NM_004130.4(GYG1):c.352_353del (p.Glu118fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 17, 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:: RCV002918700.2

Allele description [Variation Report for NM_004130.4(GYG1):c.352_353del (p.Glu118fs)]

NM_004130.4(GYG1):c.352_353del (p.Glu118fs)

Gene:

GYG1:glycogenin 1 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

3q24

Genomic location:

Preferred name:

NM_004130.4(GYG1):c.352_353del (p.Glu118fs)

HGVS:

NC_000003.12:g.148996773GA[1]
NG_027677.1:g.10366GA[1]
NG_027677.2:g.10235GA[1]
NM_001184720.2:c.352_353del
NM_001184721.2:c.352_353del
NM_004130.4:c.352_353delMANE SELECT
NP_001171649.1:p.Glu118fs
NP_001171650.1:p.Glu118fs
NP_004121.2:p.Glu118fs
NC_000003.11:g.148714559_148714560del
NC_000003.11:g.148714560GA[1]

Protein change:

E118fs

Molecular consequence:

NM_001184720.2:c.352_353del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001184721.2:c.352_353del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004130.4:c.352_353del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Glycogen storage disease XV (GSD15)
Synonyms:: GLYCOGENIN DEFICIENCY; GSD XV
Identifiers:: MONDO: MONDO:0013291; MedGen: C3150754; Orphanet: 263297; OMIM: 613507

Name:: Polyglucosan body myopathy type 2
Identifiers:: MONDO: MONDO:0014526; MedGen: C4015452; Orphanet: 456369; OMIM: 616199

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003255768	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 17, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20357282, 25272951, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003255768

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 17, 2023)

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

Glycogenin-1 deficiency and inactivated priming of glycogen synthesis.

Moslemi AR, Lindberg C, Nilsson J, Tajsharghi H, Andersson B, Oldfors A.

N Engl J Med. 2010 Apr 1;362(13):1203-10. doi: 10.1056/NEJMoa0900661.

PubMed [citation]

PMID:: 20357282

A new muscle glycogen storage disease associated with glycogenin-1 deficiency.

Malfatti E, Nilsson J, Hedberg-Oldfors C, Hernandez-Lain A, Michel F, Dominguez-Gonzalez C, Viennet G, Akman HO, Kornblum C, Van den Bergh P, Romero NB, Engel AG, DiMauro S, Oldfors A.

Ann Neurol. 2014 Dec;76(6):891-8. doi: 10.1002/ana.24284. Epub 2014 Oct 31.

PubMed [citation]

PMID:: 25272951
PMCID:: PMC4348070

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003255768.2

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

Description

This sequence change creates a premature translational stop signal (p.Glu118Argfs*12) in the GYG1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GYG1 are known to be pathogenic (PMID: 20357282, 25272951). This variant is present in population databases (rs753901064, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with GYG1-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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: Mar 5, 2024

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