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NM_013382.7(POMT2):c.1333-14G>A AND Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 2, 2024
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:
RCV003480018.1

Allele description [Variation Report for NM_013382.7(POMT2):c.1333-14G>A]

NM_013382.7(POMT2):c.1333-14G>A

Gene:
POMT2:protein O-mannosyltransferase 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q24.3
Genomic location:
Preferred name:
NM_013382.7(POMT2):c.1333-14G>A
HGVS:
  • NC_000014.9:g.77285646C>T
  • NG_008897.1:g.40237G>A
  • NM_013382.7:c.1333-14G>AMANE SELECT
  • LRG_844:g.40237G>A
  • NC_000014.8:g.77751989C>T
Nucleotide change:
IVS12AS, G-A, -14
Links:
OMIM: 607439.0018; dbSNP: rs918556979
NCBI 1000 Genomes Browser:
rs918556979
Molecular consequence:
  • NM_013382.7:c.1333-14G>A - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Name:
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2 (MDDGB2)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT2-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 2
Identifiers:
MONDO: MONDO:0013160; MedGen: C3150416; OMIM: 613156

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV004222605Laboratorio de Biologia Molecular - Genetica, Hospital de Pediatria Garrahan
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 2, 2024)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

POMT2 intragenic deletions and splicing abnormalities causing congenital muscular dystrophy with mental retardation.

Yanagisawa A, Bouchet C, Quijano-Roy S, Vuillaumier-Barrot S, Clarke N, Odent S, Rodriguez D, Romero NB, Osawa M, Endo T, Taratuto AL, Seta N, Guicheney P.

Eur J Med Genet. 2009 Jul-Aug;52(4):201-6. doi: 10.1016/j.ejmg.2008.12.004. Epub 2008 Dec 27.

PubMed [citation]
PMID:
19138766

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 Laboratorio de Biologia Molecular - Genetica, Hospital de Pediatria Garrahan, SCV004222605.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
11not providednot providedclinical testing PubMed (2)

Description

This variant was detected in a homozygous state in the present case and in an affected sibling. Both parents are asymptomatic carriers. RNA analysis of this variant has shown that it creates a cryptic splicing acceptor site, leading to the insertion of 12 base pairs at the beginning of exon 13. This alteration is expected to result in the insertion of 4 amino acids (p.Ile444_Asn445insLeuLeuTrpGln) at the protein level; it is expected to preserve the reading frame integrity (PMID: 19138766). The variant has been observed in one Portuguese patient and two Argentinean siblings with congenital muscular dystrophy (PMID: 19138766). Consequently, it has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Mar 5, 2024