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NM_001077365.2(POMT1):c.1698+1G>A AND Autosomal recessive limb-girdle muscular dystrophy

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Nov 16, 2022
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:
RCV002469286.1

Allele description [Variation Report for NM_001077365.2(POMT1):c.1698+1G>A]

NM_001077365.2(POMT1):c.1698+1G>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.1698+1G>A
HGVS:
  • NC_000009.12:g.131520194G>A
  • NG_008896.2:g.22293G>A
  • NM_001077365.2:c.1698+1G>AMANE SELECT
  • NM_001077366.2:c.1536+1G>A
  • NM_001136113.2:c.1698+1G>A
  • NM_001136114.2:c.1347+1G>A
  • NM_001353193.2:c.1764+1G>A
  • NM_001353194.2:c.1536+1G>A
  • NM_001353195.2:c.1347+1G>A
  • NM_001353196.2:c.1608+1G>A
  • NM_001353197.2:c.1602+1G>A
  • NM_001353198.2:c.1602+1G>A
  • NM_001353199.2:c.1413+1G>A
  • NM_001353200.2:c.1242+1G>A
  • NM_001374689.1:c.1686+1G>A
  • NM_001374690.1:c.1479+1G>A
  • NM_001374691.1:c.1347+1G>A
  • NM_001374692.1:c.1347+1G>A
  • NM_001374693.1:c.1347+1G>A
  • NM_001374695.1:c.1308+1G>A
  • NM_001411024.1:c.567+1G>A
  • NM_007171.4:c.1764+1G>A
  • LRG_842t1:c.1764+1G>A
  • LRG_842t2:c.1698+1G>A
  • LRG_842:g.22293G>A
  • NC_000009.11:g.134395581G>A
  • NM_007171.3:c.1764+1G>A
Links:
dbSNP: rs763586263
NCBI 1000 Genomes Browser:
rs763586263
Molecular consequence:
  • NM_001077365.2:c.1698+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001077366.2:c.1536+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001136113.2:c.1698+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001136114.2:c.1347+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353193.2:c.1764+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353194.2:c.1536+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353195.2:c.1347+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353196.2:c.1608+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353197.2:c.1602+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353198.2:c.1602+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353199.2:c.1413+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353200.2:c.1242+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374689.1:c.1686+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374690.1:c.1479+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374691.1:c.1347+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374692.1:c.1347+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374693.1:c.1347+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374695.1:c.1308+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001411024.1:c.567+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_007171.4:c.1764+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy
Identifiers:
MONDO: MONDO:0015152; MedGen: C2931907; OMIM: PS253600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002766345Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Likely pathogenic
(Nov 16, 2022)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Summary from all submissions

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

Citations

PubMed

Molecular heterogeneity in fetal forms of type II lissencephaly.

Bouchet C, Gonzales M, Vuillaumier-Barrot S, Devisme L, Lebizec C, Alanio E, Bazin A, Bessières-Grattagliano B, Bigi N, Blanchet P, Bonneau D, Bonnières M, Carles D, Delahaye S, Fallet-Bianco C, Figarella-Branger D, Gaillard D, Gasser B, Guimiot F, Joubert M, Laurent N, Liprandi A, et al.

Hum Mutat. 2007 Oct;28(10):1020-7.

PubMed [citation]
PMID:
17559086

Cobblestone lissencephaly: neuropathological subtypes and correlations with genes of dystroglycanopathies.

Devisme L, Bouchet C, Gonzalès M, Alanio E, Bazin A, Bessières B, Bigi N, Blanchet P, Bonneau D, Bonnières M, Bucourt M, Carles D, Clarisse B, Delahaye S, Fallet-Bianco C, Figarella-Branger D, Gaillard D, Gasser B, Delezoide AL, Guimiot F, Joubert M, Laurent N, et al.

Brain. 2012 Feb;135(Pt 2):469-82. doi: 10.1093/brain/awr357. Epub 2012 Feb 9.

PubMed [citation]
PMID:
22323514
See all PubMed Citations (3)

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002766345.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

Variant summary: POMT1 c.1764+1G>A is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: four predict the variant abolishes a 5' splicing donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing, demonstrating in a patient derived sample that the variant resulted in an in-frame skipping of exon 17 (Bouchet_2007), with a predicted protein level effect of p.Trp551_Ser588del, which would affect the C-terminal four TM domain (amino acids 542-740; IPR032421) of the protein. The variant allele was found at a frequency of 8e-06 in 250470 control chromosomes (gnomAD). The variant, c.1764+1G>A, has been reported in the literature in compound heterozygous state in a fetus affected with cobblestone lissencephaly (Bouchet_2007, Devisme_2012). Four submitters have provided clinical-significance assessments for this variant in ClinVar after 2014, and classified the variant as pathogenic (n=1), likely pathogenic (n=2), or unknown significance but suspicious for pathogenicity (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Jun 17, 2024