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NM_000702.4(ATP1A2):c.2961C>T (p.Cys987=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7 (Most recent: Sep 28, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000128484.9
Variation ID:
128484
Description:
single nucleotide variant
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NM_000702.4(ATP1A2):c.2961C>T (p.Cys987=)

Allele ID
133933
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q23.2
Genomic location
1: 160139911 (GRCh38) GRCh38 UCSC
1: 160109701 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_6:g.29154C>T
NC_000001.10:g.160109701C>T
NC_000001.11:g.160139911C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:160139910:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.02396 (T)

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00814
The Genome Aggregation Database (gnomAD) 0.02540
The Genome Aggregation Database (gnomAD) 0.02789
Trans-Omics for Precision Medicine (TOPMed) 0.02824
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.02837
The Genome Aggregation Database (gnomAD), exomes 0.00701
Trans-Omics for Precision Medicine (TOPMed) 0.02971
1000 Genomes Project 0.02396
Links
ClinGen: CA151974
dbSNP: rs74123254
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 8, 2020 RCV000390132.7
Benign 2 criteria provided, multiple submitters, no conflicts Aug 15, 2017 RCV000710691.4
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV000340757.2
Benign 1 criteria provided, single submitter Jan 13, 2018 RCV001093789.1
Likely benign 1 no assertion criteria provided - RCV000116453.3
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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
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: SCV000349922.3
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
Familial hemiplegic migraine type 2
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000349923.3
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
(Aug 15, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000840976.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(Mar 18, 2016)
criteria provided, single submitter
Method: clinical testing
Familial hemiplegic migraine
Allele origin: germline
Ambry Genetics
Accession: SCV000847432.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Familial hemiplegic migraine
Allele origin: germline
Invitae
Accession: SCV000556863.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Mar 03, 2015)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001944557.1
Submitted: (Sep 28, 2021)
Evidence details
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory,University of Chicago
Accession: SCV000150378.2
Submitted: (Jun 27, 2014)
Evidence details
Comment:
Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated … (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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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 rs74123254...

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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