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NM_152296.5(ATP1A3):c.357C>T (p.Asn119=)

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Interpretation:
Benign/Likely benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
10 (Most recent: Sep 23, 2021)
Last evaluated:
Dec 5, 2020
Accession:
VCV000329427.13
Variation ID:
329427
Description:
single nucleotide variant
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NM_152296.5(ATP1A3):c.357C>T (p.Asn119=)

Allele ID
349931
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19q13.2
Genomic location
19: 41987936 (GRCh38) GRCh38 UCSC
19: 42492088 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_1186:g.11295C>T
LRG_1186t1:c.357C>T LRG_1186p1:p.Asn119=
NC_000019.9:g.42492088G>A
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:41987935:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00200 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00105
Trans-Omics for Precision Medicine (TOPMed) 0.00113
1000 Genomes Project 0.00200
Exome Aggregation Consortium (ExAC) 0.00264
The Genome Aggregation Database (gnomAD) 0.00108
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00177
Trans-Omics for Precision Medicine (TOPMed) 0.00130
The Genome Aggregation Database (gnomAD), exomes 0.00241
Links
ClinGen: CA9467899
dbSNP: rs143547136
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 Dec 5, 2020 RCV000311209.6
Benign/Likely benign 7 criteria provided, multiple submitters, no conflicts Jan 7, 2019 RCV000513805.10
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000404431.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATP1A3 - - GRCh38
GRCh37
611 625

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Oct 03, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics
Accession: SCV000610631.1
Submitted: (Oct 05, 2017)
Evidence details
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Alternating hemiplegia of childhood 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000413459.3
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)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Dystonia 12
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000413460.3
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)
Benign
(Dec 05, 2020)
criteria provided, single submitter
Method: clinical testing
Dystonia 12
Allele origin: germline
Invitae
Accession: SCV000645412.5
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Jan 07, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143141.1
Submitted: (Sep 25, 2019)
Evidence details
Benign
(Oct 16, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001907198.1
Submitted: (Sep 21, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Study: VKGL Data-share Consensus
Accession: SCV001800568.1
Submitted: (Aug 19, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001742845.3
Submitted: (Sep 02, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001926896.1
Submitted: (Sep 23, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001964030.1
Submitted: (Sep 21, 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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs143547136...

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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 Nov 27, 2021