NM_000023.4(SGCA):c.409G>A (p.Glu137Lys) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: May 4, 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:: RCV000725776.5

Allele description [Variation Report for NM_000023.4(SGCA):c.409G>A (p.Glu137Lys)]

NM_000023.4(SGCA):c.409G>A (p.Glu137Lys)

Gene:

SGCA:sarcoglycan alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.33

Genomic location:

Preferred name:

NM_000023.4(SGCA):c.409G>A (p.Glu137Lys)

HGVS:

NC_000017.11:g.50168397G>A
NG_008889.1:g.7393G>A
NM_000023.4:c.409G>AMANE SELECT
NM_001135697.3:c.409G>A
NP_000014.1:p.Glu137Lys
NP_001129169.1:p.Glu137Lys
LRG_203t1:c.409G>A
LRG_203:g.7393G>A
NC_000017.10:g.48245758G>A
NM_000023.2:c.409G>A
NR_135553.2:n.445G>A
Q16586:p.Glu137Lys

Protein change:

E137K

Links:

UniProtKB: Q16586#VAR_010416; dbSNP: rs372210292

NCBI 1000 Genomes Browser:

rs372210292

Molecular consequence:

NM_000023.4:c.409G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001135697.3:c.409G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_135553.2:n.445G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000339307	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Pathogenic (Jul 12, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link,
SCV004168957	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (May 4, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000339307

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Pathogenic
(Jul 12, 2017)

germline

clinical testing

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

Citation Link,

SCV004168957

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(May 4, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	4	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Details of each submission

From Eurofins Ntd Llc (ga), SCV000339307.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	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		4	not provided	not provided	not provided

From GeneDx, SCV004168957.1

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 34426522, 31589614, 22095924, 9192266, 30703231, 21031578, 30764848, 16778590, 31069529, 12075495, 18285821, 25214167, 31980526, 19798725, 26916285, 24077912, 30107846)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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