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NM_001243766.2(POMGNT1):c.-50-671_-50-663dup AND Autosomal recessive limb-girdle muscular dystrophy type 2O

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 1, 2012
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV002295346.8

Allele description [Variation Report for NM_001243766.2(POMGNT1):c.-50-671_-50-663dup]

NM_001243766.2(POMGNT1):c.-50-671_-50-663dup

Genes:
LOC129930471:ATAC-STARR-seq lymphoblastoid silent region 837 [Gene]
POMGNT1:protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_001243766.2(POMGNT1):c.-50-671_-50-663dup
HGVS:
  • NC_000001.11:g.46198540_46198548dup
  • NG_009205.3:g.26764_26772dup
  • NG_163522.1:g.278_286dup
  • NM_001243766.2:c.-50-671_-50-663dup
  • LRG_701t1:c.-50-671_-50-663dup
  • LRG_701:g.26764_26772dup
  • NC_000001.10:g.46664212_46664220dup
Nucleotide change:
9-BP DUP, -83
Links:
OMIM: 606822.0017; dbSNP: rs966546165
NCBI 1000 Genomes Browser:
rs966546165
Molecular consequence:
  • NM_001243766.2:c.-50-671_-50-663dup - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy type 2O
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 3; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY, LIMB-GIRDLE, POMGNT1-RELATED; Limb-Girdle Muscular Dystrophy Type 3C; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0013161; MedGen: C3150417; Orphanet: 206564; OMIM: 613157

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000056703OMIM
no assertion criteria provided
Pathogenic
(Sep 1, 2012)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Promoter alteration causes transcriptional repression of the POMGNT1 gene in limb-girdle muscular dystrophy type 2O.

Raducu M, Baets J, Fano O, Van Coster R, Cruces J.

Eur J Hum Genet. 2012 Sep;20(9):945-52. doi: 10.1038/ejhg.2012.40. Epub 2012 Mar 14.

PubMed [citation]
PMID:
22419172
PMCID:
PMC3421125

Details of each submission

From OMIM, SCV000056703.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In an 11-year-old Belgian boy with limb-girdle muscular dystrophy without brain or eye anomalies (MDDGC3; 613157), Raducu et al. (2012) identified a homozygous 9-bp duplication (-83_-75dup) upstream of the transcriptional start site of the POMGNT1 gene in the 5-prime flanking region. Each unaffected parent was heterozygous for the mutation, which was not found in 200 control individuals. Transfection of the mutation in COS-7 and HEK293T cells resulted in a 75% decrease in promoter activity compared to wildtype. Electrophoretic mobility shift assay (EMSA) revealed binding sites for several transcription factors in this region. The mutation generated an additional binding site for the transcriptional repressor ZNF202 (603430), resulting in the downregulation of POMGNT1 gene expression and, ultimately, defective glycosylation. The patient had slightly delayed initial motor development and had unsteady standing at age 2 years. He had muscle weakness, slight generalized amyotrophy, a positive Gowers sign, and lack of reflexes. At age 7 to 8 years, he had lumbar hyperlordosis, difficulties in climbing stairs, and weakness of the shoulder muscles. Laboratory studies showed a mild elevation of serum creatine kinase, and muscle biopsy showed dystrophic changes and defects in alpha-dystroglycan staining.

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

Last Updated: Jun 2, 2024