NM_004130.4(GYG1):c.143+3G>C AND multiple conditions

Clinical significance:Pathogenic (Last evaluated: Jan 3, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001054146.1

Allele description [Variation Report for NM_004130.4(GYG1):c.143+3G>C]

NM_004130.4(GYG1):c.143+3G>C

Gene:
GYG1:glycogenin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q24
Genomic location:
Preferred name:
NM_004130.4(GYG1):c.143+3G>C
HGVS:
  • NC_000003.12:g.148994280G>C
  • NG_027677.1:g.7873G>C
  • NM_001184720.2:c.143+3G>C
  • NM_001184721.2:c.143+3G>C
  • NM_004130.4:c.143+3G>CMANE SELECT
  • NC_000003.11:g.148712067G>C
  • NM_004130.3:c.143+3G>C
  • p.Asp3Glufs*4
Nucleotide change:
IVS2DS, G-C, +3
Links:
OMIM: 603942.0003; dbSNP: rs370652040
NCBI 1000 Genomes Browser:
rs370652040
Molecular consequence:
  • NM_001184720.2:c.143+3G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001184721.2:c.143+3G>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_004130.4:c.143+3G>C - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Glycogen storage disease XV (GSD15)
Synonyms:
GLYCOGENIN DEFICIENCY; GSD XV; GYG1 DEFICIENCY
Identifiers:
MONDO: MONDO:0013291; MedGen: C3150754; Orphanet: 263297; OMIM: 613507
Name:
Polyglucosan body myopathy 2 (PGBM2)
Identifiers:
MONDO: MONDO:0014526; MedGen: C4015452; Orphanet: 456369; OMIM: 616199

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001218447Invitaecriteria provided, single submitter
Pathogenic
(Jan 3, 2020)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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

Late-onset polyglucosan body myopathy in five patients with a homozygous mutation in GYG1.

Akman HO, Aykit Y, Amuk OC, Malfatti E, Romero NB, Maioli MA, Piras R, DiMauro S, Marrosu G.

Neuromuscul Disord. 2016 Jan;26(1):16-20. doi: 10.1016/j.nmd.2015.10.012. Epub 2015 Nov 10.

PubMed [citation]
PMID:
26652229
PMCID:
PMC4724519
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001218447.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change falls in intron 2 of the GYG1 gene. It does not directly change the encoded amino acid sequence of the GYG1 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is present in population databases (rs370652040, ExAC 0.03%). This variant has been observed in several individuals and families affected with polyglucosan body myopathy (PMID: 26652229, 25272951, 29264399). ClinVar contains an entry for this variant (Variation ID: 162661). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Experimental studies have shown that this variant disrupts mRNA splicing (PMID:25272951, 29264399). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 4, 2021

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