NM_000158.4(GBE1):c.202_203del (p.Lys68fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 5, 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:: RCV001053285.5

Allele description [Variation Report for NM_000158.4(GBE1):c.202_203del (p.Lys68fs)]

NM_000158.4(GBE1):c.202_203del (p.Lys68fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

3p12.2

Genomic location:

Preferred name:

NM_000158.4(GBE1):c.202_203del (p.Lys68fs)

HGVS:

NC_000003.12:g.81705554_81705555del
NG_011810.1:g.61246_61247del
NM_000158.4:c.202_203delMANE SELECT
NP_000149.4:p.Lys68fs
NC_000003.11:g.81754705_81754706del
NM_000158.3:c.202_203del

Protein change:

K68fs

Links:

dbSNP: rs1705761854

NCBI 1000 Genomes Browser:

rs1705761854

Molecular consequence:

NM_000158.4:c.202_203del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Glycogen storage disease, type IV (GSD4)
Synonyms:: GBE1 DEFICIENCY; GLYCOGENOSIS IV; GSD IV; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009292; MedGen: C0017923; Orphanet: 367; OMIM: 232500

Name:: Glycogen storage disease IV, classic hepatic
Synonyms:: GSD IV, CLASSIC HEPATIC
Identifiers:: MedGen: C1856301

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001217543	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 5, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 15452297, 20058079, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001217543

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 5, 2019)

germline

clinical testing

PubMed (3)
[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

Clinical and genetic heterogeneity of branching enzyme deficiency (glycogenosis type IV).

Bruno C, van Diggelen OP, Cassandrini D, Gimpelev M, Giuffrè B, Donati MA, Introvini P, Alegria A, Assereto S, Morandi L, Mora M, Tonoli E, Mascelli S, Traverso M, Pasquini E, Bado M, Vilarinho L, van Noort G, Mosca F, DiMauro S, Zara F, Minetti C.

Neurology. 2004 Sep 28;63(6):1053-8.

PubMed [citation]

PMID:: 15452297

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001217543.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in GBE1 are known to be pathogenic (PMID: 15452297, 20058079). This variant has not been reported in the literature in individuals with GBE1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Lys68Valfs*6) in the GBE1 gene. It is expected to result in an absent or disrupted protein product.

#	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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