NM_001164277.2(SLC37A4):c.944T>G (p.Met315Arg) AND Glucose-6-phosphate transport defect

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 27, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003872493.2

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.944T>G (p.Met315Arg)]

NM_001164277.2(SLC37A4):c.944T>G (p.Met315Arg)

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.944T>G (p.Met315Arg)

HGVS:

NC_000011.10:g.119026007A>C
NG_013331.1:g.9899T>G
NM_001164277.2:c.944T>GMANE SELECT
NM_001164278.2:c.944T>G
NM_001164279.2:c.725T>G
NM_001164280.2:c.944T>G
NM_001467.6:c.944T>G
NP_001157749.1:p.Met315Arg
NP_001157749.1:p.Met315Arg
NP_001157750.1:p.Met315Arg
NP_001157751.1:p.Met242Arg
NP_001157752.1:p.Met315Arg
NP_001458.1:p.Met315Arg
NP_001458.1:p.Met315Arg
LRG_187t1:c.944T>G
LRG_187:g.9899T>G
LRG_187p1:p.Met315Arg
NC_000011.9:g.118896717A>C
NM_001164277.1:c.944T>G
NM_001467.4:c.944T>G

Protein change:

M242R

Molecular consequence:

NM_001164277.2:c.944T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001164278.2:c.944T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001164279.2:c.725T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001164280.2:c.944T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001467.6:c.944T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Glucose-6-phosphate transport defect (GSD1B)
Synonyms:: Glycogen storage disease type 1B; GSD Ib
Identifiers:: MONDO: MONDO:0009288; MedGen: C0268146; Orphanet: 364; Orphanet: 79259; OMIM: 232220

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PREDICTED: Homo sapiens BLACAT1 overlapping LEMD1 locus (BLACAT1), transcript va...
PREDICTED: Homo sapiens BLACAT1 overlapping LEMD1 locus (BLACAT1), transcript variant X4, mRNA
gi|2462501942|ref|XM_054333730.1|

Nucleotide
isthmin-1 precursor [Homo sapiens]
isthmin-1 precursor [Homo sapiens]
gi|153791192|ref|NP_543016.1|

Protein
CD93 [Ursus americanus]
CD93 [Ursus americanus]
Gene ID:123779053

Gene
LOC130009528 [Homo sapiens]
LOC130009528 [Homo sapiens]
Gene ID:130009528

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004685517	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 27, 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

SCV004685517

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 27, 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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004685517.1

#	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 methionine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 315 of the SLC37A4 protein (p.Met315Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC37A4-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SLC37A4 protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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

Last Updated: Sep 29, 2024

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