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NM_001077365.2(POMT1):c.1698+1G>A AND POMT1-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 5, 2019
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:
RCV000778149.4

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:
POMT1-related disorder
Synonyms:
POMT1-Related Disorders; POMT1-related condition
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000914281Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 09 May 2019)
Uncertain significance
(Apr 5, 2019)
germlineclinical testing

PubMed (2)
[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

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

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000914281.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The POMT1 c.1764+1G>A variant occurs in a canonical splice site (donor) and is therefore predicted to disrupt or distort the normal gene product. The c.1764+1G>A variant has been reported in two studies in which it is found in a compound heterozygous state with a missense/splice variant in one fetus with cobblestone lissencephaly (Bouchet et al. 2007; Devisme et al. 2012). Control data are unavailable for this variant, which is reported at a frequency of 0.000061 in the South Asian population from the Exome Aggregation Consortium; however, this is based on one allele in a region of good sequencing coverage so the variant is presumed to be rare. RNA analysis showed that the c.1764+1G>A variant causes aberrant splicing, resulting in a transcript lacking exon 17 (Bouchet et al. 2007). Based on the evidence and the potential impact of splice donor variants, the c.1764+1G>A variant is classified as a variant of unknown significance but suspicious for pathogenicity for POMT1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

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

Last Updated: Jun 17, 2024