NM_001164277.2(SLC37A4):c.955C>T (p.Arg319Trp) AND Glucose-6-phosphate transport defect

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Nov 6, 2019
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:: RCV001049603.2

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.955C>T (p.Arg319Trp)]

NM_001164277.2(SLC37A4):c.955C>T (p.Arg319Trp)

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.955C>T (p.Arg319Trp)

HGVS:

NC_000011.10:g.119025996G>A
NG_013331.1:g.9910C>T
NM_001164277.2:c.955C>TMANE SELECT
NM_001164278.2:c.955C>T
NM_001164279.2:c.736C>T
NM_001164280.2:c.955C>T
NM_001467.6:c.955C>T
NP_001157749.1:p.Arg319Trp
NP_001157749.1:p.Arg319Trp
NP_001157750.1:p.Arg319Trp
NP_001157751.1:p.Arg246Trp
NP_001157752.1:p.Arg319Trp
NP_001458.1:p.Arg319Trp
LRG_187t1:c.955C>T
LRG_187:g.9910C>T
LRG_187p1:p.Arg319Trp
NC_000011.9:g.118896706G>A
NM_001164277.1:c.955C>T

Protein change:

R246W

Links:

dbSNP: rs376730573

NCBI 1000 Genomes Browser:

rs376730573

Molecular consequence:

NM_001164277.2:c.955C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164278.2:c.955C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164279.2:c.736C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001164280.2:c.955C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001467.6:c.955C>T - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001213661	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 6, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001457663	Natera, Inc.	no assertion criteria provided	Uncertain significance (Sep 16, 2020)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001213661

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 6, 2019)

germline

clinical testing

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

SCV001457663

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Sep 16, 2020)

germline

clinical testing

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 Invitae, SCV001213661.1

#	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 arginine with tryptophan at codon 319 of the SLC37A4 protein (p.Arg319Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs376730573, ExAC 0.01%). This variant has not been reported in the literature in individuals with SLC37A4-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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

From Natera, Inc., SCV001457663.1

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

Last Updated: Apr 15, 2024

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