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

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: May 11, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000664487.6

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

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

HGVS:

NC_000011.10:g.119029220A>G
NG_013331.1:g.6687T>C
NM_001164277.2:c.148+2T>CMANE SELECT
NM_001164278.2:c.148+2T>C
NM_001164279.2:c.-172+172T>C
NM_001164280.2:c.148+2T>C
NM_001467.6:c.148+2T>C
LRG_187t1:c.148+2T>C
LRG_187:g.6687T>C
NC_000011.9:g.118899930A>G
NM_001164277.1:c.148+2T>C

Links:

dbSNP: rs1449998297

NCBI 1000 Genomes Browser:

rs1449998297

Molecular consequence:

NM_001164279.2:c.-172+172T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001164277.2:c.148+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001164278.2:c.148+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001164280.2:c.148+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001467.6:c.148+2T>C - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000788453	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Feb 15, 2018)	unknown	clinical testing	Citation Link,
SCV002243900	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 3, 2021)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 9675154, 10323254, 16199547, 9758626, 10940311, 28492532
SCV004202464	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (May 11, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000788453

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Feb 15, 2018)

unknown

clinical testing

Citation Link,

SCV002243900

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 3, 2021)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV004202464

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(May 11, 2023)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Molecular analysis of glycogen storage disease type Ib: identification of a prevalent mutation among Japanese patients and assignment of a putative glucose-6-phosphate translocase gene to chromosome 11.

Kure S, Suzuki Y, Matsubara Y, Sakamoto O, Shintaku H, Isshiki G, Hoshida C, Izumi I, Sakura N, Narisawa K.

Biochem Biophys Res Commun. 1998 Jul 20;248(2):426-31.

PubMed [citation]

PMID:: 9675154

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

See all PubMed Citations (7)

Details of each submission

From Counsyl, SCV000788453.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002243900.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

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. ClinVar contains an entry for this variant (Variation ID: 549913). Disruption of this splice site has been observed in individual(s) with SLC37A4-related conditions (PMID: 9675154, 10323254). In at least one individual the data is consistent with the variant being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (ExAC no frequency). This sequence change affects a donor splice site in intron 3 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).

#	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

From Baylor Genetics, SCV004202464.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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