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

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
2 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 20, 2020
Accession:
VCV000593922.2
Variation ID:
593922
Description:
single nucleotide variant
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NM_001077365.2(POMT1):c.699+67G>A

Allele ID
584985
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 131510063 (GRCh38) GRCh38 UCSC
9: 134385450 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.12:g.131510063G>A
NC_000009.11:g.134385450G>A
NM_001077365.2:c.699+67G>A MANE Select
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:131510062:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD) 0.00003
Links
dbSNP: rs776061161
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter Sep 6, 2017 RCV000729095.1
Likely pathogenic 1 criteria provided, single submitter Jun 20, 2020 RCV001379440.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
POMT1 - - GRCh38
GRCh37
561 599

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Sep 06, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000856733.1
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely pathogenic
(Jun 20, 2020)
criteria provided, single submitter
Method: clinical testing
Congenital muscular dystrophy-dystroglycanopathy with mental retardation, type B1
Walker-Warburg congenital muscular dystrophy
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Allele origin: germline
Invitae
Accession: SCV001577243.1
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (4)
Comment:
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 … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
The expanding phenotype of POMT1 mutations: from Walker-Warburg syndrome to congenital muscular dystrophy, microcephaly, and mental retardation. van Reeuwijk J Human mutation 2006 PMID: 16575835
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Mutations in POMT1 are found in a minority of patients with Walker-Warburg syndrome. Currier SC American journal of medical genetics. Part A 2005 PMID: 15637732
Mutations in the O-mannosyltransferase gene POMT1 give rise to the severe neuronal migration disorder Walker-Warburg syndrome. Beltrán-Valero de Bernabé D American journal of human genetics 2002 PMID: 12369018
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=POMT1 - - - -

Text-mined citations for rs776061161...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 14, 2021