NM_001164277.2(SLC37A4):c.1016G>A (p.Gly339Asp) AND Glucose-6-phosphate transport defect

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Dec 19, 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:: RCV000007347.8

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1016G>A (p.Gly339Asp)]

NM_001164277.2(SLC37A4):c.1016G>A (p.Gly339Asp)

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.1016G>A (p.Gly339Asp)

HGVS:

NC_000011.10:g.119025298C>T
NG_013331.1:g.10608G>A
NM_001164277.2:c.1016G>AMANE SELECT
NM_001164278.2:c.1082G>A
NM_001164279.2:c.797G>A
NM_001164280.2:c.1016G>A
NM_001467.6:c.1016G>A
NP_001157749.1:p.Gly339Asp
NP_001157749.1:p.Gly339Asp
NP_001157750.1:p.Gly361Asp
NP_001157751.1:p.Gly266Asp
NP_001157752.1:p.Gly339Asp
NP_001458.1:p.Gly339Asp
LRG_187t1:c.1016G>A
LRG_187:g.10608G>A
LRG_187p1:p.Gly339Asp
NC_000011.9:g.118896008C>T
NM_001164277.1:c.1016G>A

Protein change:

G266D; GLY339ASP

Links:

UniProtKB/Swiss-Prot: VAR_025601; OMIM: 602671.0015; dbSNP: rs121908980

NCBI 1000 Genomes Browser:

rs121908980

Molecular consequence:

NM_001164277.2:c.1016G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001164278.2:c.1082G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001164279.2:c.797G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001164280.2:c.1016G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001467.6:c.1016G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000027545	OMIM	no assertion criteria provided	Pathogenic (Aug 1, 2000)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002228669	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 24, 2022)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 10931421, 15669677, 12444104, 9428641, 9758626, 10482962, 10923042, 28492532
SCV004202486	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 19, 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

SCV000027545

OMIM

no assertion criteria provided

Pathogenic
(Aug 1, 2000)

germline

literature only

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

SCV002228669

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 24, 2022)

germline

clinical testing

PubMed (8)
[See all records that cite these PMIDs]

SCV004202486

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 19, 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	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Glycogen storage disease type Ib without neutropenia.

Kure S, Hou DC, Suzuki Y, Yamagishi A, Hiratsuka M, Fukuda T, Sugie H, Kondo N, Matsubara Y, Narisawa K.

J Pediatr. 2000 Aug;137(2):253-6.

PubMed [citation]

PMID:: 10931421

Allelic heterogeneity of glycogen storage disease type Ib in French patients: a study of 11 cases.

Trioche P, Petit F, Francoual J, Gajdos V, Capel L, Poüs C, Labrune P.

J Inherit Metab Dis. 2004;27(5):621-3.

PubMed [citation]

PMID:: 15669677

See all PubMed Citations (9)

Details of each submission

From OMIM, SCV000027545.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a 25-year-old patient with glycogen storage disease type Ib (GSD1B; 232220) based on enzymatic analysis but no evidence of neutropenia or recurrent infections, Kure et al. (2000) identified an arg415-to-ter mutation (R415X; 606671.0014), which has been reported in patients with neutropenia, in compound heterozygosity with a gly339-to-asp mutation (G339D) due to a G-to-A transition at nucleotide 1185 in exon 7 of the G6PT1 gene.

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

From Invitae, SCV002228669.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 339 of the SLC37A4 protein (p.Gly339Asp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with glycogen storage disease type 1b (PMID: 10931421, 15669677). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as p.G339D in the G6PT or G6PT1 gene. ClinVar contains an entry for this variant (Variation ID: 6935). Experimental studies have shown that this missense change affects SLC37A4 function (PMID: 12444104). This variant disrupts the p.Gly339 amino acid residue in SLC37A4. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9428641, 9758626, 10482962, 10923042). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as 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

From Baylor Genetics, SCV004202486.1

#	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: May 12, 2024

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