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NM_000337.6(SGCD):c.15G>C (p.Glu5Asp)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
8 (Most recent: Sep 24, 2021)
Last evaluated:
Jun 22, 2021
Accession:
VCV000202085.8
Variation ID:
202085
Description:
single nucleotide variant
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NM_000337.6(SGCD):c.15G>C (p.Glu5Asp)

Allele ID
198172
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q33.3
Genomic location
5: 156344500 (GRCh38) GRCh38 UCSC
5: 155771510 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.156344500G>C
NG_008693.2:g.479157G>C
NM_000337.6:c.15G>C MANE Select NP_000328.2:p.Glu5Asp missense
... more HGVS
Protein change
E5D, E4D
Other names
p.E5D:GAG>GAC
Canonical SPDI
NC_000005.10:156344499:G:C
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (C)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00004
Trans-Omics for Precision Medicine (TOPMed) 0.00009
1000 Genomes Project 0.00140
Trans-Omics for Precision Medicine (TOPMed) 0.00011
Links
ClinGen: CA308779
dbSNP: rs549319429
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 criteria provided, single submitter Jan 22, 2016 RCV000183899.7
Likely benign 1 criteria provided, single submitter Jun 14, 2016 RCV000331989.2
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV000389000.2
Benign 1 criteria provided, single submitter Nov 16, 2020 RCV000639556.4
Benign 1 criteria provided, single submitter Mar 9, 2018 RCV001170139.1
Likely benign 3 criteria provided, single submitter Jun 22, 2021 RCV001701634.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
SGCD - - GRCh38
GRCh37
492 508

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jun 14, 2016)
criteria provided, single submitter
Method: clinical testing
Limb-Girdle Muscular Dystrophy, Recessive
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000455467.2
Submitted: (Oct 18, 2016)
Evidence details
Benign
(Jan 22, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000338346.3
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Qualitative or quantitative defects of delta-sarcoglycan
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000455468.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Mar 09, 2018)
criteria provided, single submitter
Method: clinical testing
Cardiomyopathy
Allele origin: germline
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario
Accession: SCV001332680.1
Submitted: (Mar 03, 2020)
Evidence details
Benign
(Nov 16, 2020)
criteria provided, single submitter
Method: clinical testing
Autosomal recessive limb-girdle muscular dystrophy type 2F
Allele origin: germline
Invitae
Accession: SCV000761132.4
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jun 22, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000236382.13
Submitted: (Sep 24, 2021)
Evidence details
Comment:
This variant is associated with the following publications: (PMID: 28144010, 27488758, 30564623)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001930302.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001965770.1
Submitted: (Sep 21, 2021)
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=SGCD - - - -

Text-mined citations for rs549319429...

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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 Nov 27, 2021