NM_001164277.2(SLC37A4):c.381+2T>G AND Glucose-6-phosphate transport defect

Clinical significance:Likely pathogenic (Last evaluated: May 21, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000781850.1

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.381+2T>G]

NM_001164277.2(SLC37A4):c.381+2T>G

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.381+2T>G
HGVS:
  • NC_000011.10:g.119028192A>C
  • NG_013331.1:g.7715T>G
  • NM_001164277.1:c.381+2T>G
  • NM_001164277.2:c.381+2T>G
  • NM_001164278.2:c.381+2T>G
  • NM_001164279.2:c.162+2T>G
  • NM_001164280.2:c.381+2T>G
  • NM_001467.6:c.381+2T>G
  • LRG_187t1:c.381+2T>G
  • LRG_187:g.7715T>G
  • NC_000011.9:g.118898902A>C
Links:
dbSNP: rs782645078
NCBI 1000 Genomes Browser:
rs782645078
Molecular consequence:
  • NM_001164277.1:c.381+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164277.2:c.381+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164278.2:c.381+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164279.2:c.162+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164280.2:c.381+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001467.6:c.381+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]

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
SCV000920221Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Likely pathogenic
(May 21, 2018)
germlineclinical testing

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

The SLC37 family of sugar-phosphate/phosphate exchangers.

Chou JY, Mansfield BC.

Curr Top Membr. 2014;73:357-82. doi: 10.1016/B978-0-12-800223-0.00010-4. Review.

PubMed [citation]
PMID:
24745989
PMCID:
PMC4180117

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000920221.1

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

Description

Variant summary: SLC37A4 c.381+2T>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Five predict the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 3.2e-05 in 30900 control chromosomes (gnomAD). To our knowledge, no occurrence of c.381+2T>G in individuals affected with Glycogen Storage Disease Type Ib and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic

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

Last Updated: Oct 25, 2021

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