NM_001164277.2(SLC37A4):c.686del (p.Leu229fs) AND Glucose-6-phosphate transport defect

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 17, 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:: RCV003017524.2

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.686del (p.Leu229fs)]

NM_001164277.2(SLC37A4):c.686del (p.Leu229fs)

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.686del (p.Leu229fs)

HGVS:

NC_000011.10:g.119027035del
NG_013331.1:g.8871del
NM_001164277.2:c.686delMANE SELECT
NM_001164278.2:c.686del
NM_001164279.2:c.467del
NM_001164280.2:c.686del
NM_001467.6:c.686del
NP_001157749.1:p.Leu229Profs
NP_001157749.1:p.Leu229fs
NP_001157750.1:p.Leu229fs
NP_001157751.1:p.Leu156fs
NP_001157752.1:p.Leu229fs
NP_001458.1:p.Leu229Profs
NP_001458.1:p.Leu229fs
LRG_187t1:c.686del
LRG_187:g.8871del
LRG_187p1:p.Leu229Profs
NC_000011.9:g.118897745del
NM_001164277.1:c.686delT
NM_001467.4:c.686delT

Protein change:

L156fs

Molecular consequence:

NM_001164277.2:c.686del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164278.2:c.686del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164279.2:c.467del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164280.2:c.686del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001467.6:c.686del - 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

Recent activity

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gi|1908122435|ref|NM_001278538.2|

Nucleotide
"CeGaT Center for Human Genetics Tuebingen"[submitter] AND "LOC12... (1)
"CeGaT Center for Human Genetics Tuebingen"[submitter] AND "LOC126861153"[gene]
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003325144	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 17, 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

SCV003325144

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 17, 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 Invitae, SCV003325144.2

#	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. 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.Leu229Profs*11) 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: Apr 15, 2024

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