NM_001164277.2(SLC37A4):c.1028_1036delinsTGCCTCG (p.Tyr343fs) AND Glucose-6-phosphate transport defect

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 14, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003027110.2

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1028_1036delinsTGCCTCG (p.Tyr343fs)]

NM_001164277.2(SLC37A4):c.1028_1036delinsTGCCTCG (p.Tyr343fs)

Gene:

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

Variant type:

Indel

Cytogenetic location:

11q23.3

Genomic location:

Preferred name:

NM_001164277.2(SLC37A4):c.1028_1036delinsTGCCTCG (p.Tyr343fs)

HGVS:

NC_000011.10:g.119025278_119025286delinsCGAGGCA
NG_013331.1:g.10620_10628delinsTGCCTCG
NM_001164277.2:c.1028_1036delinsTGCCTCGMANE SELECT
NM_001164278.2:c.1094_1102delinsTGCCTCG
NM_001164279.2:c.809_817delinsTGCCTCG
NM_001164280.2:c.1028_1036delinsTGCCTCG
NM_001467.6:c.1028_1036delinsTGCCTCG
NP_001157749.1:p.Tyr343Leufs
NP_001157749.1:p.Tyr343fs
NP_001157750.1:p.Tyr365fs
NP_001157751.1:p.Tyr270fs
NP_001157752.1:p.Tyr343fs
NP_001458.1:p.Tyr343Leufs
NP_001458.1:p.Tyr343fs
LRG_187t1:c.1028_1036delATGGCCCCAinsTGCCTCG
LRG_187:g.10620_10628delinsTGCCTCG
LRG_187p1:p.Tyr343Leufs
NC_000011.9:g.118895988_118895996delinsCGAGGCA
NM_001164277.1:c.1028_1036delATGGCCCCAinsTGCCTCG
NM_001467.4:c.1028_1036delATGGCCCCAinsTGCCTCG

Protein change:

Y270fs

Molecular consequence:

NM_001164277.2:c.1028_1036delinsTGCCTCG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164278.2:c.1094_1102delinsTGCCTCG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164279.2:c.809_817delinsTGCCTCG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164280.2:c.1028_1036delinsTGCCTCG - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001467.6:c.1028_1036delinsTGCCTCG - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV003324312	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 14, 2022)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 10482962, 10931421, 15059622, 21575371, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003324312

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 14, 2022)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

Citations

PubMed

The putative glucose 6-phosphate translocase gene is mutated in essentially all cases of glycogen storage disease type I non-a.

Veiga-da-Cunha M, Gerin I, Chen YT, Lee PJ, Leonard JV, Maire I, Wendel U, Vikkula M, Van Schaftingen E.

Eur J Hum Genet. 1999 Sep;7(6):717-23.

PubMed [citation]

PMID:: 10482962

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

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV003324312.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. This sequence change creates a premature translational stop signal (p.Tyr343Leufs*58) in the SLC37A4 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 87 amino acid(s) of the SLC37A4 protein. This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SLC37A4-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant disrupts a region of the SLC37A4 protein in which other variant(s) (p.Arg415*) have been determined to be pathogenic (PMID: 10482962, 10931421, 15059622, 21575371). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing.

#	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

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