NM_000158.4(GBE1):c.760A>G (p.Thr254Ala) AND Adult polyglucosan body disease

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Sep 28, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV001147052.9

Allele description [Variation Report for NM_000158.4(GBE1):c.760A>G (p.Thr254Ala)]

NM_000158.4(GBE1):c.760A>G (p.Thr254Ala)

Gene:

GBE1:1,4-alpha-glucan branching enzyme 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p12.2

Genomic location:

Preferred name:

NM_000158.4(GBE1):c.760A>G (p.Thr254Ala)

Other names:

NM_000158.4(GBE1):c.760A>G; p.Thr254Ala

HGVS:

NC_000003.12:g.81646414T>C
NG_011810.1:g.120387A>G
NM_000158.4:c.760A>GMANE SELECT
NP_000149.4:p.Thr254Ala
NC_000003.11:g.81695565T>C
NM_000158.3:c.760A>G

Protein change:

T254A

Links:

dbSNP: rs770427750

NCBI 1000 Genomes Browser:

rs770427750

Molecular consequence:

NM_000158.4:c.760A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Adult polyglucosan body disease (APBN)
Synonyms:: Polyglucosan body disease, adult form
Identifiers:: MONDO: MONDO:0009897; MedGen: C1849722; OMIM: 263570

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001307824	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 27107456, 20058079 Citation Link,
SCV004100752	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 28, 2023)	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

SCV001307824

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

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

Citation Link,

SCV004100752

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 28, 2023)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A novel GBE1 gene variant in a child with glycogen storage disease type IV.

Said SM, Murphree MI, Mounajjed T, El-Youssef M, Zhang L.

Hum Pathol. 2016 Aug;54:152-6. doi: 10.1016/j.humpath.2016.03.021. Epub 2016 Apr 20.

PubMed [citation]

PMID:: 27107456

Glycogen storage disease type IV: novel mutations and molecular characterization of a heterogeneous disorder.

Li SC, Chen CM, Goldstein JL, Wu JY, Lemyre E, Burrow TA, Kang PB, Chen YT, Bali DS.

J Inherit Metab Dis. 2010 Dec;33 Suppl 3:S83-90. doi: 10.1007/s10545-009-9026-5. Epub 2010 Jan 8.

PubMed [citation]

PMID:: 20058079

See all PubMed Citations (3)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001307824.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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 Institute of Human Genetics, University of Leipzig Medical Center, SCV004100752.2

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

Description

Criteria applied: PM3_VSTR,PM2_SUP,PP3

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

Last Updated: Aug 25, 2024

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