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NM_000702.4(ATP1A2):c.129G>A (p.Lys43=)

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Interpretation:
Benign​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000128478.6
Variation ID:
128478
Description:
single nucleotide variant
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NM_000702.4(ATP1A2):c.129G>A (p.Lys43=)

Allele ID
133927
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1q23.2
Genomic location
1: 160121203 (GRCh38) GRCh38 UCSC
1: 160090993 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.160090993G>A
NC_000001.11:g.160121203G>A
NM_000702.4:c.129G>A MANE Select NP_000693.1:p.Lys43= synonymous
... more HGVS
Protein change
-
Other names
p.K43K:AAG>AAA
Canonical SPDI
NC_000001.11:160121202:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00659 (A)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00188
1000 Genomes Project 0.00659
Exome Aggregation Consortium (ExAC) 0.00230
The Genome Aggregation Database (gnomAD) 0.00630
Trans-Omics for Precision Medicine (TOPMed) 0.00803
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00946
Links
ClinGen: CA288685
dbSNP: rs61734527
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 RCV000226425.7
Benign 2 criteria provided, single submitter Nov 26, 2012 RCV000116447.5
Benign 1 criteria provided, single submitter Feb 19, 2018 RCV000710687.3
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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
677 693

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Nov 26, 2012)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000167115.12
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
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
Familial hemiplegic migraine
Allele origin: germline
Invitae
Accession: SCV000285579.6
Submitted: (Jan 07, 2021)
Evidence details
Benign
(Feb 19, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV000840971.1
Submitted: (Aug 31, 2018)
Evidence details
Benign
(May 02, 2016)
criteria provided, single submitter
Method: clinical testing
Familial hemiplegic migraine
Allele origin: germline
Ambry Genetics
Accession: SCV000846456.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
AllHighlyPenetrant
(Autosomal dominant inheritance)
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000150372.2
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 rs61734527...

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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 Jun 14, 2021