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NM_017739.4(POMGNT1):c.1212-3_1212-2del AND Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 2, 2021
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:
RCV001788235.4

Allele description [Variation Report for NM_017739.4(POMGNT1):c.1212-3_1212-2del]

NM_017739.4(POMGNT1):c.1212-3_1212-2del

Genes:
POMGNT1:protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-) [Gene - OMIM - HGNC]
TSPAN1:tetraspanin 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
1p34.1
Genomic location:
Preferred name:
NM_017739.4(POMGNT1):c.1212-3_1212-2del
HGVS:
  • NC_000001.11:g.46192592_46192593del
  • NG_009205.3:g.32713_32714del
  • NM_001243766.2:c.1212-3_1212-2del
  • NM_001290129.2:c.1146-3_1146-2del
  • NM_001290130.2:c.783-3_783-2del
  • NM_017739.4:c.1212-3_1212-2delMANE SELECT
  • LRG_701t1:c.1212-3_1212-2del
  • LRG_701t2:c.1212-3_1212-2del
  • LRG_701:g.32713_32714del
  • NC_000001.10:g.46658264_46658265del
  • NG_009205.2:g.32713_32714del
  • NM_017739.4:c.1212-3_1212-2delCAMANE SELECT
Links:
dbSNP: rs1064797111
NCBI 1000 Genomes Browser:
rs1064797111
Molecular consequence:
  • NM_001243766.2:c.1212-3_1212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001290129.2:c.1146-3_1146-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001290130.2:c.783-3_783-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_017739.4:c.1212-3_1212-2del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 (MDDGB3)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMGNT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 3
Identifiers:
MONDO: MONDO:0013155; MedGen: C3150412; OMIM: 613151

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002029242Molecular Genetics, Royal Melbourne Hospital

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Dec 2, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Molecular Genetics, Royal Melbourne Hospital, SCV002029242.3

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

Description

This sequence change in POMGNT1 occurs within the canonical splice acceptor site (-2) of intron 14. It is predicted to cause an in-frame deletion (removes amino acids 405-407) that is predicted to escape nonsense mediated decay and remove <10% of the protein. This variant is present in a single individual in gnomAD v2.1 (1/18,386 alleles) in the East Asian population, which is consistent with a recessive condition. To our knowledge, this variant has not been reported in the literature in any individuals with POMGNT1-related disease. It has been reported as likely pathogenic (ClinVar Variation ID: 424898). This variant has been observed in trans with the variant c.385C>T, p.(Arg129Trp) which is classified as likely pathogenic in an individual with muscular dystrophy (Royal Melbourne Hospital). Based on the classification scheme RMH Modified ACMG Guidelines v1.4.0, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: PVS1_Moderate, PM3, PM2_Supporting.

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

Last Updated: Oct 20, 2024