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NM_000702.4(ATP1A2):c.2751G>A (p.Thr917=)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(4);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
8 (Most recent: Sep 23, 2021)
Last evaluated:
Nov 14, 2020
Accession:
VCV000195466.7
Variation ID:
195466
Description:
single nucleotide variant
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NM_000702.4(ATP1A2):c.2751G>A (p.Thr917=)

Allele ID
192627
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q23.2
Genomic location
1: 160136942 (GRCh38) GRCh38 UCSC
1: 160106732 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_6:g.26185G>A
NC_000001.10:g.160106732G>A
NC_000001.11:g.160136942G>A
... more HGVS
Protein change
-
Other names
p.T917T:ACG>ACA
Canonical SPDI
NC_000001.11:160136941:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (A)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00064
The Genome Aggregation Database (gnomAD) 0.00069
Trans-Omics for Precision Medicine (TOPMed) 0.00072
Trans-Omics for Precision Medicine (TOPMed) 0.00075
Exome Aggregation Consortium (ExAC) 0.00091
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00100
1000 Genomes Project 0.00040
The Genome Aggregation Database (gnomAD), exomes 0.00084
Links
ClinGen: CA241895
dbSNP: rs146839867
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 Nov 30, 2016 RCV000186775.3
Benign 1 criteria provided, single submitter Nov 14, 2020 RCV000333644.6
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000388105.2
Likely benign 1 criteria provided, single submitter Jan 13, 2018 RCV001093738.1
Uncertain significance 3 criteria provided, single submitter May 15, 2015 RCV000724819.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ATP1A2 - - GRCh38
GRCh37
710 726

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(May 15, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000227633.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Alternating hemiplegia of childhood 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000349917.3
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)
Likely benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Familial hemiplegic migraine type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000349916.3
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
(Jul 07, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000240343.11
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Nov 30, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000612443.1
Submitted: (Aug 17, 2017)
Evidence details
Benign
(Nov 14, 2020)
criteria provided, single submitter
Method: clinical testing
Familial hemiplegic migraine
Allele origin: germline
Invitae
Accession: SCV000556873.6
Submitted: (Jan 07, 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: SCV001967084.1
Submitted: (Sep 21, 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: SCV001926767.1
Submitted: (Sep 23, 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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=ATP1A2 - - - -

Text-mined citations for rs146839867...

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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