NM_001164277.2(SLC37A4):c.962_963del (p.Thr321fs) AND Glucose-6-phosphate transport defect

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 12, 2022
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:: RCV003031249.3

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.962_963del (p.Thr321fs)]

NM_001164277.2(SLC37A4):c.962_963del (p.Thr321fs)

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.962_963del (p.Thr321fs)

HGVS:

NC_000011.10:g.119025989_119025990del
NG_013331.1:g.9917_9918del
NM_001164277.2:c.962_963delMANE SELECT
NM_001164278.2:c.962_963del
NM_001164279.2:c.743_744del
NM_001164280.2:c.962_963del
NM_001467.6:c.962_963del
NP_001157749.1:p.Thr321Serfs
NP_001157749.1:p.Thr321fs
NP_001157750.1:p.Thr321fs
NP_001157751.1:p.Thr248fs
NP_001157752.1:p.Thr321fs
NP_001458.1:p.Thr321Serfs
NP_001458.1:p.Thr321fs
LRG_187t1:c.961_962del
LRG_187:g.9917_9918del
LRG_187p1:p.Thr321Serfs
NC_000011.9:g.118896698_118896699del
NC_000011.9:g.118896699_118896700del
NM_001164277.1:c.961_962delAC
NM_001467.4:c.961_962delAC

Protein change:

T248fs

Molecular consequence:

NM_001164277.2:c.962_963del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164278.2:c.962_963del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164279.2:c.743_744del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164280.2:c.962_963del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001467.6:c.962_963del - frameshift variant - [Sequence Ontology: SO:0001589]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003322460	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 12, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9758626, 10940311, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003322460

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 12, 2022)

germline

clinical testing

PubMed (3)
[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

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

Structural requirements for the stability and microsomal transport activity of the human glucose 6-phosphate transporter.

Chen LY, Lin B, Pan CJ, Hiraiwa H, Chou JY.

J Biol Chem. 2000 Nov 3;275(44):34280-6.

PubMed [citation]

PMID:: 10940311

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003322460.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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 creates a premature translational stop signal (p.Thr321Serfs*4) in the SLC37A4 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC37A4 are known to be pathogenic (PMID: 9758626, 10940311).

#	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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