NM_001077365.2(POMT1):c.699+67G>A AND multiple conditions

Clinical significance:Likely pathogenic (Last evaluated: Jun 20, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001379440.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.699+67G>A]

NM_001077365.2(POMT1):c.699+67G>A

Gene:
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_001077365.2(POMT1):c.699+67G>A
HGVS:
  • NC_000009.12:g.131510063G>A
  • NG_008896.1:g.12162G>A
  • NM_001077365.2:c.699+67G>AMANE SELECT
  • NM_001077366.2:c.537+67G>A
  • NM_001136113.1:c.699+67G>A
  • NM_001136114.1:c.348+67G>A
  • NM_001353193.2:c.765+1G>A
  • NM_001353194.2:c.537+67G>A
  • NM_001353195.2:c.348+67G>A
  • NM_001353196.2:c.609+67G>A
  • NM_001353197.2:c.603+1G>A
  • NM_001353198.2:c.603+1G>A
  • NM_001353199.2:c.414+1G>A
  • NM_001353200.2:c.243+67G>A
  • NM_007171.3:c.765+1G>A
  • LRG_842t2:c.699+67G>A
  • NC_000009.11:g.134385450G>A
Links:
dbSNP: rs776061161
NCBI 1000 Genomes Browser:
rs776061161
Molecular consequence:
  • NM_001077365.2:c.699+67G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001077366.2:c.537+67G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001136113.1:c.699+67G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001136114.1:c.348+67G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353194.2:c.537+67G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353195.2:c.348+67G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353196.2:c.609+67G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353200.2:c.243+67G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353193.2:c.765+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353197.2:c.603+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353198.2:c.603+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353199.2:c.414+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_007171.3:c.765+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1 (MDDGC1)
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 1; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K; MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 11
Identifiers:
MONDO: MONDO:0012248; MedGen: C1836373; Orphanet: 86812; OMIM: 609308
Name:
Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1 (MDDGB1)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL IMPAIRMENT), TYPE B, 1; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1
Identifiers:
MONDO: MONDO:0013159; MedGen: C3150415; OMIM: 613155
Name:
Walker-Warburg congenital muscular dystrophy (MDDGA1)
Synonyms:
HARD syndrome; Muscular dystrophy-dystroglycanopathy, type A; Walker-Warburg syndrome
Identifiers:
MONDO: MONDO:0000171; MedGen: C0265221; Orphanet: 899; OMIM: PS236670

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001577243Invitaecriteria provided, single submitter
Likely pathogenic
(Jun 20, 2020)
germlineclinical testing

PubMed (5)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Mutations in the O-mannosyltransferase gene POMT1 give rise to the severe neuronal migration disorder Walker-Warburg syndrome.

Beltrán-Valero de Bernabé D, Currier S, Steinbrecher A, Celli J, van Beusekom E, van der Zwaag B, Kayserili H, Merlini L, Chitayat D, Dobyns WB, Cormand B, Lehesjoki AE, Cruces J, Voit T, Walsh CA, van Bokhoven H, Brunner HG.

Am J Hum Genet. 2002 Nov;71(5):1033-43. Epub 2002 Oct 4.

PubMed [citation]
PMID:
12369018
PMCID:
PMC419999
See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001577243.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change affects a donor splice site in intron 8 of the POMT1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is present in population databases (rs776061161, ExAC 0.003%). This variant has not been reported in the literature in individuals with POMT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 593922). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in POMT1 are known to be pathogenic (PMID: 12369018, 15637732, 16575835). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Jun 14, 2021

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