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NM_001077365.2(POMT1):c.2178G>A (p.Ter726=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jul 16, 2021)
Last evaluated:
Mar 30, 2021
Accession:
VCV000211947.13
Variation ID:
211947
Description:
single nucleotide variant
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NM_001077365.2(POMT1):c.2178G>A (p.Ter726=)

Allele ID
207639
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9q34.13
Genomic location
9: 131523106 (GRCh38) GRCh38 UCSC
9: 134398493 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.134398493G>A
NC_000009.12:g.131523106G>A
NM_001077365.2:c.2178G>A MANE Select NP_001070833.1:p.Ter726= synonymous
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000009.12:131523105:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00095
The Genome Aggregation Database (gnomAD) 0.00099
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00108
1000 Genomes Project 0.00040
Trans-Omics for Precision Medicine (TOPMed) 0.00052
Links
ClinGen: CA208025
dbSNP: rs147143094
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Nov 23, 2020 RCV001084644.2
Uncertain significance 1 criteria provided, single submitter Jan 12, 2018 RCV001169207.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Aug 4, 2015 RCV000194092.2
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Mar 30, 2021 RCV000712824.5
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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
555 593

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 02, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000248587.1
Submitted: (Sep 15, 2015)
Evidence details
Likely benign
(Jul 25, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000843359.1
Submitted: (Aug 31, 2018)
Evidence details
Likely benign
(Nov 23, 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: SCV000649896.5
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(May 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV001155779.6
Submitted: (Jul 04, 2021)
Evidence details
Likely benign
(Mar 30, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001754274.1
Submitted: (Jul 16, 2021)
Evidence details
Likely benign
(Aug 04, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000331134.4
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Limb-girdle muscular dystrophy-dystroglycanopathy, type C1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001331883.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=POMT1 - - - -

Text-mined citations for rs147143094...

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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 Aug 17, 2021