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NM_000023.4(SGCA):c.421C>A (p.Arg141Ser)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(6)

Review status:
criteria provided, conflicting interpretations
Submissions:
10 (Most recent: Sep 13, 2021)
Last evaluated:
Jul 22, 2021
Accession:
VCV000197618.16
Variation ID:
197618
Description:
single nucleotide variant
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NM_000023.4(SGCA):c.421C>A (p.Arg141Ser)

Allele ID
194779
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q21.33
Genomic location
17: 50168409 (GRCh38) GRCh38 UCSC
17: 48245770 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.48245770C>A
NC_000017.11:g.50168409C>A
NG_008889.1:g.7405C>A
... more HGVS
Protein change
R141S
Other names
-
Canonical SPDI
NC_000017.11:50168408:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00035
1000 Genomes Project 0.00140
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00046
Trans-Omics for Precision Medicine (TOPMed) 0.00063
Exome Aggregation Consortium (ExAC) 0.00116
Links
ClinGen: CA245881
dbSNP: rs35130237
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 4 criteria provided, multiple submitters, no conflicts Nov 17, 2020 RCV000713237.7
Likely benign 1 criteria provided, single submitter Dec 6, 2017 RCV000852723.1
Likely benign 1 criteria provided, single submitter Jan 24, 2018 RCV001122688.1
Conflicting interpretations of pathogenicity 4 criteria provided, conflicting interpretations Jul 22, 2021 RCV001086384.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SGCA - - GRCh38
GRCh37
405 418

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 24, 2018)
criteria provided, single submitter
Method: clinical testing
Sarcoglycanopathy
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001281434.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Jan 28, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal recessive limb-girdle muscular dystrophy type 2D
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories
Accession: SCV001474179.1
Submitted: (Dec 11, 2020)
Evidence details
Comment:
The SGCA c.421C>A; p.Arg141Ser variant (rs35130237) is reported in the literature in several individuals affected with limb-girdle muscular dystrophy or a related sarcoglycanopathy, although a … (more)
Likely benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal recessive limb-girdle muscular dystrophy type 2D
Allele origin: germline
Invitae
Accession: SCV000649772.4
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Nov 17, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: unknown
Athena Diagnostics Inc
Accession: SCV000843823.2
Submitted: (Sep 13, 2021)
Evidence details
Publications
PubMed (3)
Uncertain significance
(Mar 08, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230831.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Jul 16, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000565557.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
A variant of uncertain significance has been identified in the SGCA gene. The c.421 C>A variant has been reported previously in an individual with limb-girdle … (more)
Likely benign
(Dec 06, 2017)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
Center for Advanced Laboratory Medicine, UC San Diego Health,University of California San Diego
Accession: SCV000995438.1
Submitted: (Jun 12, 2019)
Evidence details
Uncertain significance
(Jan 01, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001246754.5
Submitted: (Jul 04, 2021)
Evidence details
Uncertain significance
(Jul 22, 2021)
criteria provided, single submitter
Method: clinical testing
Autosomal recessive limb-girdle muscular dystrophy type 2D
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001806722.1
Submitted: (Aug 23, 2021)
Evidence details
Uncertain significance
(Apr 03, 2020)
no assertion criteria provided
Method: clinical testing
Limb-girdle muscular dystrophy type 2D
Allele origin: germline
Natera, Inc.
Accession: SCV001465521.1
Submitted: (Dec 28, 2020)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
The Latin American experience with a next generation sequencing genetic panel for recessive limb-girdle muscular weakness and Pompe disease. Bevilacqua JA Orphanet journal of rare diseases 2020 PMID: 31931849
Revised spectrum of mutations in sarcoglycanopathies. Trabelsi M European journal of human genetics : EJHG 2008 PMID: 18285821
Novel sarcoglycan gene mutations in a large cohort of Italian patients. Boito C Journal of medical genetics 2003 PMID: 12746421
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SGCA - - - -

Text-mined citations for rs35130237...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Sep 18, 2021