NC_000003.11:g.(?_81627066)_(81643184_?)del AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 16, 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:: RCV003119444.3

Allele description [Variation Report for NC_000003.11:g.(?_81627066)_(81643184_?)del]

NC_000003.11:g.(?_81627066)_(81643184_?)del

Gene:: GBE1:1,4-alpha-glucan branching enzyme 1 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 3p12.2
Genomic location:: Chr3: 81627066 - 81643184 (on Assembly GRCh37)
Preferred name:: NC_000003.11:g.(?_81627066)_(81643184_?)del
HGVS:: NC_000003.11:g.(?_81627066)_(81643184_?)del
This HGVS expression did not pass validation

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
SCV003790766	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 16, 2022)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 15452297, 20058079, 15019703, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003790766

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 16, 2022)

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

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 (4)

Details of each submission

From Invitae, SCV003790766.2

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

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 8-12 of the GBE1 gene. This deletion is out-of-frame, and is expected to create a premature termination codon and result in an absent or disrupted protein product. Loss-of-function variants in GBE1 are known to be pathogenic (PMID: 15452297, 20058079). A similar copy number variant has been observed in individual(s) with glycogen storage disease (PMID: 15019703). 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: Nov 11, 2023

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