NM_001164277.2(SLC37A4):c.872-2A>C AND Glucose-6-phosphate transport defect

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: May 22, 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:: RCV000666410.2

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.872-2A>C]

NM_001164277.2(SLC37A4):c.872-2A>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.872-2A>C

HGVS:

NC_000011.10:g.119026082T>G
NG_013331.1:g.9824A>C
NM_001164277.2:c.872-2A>CMANE SELECT
NM_001164278.2:c.872-2A>C
NM_001164279.2:c.653-2A>C
NM_001164280.2:c.872-2A>C
NM_001467.6:c.872-2A>C
LRG_187t1:c.871-2A>C
LRG_187:g.9824A>C
NC_000011.9:g.118896792T>G
NM_001164277.1:c.871-2A>C

Links:

dbSNP: rs920196110

NCBI 1000 Genomes Browser:

rs920196110

Molecular consequence:

NM_001164277.2:c.872-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001164278.2:c.872-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001164279.2:c.653-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001164280.2:c.872-2A>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001467.6:c.872-2A>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

Recent activity

Clear Turn Off Turn On

phosphatidylinositol 3-kinase regulatory subunit gamma isoform 1 [Rattus norvegi...
phosphatidylinositol 3-kinase regulatory subunit gamma isoform 1 [Rattus norvegicus]
gi|2725386671|ref|NP_001416846.1|

Protein
Kre28p [Saccharomyces cerevisiae S288C]
Kre28p [Saccharomyces cerevisiae S288C]
gi|398366685|ref|NP_010821.3|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000790697	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Apr 5, 2017)	unknown	clinical testing	Citation Link,
SCV003934753	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (May 22, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000790697

Counsyl

criteria provided, single submitter

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

Likely pathogenic
(Apr 5, 2017)

unknown

clinical testing

Citation Link,

SCV003934753

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(May 22, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Counsyl, SCV000790697.1

#	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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV003934753.1

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

Description

Variant summary: SLC37A4 c.871-2A>C is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 3' acceptor site. However, these predictions have yet to be confirmed by functional studies. The variant was absent in 204102 control chromosomes. To our knowledge, no occurrence of c.871-2A>C in individuals affected with Glycogen Storage Disease Type Ib and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was 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: Apr 15, 2024

ClinVar

Relating variation to medicine