G315R

Links:

dbSNP: rs150395645

NCBI 1000 Genomes Browser:

rs150395645

Molecular consequence:

NM_000232.5:c.943G>A - missense variant - [Sequence Ontology: SO:0001583]

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

Recent activity

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Lds2p [Saccharomyces cerevisiae S288C]
Lds2p [Saccharomyces cerevisiae S288C]
gi|9755359|ref|NP_014595.2|

Protein
Macrognathus pancalus voucher SR_GU_Mp_02 cytochrome oxidase subunit I (COI) gen...
Macrognathus pancalus voucher SR_GU_Mp_02 cytochrome oxidase subunit I (COI) gene, partial cds; mitochondrial
gi|1040784488|gb|KX355469.1|

Nucleotide
Qipengyuania zhejiangensis 16S ribosomal RNA gene, partial sequence
Qipengyuania zhejiangensis 16S ribosomal RNA gene, partial sequence
gi|2577544167|gb|OR563694.1|

Nucleotide
MAG: Gammaproteobacteria bacterium RIFCSPHIGHO2_01_FULL_42_8 rifcsphigho2_01_sca...
MAG: Gammaproteobacteria bacterium RIFCSPHIGHO2_01_FULL_42_8 rifcsphigho2_01_scaffold_103981, whole genome shotgun sequence
gi|1085137607|gb|MGXN01000002.1||gn :MGXN01|rifcsphigho2_01_scaffold_103981

Nucleotide
Metastatic Hydatidiform Mole
Metastatic Hydatidiform Mole

MedGen

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000955676	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001462201	Natera, Inc.	no assertion criteria provided	Uncertain significance (Jan 6, 2020)	germline	clinical testing
SCV003827622	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 2, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000955676

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 2022)

germline

clinical testing

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

SCV001462201

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Jan 6, 2020)

germline

clinical testing

SCV003827622

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Oct 2, 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

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

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000955676.3

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 315 of the SGCB protein (p.Gly315Arg). This variant is present in population databases (rs150395645, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. 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: 255606). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.

#	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 Natera, Inc., SCV001462201.1

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

From Revvity Omics, Revvity, SCV003827622.2

#	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

Last Updated: Oct 20, 2024

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