NM_001164277.2(SLC37A4):c.1212T>A (p.Cys404Ter) AND Glucose-6-phosphate transport defect

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 8, 2023
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:: RCV003618735.2

Allele description [Variation Report for NM_001164277.2(SLC37A4):c.1212T>A (p.Cys404Ter)]

NM_001164277.2(SLC37A4):c.1212T>A (p.Cys404Ter)

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.1212T>A (p.Cys404Ter)

HGVS:

NC_000011.10:g.119024988A>T
NG_013331.1:g.10918T>A
NM_001164277.2:c.1212T>AMANE SELECT
NM_001164278.2:c.1278T>A
NM_001164279.2:c.993T>A
NM_001164280.2:c.1212T>A
NM_001467.6:c.1212T>A
NP_001157749.1:p.Cys404Ter
NP_001157749.1:p.Cys404Ter
NP_001157750.1:p.Cys426Ter
NP_001157751.1:p.Cys331Ter
NP_001157752.1:p.Cys404Ter
NP_001458.1:p.Cys404Ter
NP_001458.1:p.Cys404Ter
LRG_187t1:c.1212T>A
LRG_187:g.10918T>A
LRG_187p1:p.Cys404Ter
NC_000011.9:g.118895698A>T
NM_001164277.1:c.1212T>A
NM_001467.4:c.1212T>A

Protein change:

C331*

Molecular consequence:

NM_001164277.2:c.1212T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001164278.2:c.1278T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001164279.2:c.993T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001164280.2:c.1212T>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001467.6:c.1212T>A - nonsense - [Sequence Ontology: SO:0001587]

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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ORF065L [Infectious spleen and kidney necrosis virus]
ORF065L [Infectious spleen and kidney necrosis virus]
gi|19881470|ref|NP_612287.1|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004435493	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 8, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10931421, 15059622, 21575371, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004435493

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Feb 8, 2023)

germline

clinical testing

PubMed (4)
[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

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

Genetic testing of glycogen storage disease type Ib in Japan: five novel G6PT1 mutations and a rapid detection method for a prevalent mutation W118R.

Kojima K, Kure S, Kamada F, Hao K, Ichinohe A, Sato K, Aoki Y, Yoichi S, Kubota M, Horikawa R, Utsumi A, Miura M, Ogawa S, Kanazawa M, Kohno Y, Inokuchi M, Hasegawa T, Narisawa K, Matsubara Y.

Mol Genet Metab. 2004 Apr;81(4):343-6.

PubMed [citation]

PMID:: 15059622

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004435493.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Cys404*) in the SLC37A4 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 26 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. This variant disrupts a region of the SLC37A4 protein in which other variant(s) (p.Arg415*) have been determined to be pathogenic (PMID: 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. 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

Last Updated: Sep 29, 2024

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