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NM_001077365.2(POMT1):c.1856C>T (p.Ala619Val)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Sep 28, 2021)
Last evaluated:
Dec 7, 2020
Accession:
VCV000130011.6
Variation ID:
130011
Description:
single nucleotide variant
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NM_001077365.2(POMT1):c.1856C>T (p.Ala619Val)

Allele ID
135457
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 131522077 (GRCh38) GRCh38 UCSC
9: 134397464 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_842t2:c.1856C>T LRG_842p2:p.Ala619Val
LRG_842t1:c.1922C>T LRG_842p1:p.Ala641Val
NC_000009.11:g.134397464C>T
... more HGVS
Protein change
A641V, A502V, A524V, A565V, A587V, A589V, A467V, A619V, A615V, A489V, A546V
Other names
-
Canonical SPDI
NC_000009.12:131522076:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.02097 (T)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00665
Exome Aggregation Consortium (ExAC) 0.00758
Trans-Omics for Precision Medicine (TOPMed) 0.01547
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.01569
The Genome Aggregation Database (gnomAD) 0.01562
1000 Genomes Project 0.02097
Links
ClinGen: CA154753
dbSNP: rs12115566
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 2 criteria provided, multiple submitters, no conflicts Aug 15, 2013 RCV000118035.2
Benign 2 criteria provided, multiple submitters, no conflicts Nov 1, 2017 RCV000712821.4
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000331368.2
Benign 1 criteria provided, single submitter Dec 7, 2020 RCV001085455.2
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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
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000311748.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000477674.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001945140.1
Submitted: (Sep 28, 2021)
Evidence details
Benign
(Aug 15, 2013)
criteria provided, single submitter
Method: clinical testing
AllHighlyPenetrant
(Autosomal recessive inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000152356.1
Submitted: (Apr 30, 2014)
Evidence details
Benign
(Nov 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000843355.1
Submitted: (Aug 31, 2018)
Evidence details
Publications
PubMed (3)
Benign
(Dec 07, 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: SCV000649888.5
Submitted: (Jan 07, 2021)
Evidence details

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
Genetic alterations of protein-o-mannosyltransferase-1 in glioneuronal and glial brain tumors with subarachnoid spread. Snoei J Neuropathology : official journal of the Japanese Society of Neuropathology 2009 PMID: 18647264
Refining genotype phenotype correlations in muscular dystrophies with defective glycosylation of dystroglycan. Godfrey C Brain : a journal of neurology 2007 PMID: 17878207
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

Text-mined citations for rs12115566...

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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 Sep 29, 2021