NM_001164277.2(SLC37A4):c.1176T>A (p.Ser392Arg) AND Glucose-6-phosphate transport defect

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 27, 2021
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:: RCV000670525.5

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1176T>A (p.Ser392Arg)]

NM_001164277.2(SLC37A4):c.1176T>A (p.Ser392Arg)

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.1176T>A (p.Ser392Arg)

HGVS:

NC_000011.10:g.119025024A>T
NG_013331.1:g.10882T>A
NM_001164277.2:c.1176T>AMANE SELECT
NM_001164278.2:c.1242T>A
NM_001164279.2:c.957T>A
NM_001164280.2:c.1176T>A
NM_001467.6:c.1176T>A
NP_001157749.1:p.Ser392Arg
NP_001157749.1:p.Ser392Arg
NP_001157750.1:p.Ser414Arg
NP_001157751.1:p.Ser319Arg
NP_001157752.1:p.Ser392Arg
NP_001458.1:p.Ser392Arg
LRG_187t1:c.1176T>A
LRG_187:g.10882T>A
LRG_187p1:p.Ser392Arg
NC_000011.9:g.118895734A>T
NM_001164277.1:c.1176T>A

Protein change:

S319R

Links:

dbSNP: rs782552989

NCBI 1000 Genomes Browser:

rs782552989

Molecular consequence:

NM_001164277.2:c.1176T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001164278.2:c.1242T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001164279.2:c.957T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001164280.2:c.1176T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001467.6:c.1176T>A - 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
SCV000795386	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Uncertain significance (Nov 8, 2017)	unknown	clinical testing	Citation Link,
SCV002197682	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 27, 2021)	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

SCV000795386

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Uncertain significance
(Nov 8, 2017)

unknown

clinical testing

Citation Link,

SCV002197682

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 27, 2021)

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	unknown	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 Counsyl, SCV000795386.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002197682.3

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

Description

Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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. ClinVar contains an entry for this variant (Variation ID: 554828). This variant has not been reported in the literature in individuals affected with SLC37A4-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces serine with arginine at codon 392 of the SLC37A4 protein (p.Ser392Arg). The serine residue is highly conserved and there is a moderate physicochemical difference between serine and arginine.

#	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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