NM_001164277.2(SLC37A4):c.1015G>T (p.Gly339Cys) AND not provided

Germline classification:: Pathogenic (5 submissions)
Last evaluated:: Apr 10, 2024
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:: RCV000059116.31

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1015G>T (p.Gly339Cys)]

NM_001164277.2(SLC37A4):c.1015G>T (p.Gly339Cys)

Gene:

SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001164277.2(SLC37A4):c.1015G>T (p.Gly339Cys)

Other names:

1184G>T

HGVS:

NC_000011.10:g.119025299C>A
NG_013331.1:g.10607G>T
NM_001164277.2:c.1015G>TMANE SELECT
NM_001164278.2:c.1081G>T
NM_001164279.2:c.796G>T
NM_001164280.2:c.1015G>T
NM_001467.6:c.1015G>T
NP_001157749.1:p.Gly339Cys
NP_001157749.1:p.Gly339Cys
NP_001157750.1:p.Gly361Cys
NP_001157751.1:p.Gly266Cys
NP_001157752.1:p.Gly339Cys
NP_001458.1:p.Gly339Cys
LRG_187t1:c.1015G>T
LRG_187:g.10607G>T
LRG_187p1:p.Gly339Cys
NC_000011.9:g.118896009C>A
NM_001164277.1:c.1015G>T
NM_001467.4:c.1015G>T
p.G339C

Protein change:

G266C; GLY339CYS

Links:

UniProtKB/Swiss-Prot: VAR_003185; OMIM: 602671.0001; dbSNP: rs80356490

NCBI 1000 Genomes Browser:

rs80356490

Molecular consequence:

NM_001164277.2:c.1015G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164278.2:c.1081G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164279.2:c.796G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164280.2:c.1015G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001467.6:c.1015G>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000090645	UniProtKB/Swiss-Prot	no classification provided	not provided	not provided	not provided	PubMed (1) [See all records that cite this PMID]
SCV000252293	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Apr 10, 2024)	germline	clinical testing	Citation Link,
SCV001446587	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 23, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002585359	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Pathogenic (Aug 1, 2022)	germline	clinical testing	Citation Link,
SCV003821197	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 20, 2022)	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
not provided	germline	yes	1	not provided	not provided	1	not provided	clinical testing
not provided	not provided	not provided	not provided	not provided	not provided	1	not provided	literature only

Citations

PubMed

A gene on chromosome 11q23 coding for a putative glucose- 6-phosphate translocase is mutated in glycogen-storage disease types Ib and Ic.

Veiga-da-Cunha M, Gerin I, Chen YT, de Barsy T, de Lonlay P, Dionisi-Vici C, Fenske CD, Lee PJ, Leonard JV, Maire I, McConkie-Rosell A, Schweitzer S, Vikkula M, Van Schaftingen E.

Am J Hum Genet. 1998 Oct;63(4):976-83.

PubMed [citation]

PMID:: 9758626
PMCID:: PMC1377500

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 UniProtKB/Swiss-Prot, SCV000090645.1

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

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

From GeneDx, SCV000252293.14

#	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; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 9428641, 10940311, 18835800, 19008136, 20578944, 12811562, 10482962, 21599942, 31980526, 31589614, 33977030, 12444104, 9758626, 12373566)

#	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

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001446587.1

#	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	yes	1	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV002585359.15

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

From Revvity Omics, Revvity, SCV003821197.2

#	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 26, 2024

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