NM_001164277.2(SLC37A4):c.59dup (p.Tyr21fs) AND Glucose-6-phosphate transport defect

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Dec 3, 2022
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:: RCV001036141.8

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.59dup (p.Tyr21fs)]

NM_001164277.2(SLC37A4):c.59dup (p.Tyr21fs)

Gene:

SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001164277.2(SLC37A4):c.59dup (p.Tyr21fs)

HGVS:

NC_000011.10:g.119029315dup
NG_013331.1:g.6596dup
NM_001164277.2:c.59dupMANE SELECT
NM_001164278.2:c.59dup
NM_001164279.2:c.-172+81dup
NM_001164280.2:c.59dup
NM_001467.6:c.59dup
NP_001157749.1:p.Tyr21fs
NP_001157749.1:p.Tyr21fs
NP_001157750.1:p.Tyr21fs
NP_001157752.1:p.Tyr21fs
NP_001458.1:p.Tyr21fs
LRG_187t1:c.59dup
LRG_187:g.6596dup
LRG_187p1:p.Tyr21fs
NC_000011.9:g.118900020_118900021insC
NC_000011.9:g.118900025dup
NM_001164277.1:c.59dup

Protein change:

Y21fs

Links:

dbSNP: rs1943676862

NCBI 1000 Genomes Browser:

rs1943676862

Molecular consequence:

NM_001164277.2:c.59dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164278.2:c.59dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164280.2:c.59dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001467.6:c.59dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164279.2:c.-172+81dup - intron variant - [Sequence Ontology: SO:0001627]

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

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
SCV001199491	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 30, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9758626, 10940311, 28492532
SCV004202488	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Dec 3, 2022)	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

SCV001199491

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 30, 2019)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004202488

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Dec 3, 2022)

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

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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001199491.5

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

Description

This sequence change creates a premature translational stop signal (p.Tyr21Leufs*28) in the SLC37A4 gene. It is expected to result in an absent or disrupted protein product. For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SLC37A4 are known to be pathogenic (PMID: 9758626, 10940311). This variant has not been reported in the literature in individuals with SLC37A4-related conditions. This variant is not present in population databases (ExAC no frequency).

#	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, SCV004202488.1

#	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: Oct 20, 2024

ClinVar

Relating variation to medicine