NM_001164277.2(SLC37A4):c.1175G>A (p.Ser392Asn) AND Glucose-6-phosphate transport defect

Clinical significance:Uncertain significance (Last evaluated: Dec 18, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000666617.3

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1175G>A (p.Ser392Asn)]

NM_001164277.2(SLC37A4):c.1175G>A (p.Ser392Asn)

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.1175G>A (p.Ser392Asn)
HGVS:
  • NC_000011.10:g.119025025C>T
  • NG_013331.1:g.10881G>A
  • NM_001164277.1:c.1175G>A
  • NM_001164277.2:c.1175G>A
  • NM_001164278.2:c.1241G>A
  • NM_001164279.2:c.956G>A
  • NM_001164280.2:c.1175G>A
  • NM_001467.6:c.1175G>A
  • NP_001157749.1:p.Ser392Asn
  • NP_001157749.1:p.Ser392Asn
  • NP_001157750.1:p.Ser414Asn
  • NP_001157751.1:p.Ser319Asn
  • NP_001157752.1:p.Ser392Asn
  • NP_001458.1:p.Ser392Asn
  • LRG_187t1:c.1175G>A
  • LRG_187:g.10881G>A
  • LRG_187p1:p.Ser392Asn
  • NC_000011.9:g.118895735C>T
Protein change:
S319N
Links:
dbSNP: rs1035199340
NCBI 1000 Genomes Browser:
rs1035199340
Molecular consequence:
  • NM_001164277.1:c.1175G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164277.2:c.1175G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164278.2:c.1241G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164279.2:c.956G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164280.2:c.1175G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001467.6:c.1175G>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:
MedGen: C0268146; Orphanet: 364; Orphanet: 79259; OMIM: 232220

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000790937Counsylcriteria provided, single submitter
Uncertain significance
(Apr 14, 2017)
unknownclinical testing

Citation Link,

SCV000930851Invitaecriteria provided, single submitter
Uncertain significance
(Dec 18, 2018)
germlineclinical testing

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

SCV001457208Natera, Inc.no assertion criteria providedUncertain significance
(Apr 16, 2020)
germlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Counsyl, SCV000790937.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000930851.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces serine with asparagine at codon 392 of the SLC37A4 protein (p.Ser392Asn). The serine residue is highly conserved and there is a small physicochemical difference between serine and asparagine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SLC37A4-related conditions. ClinVar contains an entry for this variant (Variation ID: 551534). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0". The asparagine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Natera, Inc., SCV001457208.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 25, 2021

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