NM_001164277.2(SLC37A4):c.872-8_881del AND Glucose-6-phosphate transport defect

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Nov 18, 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:: RCV003507617.2

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.872-8_881del]

NM_001164277.2(SLC37A4):c.872-8_881del

Gene:

SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001164277.2(SLC37A4):c.872-8_881del

HGVS:

NC_000011.10:g.119026080_119026097del
NG_013331.1:g.9818_9835del
NM_001164277.2:c.872-8_881delMANE SELECT
NM_001164278.2:c.872-8_881del
NM_001164279.2:c.653-8_662del
NM_001164280.2:c.872-8_881del
NM_001467.6:c.872-8_881del
LRG_187:g.9818_9835del
NC_000011.9:g.118896781_118896798del
NC_000011.9:g.118896790_118896807del

Molecular consequence:

NM_001164277.2:c.872-8_881del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001164278.2:c.872-8_881del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001164279.2:c.653-8_662del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001164280.2:c.872-8_881del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001467.6:c.872-8_881del - 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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PREDICTED: LEAF RUST 10 DISEASE-RESISTANCE LOCUS RECEPTOR-LIKE PROTEIN KINASE-li...
PREDICTED: LEAF RUST 10 DISEASE-RESISTANCE LOCUS RECEPTOR-LIKE PROTEIN KINASE-like 1.1 isoform X1 [Cucumis melo]
gi|659091595|ref|XP_008446629.1|

Protein
AMSH-like ubiquitin thioesterase 1 [Cucurbita maxima]
AMSH-like ubiquitin thioesterase 1 [Cucurbita maxima]
gi|1281033185|ref|XP_023001055.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004253456	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Nov 18, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16199547, 9758626, 10940311, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004253456

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Nov 18, 2023)

germline

clinical testing

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

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

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, SCV004253456.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant results in the deletion of part of exon 8 (c.871-8_880del) 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). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC37A4-related conditions. 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.

#	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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