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NM_001077365.2(POMT1):c.1175+4_1175+7del AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 25, 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:
RCV001238420.7

Allele description [Variation Report for NM_001077365.2(POMT1):c.1175+4_1175+7del]

NM_001077365.2(POMT1):c.1175+4_1175+7del

Gene:
POMT1:protein O-mannosyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q34.13
Genomic location:
Preferred name:
NM_001077365.2(POMT1):c.1175+4_1175+7del
HGVS:
  • NC_000009.12:g.131513335_131513338del
  • NG_008896.1:g.15434_15437del
  • NM_001077365.2:c.1175+4_1175+7delMANE SELECT
  • NM_001077366.2:c.1013+4_1013+7del
  • NM_001136113.2:c.1175+4_1175+7del
  • NM_001136114.2:c.824+4_824+7del
  • NM_001353193.2:c.1241+4_1241+7del
  • NM_001353194.2:c.1013+4_1013+7del
  • NM_001353195.2:c.824+4_824+7del
  • NM_001353196.2:c.1085+4_1085+7del
  • NM_001353197.2:c.1079+4_1079+7del
  • NM_001353198.2:c.1079+4_1079+7del
  • NM_001353199.2:c.890+4_890+7del
  • NM_001353200.2:c.719+4_719+7del
  • NM_001374689.1:c.1163+4_1163+7del
  • NM_001374690.1:c.1175+4_1175+7del
  • NM_001374691.1:c.824+4_824+7del
  • NM_001374692.1:c.824+4_824+7del
  • NM_001374693.1:c.824+1868_824+1871del
  • NM_001374695.1:c.785+4_785+7del
  • NM_007171.4:c.1241+4_1241+7del
  • LRG_842t1:c.1241+4_1241+7del
  • LRG_842t2:c.1175+4_1175+7del
  • NC_000009.11:g.134388719_134388722del
  • NC_000009.11:g.134388722_134388725del
  • NM_007171.3:c.1241+4_1241+7del
Links:
dbSNP: rs1588409344
NCBI 1000 Genomes Browser:
rs1588409344
Molecular consequence:
  • NM_001374693.1:c.824+1868_824+1871del - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001077365.2:c.1175+4_1175+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001077366.2:c.1013+4_1013+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001136113.2:c.1175+4_1175+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001136114.2:c.824+4_824+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353193.2:c.1241+4_1241+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353194.2:c.1013+4_1013+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353195.2:c.824+4_824+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353196.2:c.1085+4_1085+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353197.2:c.1079+4_1079+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353198.2:c.1079+4_1079+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353199.2:c.890+4_890+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001353200.2:c.719+4_719+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374689.1:c.1163+4_1163+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374690.1:c.1175+4_1175+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374691.1:c.824+4_824+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374692.1:c.824+4_824+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001374695.1:c.785+4_785+7del - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_007171.4:c.1241+4_1241+7del - 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
SCV001411228Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Sep 25, 2019)
germlineclinical testing

PubMed (4)
[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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV001411228.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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. This variant has been observed homozygous in an individual affected with Walker-Warburg syndrome (PMID: 28556411). This variant is also known as c.1241+3delAGTG in the literature. This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 12 of the POMT1 gene. It does not directly change the encoded amino acid sequence of the POMT1 protein, but it affects a nucleotide within the consensus splice site of the intron.

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

Last Updated: Apr 15, 2024