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NM_001164277.2(SLC37A4):c.148+1G>T AND Glucose-6-phosphate transport defect

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 14, 2020
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:
RCV001260430.1

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.148+1G>T]

NM_001164277.2(SLC37A4):c.148+1G>T

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.148+1G>T
HGVS:
  • NC_000011.10:g.119029221C>A
  • NG_013331.1:g.6686G>T
  • NM_001164277.2:c.148+1G>TMANE SELECT
  • NM_001164278.2:c.148+1G>T
  • NM_001164279.2:c.-172+171G>T
  • NM_001164280.2:c.148+1G>T
  • NM_001467.6:c.148+1G>T
  • LRG_187t1:c.148+1G>T
  • LRG_187:g.6686G>T
  • NC_000011.9:g.118899931C>A
  • NM_001164277.1:c.148+1G>T
Links:
dbSNP: rs1943672400
NCBI 1000 Genomes Browser:
rs1943672400
Molecular consequence:
  • NM_001164279.2:c.-172+171G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001164277.2:c.148+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164278.2:c.148+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164280.2:c.148+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001467.6:c.148+1G>T - 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:
MONDO: MONDO:0009288; MedGen: C0268146; Orphanet: 364; Orphanet: 79259; OMIM: 232220

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001437427Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Pathogenic
(Sep 14, 2020) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Molecular diagnosis of type 1c glycogen storage disease.

Janecke AR, Bosshard NU, Mayatepek E, Schulze A, Gitzelmann R, Burchell A, Bartram CR, Janssen B.

Hum Genet. 1999 Mar;104(3):275-7.

PubMed [citation]
PMID:
10323254

Molecular analysis in glycogen storage disease 1 non-A: DHPLC detection of the highly prevalent exon 8 mutations of the G6PT1 gene in German patients.

Santer R, Rischewski J, Block G, Kinner M, Wendel U, Schaub J, Schneppenheim R.

Hum Mutat. 2000 Aug;16(2):177.

PubMed [citation]
PMID:
10923042
See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001437427.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Variant summary: SLC37A4 c.148+1G>T 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: Four predict the variant abolishes a 5 splicing donor site. Experimental evidence supports these predictions revealing the variant causes a 170-bp deletion of nucleotides, following RT-PCR and sequencing analysis (Janecke_1999). The variant was absent in 247574 control chromosomes (gnomAD). c.148+1G>T has been reported in the literature in the homozygous state in individuals affected with Glycogen Storage Disease Type Ib (Janecke_1999, Janecke_2000, Santer_2000). These data indicate that the variant is likely to be associated with disease. Experimental evidence demonstrated the variant causes reduced/absent enzyme activity (Janecke_1999). 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 pathogenic.

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

Last Updated: Apr 15, 2024