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NM_001164277.2(SLC37A4):c.786-2A>C AND Glucose-6-phosphate transport defect

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 3, 2023
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:
RCV002881115.3

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.786-2A>C]

NM_001164277.2(SLC37A4):c.786-2A>C

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.786-2A>C
HGVS:
  • NC_000011.10:g.119026690T>G
  • NG_013331.1:g.9216A>C
  • NM_001164277.2:c.786-2A>CMANE SELECT
  • NM_001164278.2:c.786-2A>C
  • NM_001164279.2:c.567-2A>C
  • NM_001164280.2:c.786-2A>C
  • NM_001467.6:c.786-2A>C
  • LRG_187:g.9216A>C
  • NC_000011.9:g.118897400T>G
Molecular consequence:
  • NM_001164277.2:c.786-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001164278.2:c.786-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001164279.2:c.567-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001164280.2:c.786-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001467.6:c.786-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV003233900Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Jul 3, 2023) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

A gene on chromosome 11q23 coding for a putative glucose- 6-phosphate translocase is mutated in glycogen-storage disease types Ib and Ic.

Veiga-da-Cunha M, Gerin I, Chen YT, de Barsy T, de Lonlay P, Dionisi-Vici C, Fenske CD, Lee PJ, Leonard JV, Maire I, McConkie-Rosell A, Schweitzer S, Vikkula M, Van Schaftingen E.

Am J Hum Genet. 1998 Oct;63(4):976-83.

PubMed [citation]
PMID:
9758626
PMCID:
PMC1377500
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003233900.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 2030023). This variant has not been reported in the literature in individuals affected with SLC37A4-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 6 of the SLC37A4 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SLC37A4 are known to be pathogenic (PMID: 9758626, 10940311).

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

Last Updated: Sep 29, 2024