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NM_001077365.2(POMT1):c.1474C>T (p.Arg492Ter)

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Interpretation:
Pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Mar 13, 2019)
Last evaluated:
Aug 21, 2018
Accession:
VCV000003245.3
Variation ID:
3245
Description:
single nucleotide variant
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NM_001077365.2(POMT1):c.1474C>T (p.Arg492Ter)

Allele ID
18284
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 131518945 (GRCh38) GRCh38 UCSC
9: 134394332 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.12:g.131518945C>T
NC_000009.11:g.134394332C>T
NM_001077365.2:c.1474C>T MANE Select NP_001070833.1:p.Arg492Ter nonsense
... more HGVS
Protein change
R514*, R340*, R397*, R375*, R438*, R492*, R460*, R462*, R362*, R488*
Other names
-
Canonical SPDI
NC_000009.12:131518944:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA116110
OMIM: 607423.0008
dbSNP: rs119462985
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 2 criteria provided, multiple submitters, no conflicts Aug 21, 2018 RCV000760355.2
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 1
Pathogenic 1 no assertion criteria provided May 1, 2006 RCV000003401.5
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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
(Aug 21, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000890215.1
Submitted: (Mar 13, 2019)
Evidence details
Comment:
The R514X nonsense variant in the POMT1 gene has been reported previously in the homozygous state in an individual with a clinical diagnosis of Walker-Warburg … (more)
Pathogenic
(Mar 20, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000226310.5
Submitted: (Jun 30, 2017)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Pathogenic
(May 01, 2006)
no assertion criteria provided
Method: literature only
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (CONGENITAL WITH IMPAIRED INTELLECTUAL DEVELOPMENT), TYPE B, 1
Allele origin: germline
OMIM
Accession: SCV000023559.4
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)

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
Congenital muscular dystrophy associated with calf hypertrophy, microcephaly and severe mental retardation in three Italian families: evidence for a novel CMD syndrome. Villanova M Neuromuscular disorders : NMD 2000 PMID: 11053679
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=POMT1 - - - -

Text-mined citations for rs119462985...

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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 Feb 27, 2021