NM_000151.4(G6PC1):c.479G>A (p.Trp160Ter) AND Glycogen storage disease due to glucose-6-phosphatase deficiency type IA

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Oct 17, 2019
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:: RCV001193577.3

Allele description [Variation Report for NM_000151.4(G6PC1):c.479G>A (p.Trp160Ter)]

NM_000151.4(G6PC1):c.479G>A (p.Trp160Ter)

Gene:

G6PC1:glucose-6-phosphatase catalytic subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.31

Genomic location:

Preferred name:

NM_000151.4(G6PC1):c.479G>A (p.Trp160Ter)

HGVS:

NC_000017.11:g.42909335G>A
NG_011808.1:g.13538G>A
NM_000151.4:c.479G>AMANE SELECT
NM_001270397.2:c.402G>A
NP_000142.2:p.Trp160Ter
NP_001257326.1:p.Leu134=
LRG_147:g.13538G>A
NC_000017.10:g.41061352G>A
NM_000151.3:c.479G>A

Protein change:

W160*

Links:

dbSNP: rs2056081522

NCBI 1000 Genomes Browser:

rs2056081522

Molecular consequence:

NM_000151.4:c.479G>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001270397.2:c.402G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Glycogen storage disease due to glucose-6-phosphatase deficiency type IA (GSD1A)
Synonyms:: GSD Ia; Glycogen storage disease type 1A; Von Gierke disease; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009287; MedGen: C2919796; Orphanet: 364; Orphanet: 79258; OMIM: 232200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001362496	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (Oct 17, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30956637, 20509832 Citation Link,
SCV002093308	Natera, Inc.	no assertion criteria provided	Likely pathogenic (Jan 26, 2021)	germline	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001362496

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(Oct 17, 2019)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV002093308

Natera, Inc.

no assertion criteria provided

Likely pathogenic
(Jan 26, 2021)

germline

clinical testing

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

Molecular diagnosis of glycogen storage disease type I: a review.

Beyzaei Z, Geramizadeh B.

EXCLI J. 2019;18:30-46. Review.

PubMed [citation]

PMID:: 30956637
PMCID:: PMC6449677

Rapid detection of glycogen storage disease type Ia by DNA microarray.

Xu S, Qin S, Gu X, Qiu W, Ye J, Han L, He L.

Clin Chem Lab Med. 2010 Sep;48(9):1229-34. doi: 10.1515/CCLM.2010.244.

PubMed [citation]

PMID:: 20509832

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001362496.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Variant summary: G6PC c.479G>A (p.Trp160X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (eg. c.508C>T (p.Arg170X), c.1039C>T (p.Gln347X)). The variant was absent in 251484 control chromosomes (gnomAD). c.479G>A has been reported in the literature at least in an individual affected with Glycogen Storage Disease Type Ia (Xu_2010). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely 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 Natera, Inc., SCV002093308.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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 23, 2022

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