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NM_001077365.2(POMT1):c.1698+1G>A AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 10, 2023
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:
RCV001040545.7

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 type 2K
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 1; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2K; Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Identifiers:
MONDO: MONDO:0012248; MedGen: C1836373; Orphanet: 86812; OMIM: 609308
Name:
Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 (MDDGB1)
Synonyms:
MUSCULAR DYSTROPHY, CONGENITAL, POMT1-RELATED; MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 1
Identifiers:
MONDO: MONDO:0013159; MedGen: C5436962; OMIM: 613155
Name:
Walker-Warburg congenital muscular dystrophy
Synonyms:
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
SCV001204125Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Aug 10, 2023)
germlineclinical testing

PubMed (7)
[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

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 (7)

Details of each submission

From Invitae, SCV001204125.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

Disruption of this splice site has been observed in individual(s) with clinical features of Walker-Warburg syndrome (PMID: 17559086, 22323514). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 631540). This variant is present in population databases (rs763586263, gnomAD 0.003%). This sequence change affects a donor splice site in intron 17 of the POMT1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site 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).

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

Last Updated: Jun 17, 2024