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NM_001164277.2(SLC37A4):c.1124+1G>T AND Glucose-6-phosphate transport defect

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Nov 15, 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:
RCV002048277.9

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1124+1G>T]

NM_001164277.2(SLC37A4):c.1124+1G>T

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.1124+1G>T
HGVS:
  • NC_000011.10:g.119025190C>A
  • NG_013331.1:g.10716G>T
  • NM_001164277.2:c.1124+1G>TMANE SELECT
  • NM_001164278.2:c.1190+1G>T
  • NM_001164279.2:c.905+1G>T
  • NM_001164280.2:c.1124+1G>T
  • NM_001467.6:c.1124+1G>T
  • LRG_187:g.10716G>T
  • NC_000011.9:g.118895900C>A
  • NM_001164277.2:c.1123+1G>TMANE SELECT
Links:
dbSNP: rs782630676
NCBI 1000 Genomes Browser:
rs782630676
Molecular consequence:
  • NM_001164277.2:c.1124+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164278.2:c.1190+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164279.2:c.905+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001164280.2:c.1124+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001467.6:c.1124+1G>T - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002302229Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 21, 2022) 		germlineclinical testing

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

SCV004202479Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Nov 15, 2023) 		unknownclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Glycogen storage disease type Ib: structural and mutational analysis of the microsomal glucose-6-phosphate transporter gene.

Hou DC, Kure S, Suzuki Y, Hasegawa Y, Hara Y, Inoue T, Kida Y, Matsubara Y, Narisawa K.

Am J Med Genet. 1999 Sep 17;86(3):253-7.

PubMed [citation]
PMID:
10482875

Mutation analysis in glycogen storage disease type 1 non-a.

Janecke AR, Lindner M, Erdel M, Mayatepek E, Möslinger D, Podskarbi T, Fresser F, Stöckler-Ipsiroglu S, Hoffmann GF, Utermann G.

Hum Genet. 2000 Sep;107(3):285-9.

PubMed [citation]
PMID:
11071391
See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002302229.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

ClinVar contains an entry for this variant (Variation ID: 1514493). This variant is also known as IVS7+1G‚ÜíT. Disruption of this splice site has been observed in individual(s) with clinical features of autosomal recessive SLC37A4-related conditions (PMID: 10482875, 11071391, 16716283; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs782630676, gnomAD 0.007%). This sequence change affects a donor splice site in intron 9 of the SLC37A4 gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Baylor Genetics, SCV004202479.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024