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NM_152296.5(ATP1A3):c.2146AAG[1] (p.Lys717del) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jul 29, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000480245.1

Allele description [Variation Report for NM_152296.5(ATP1A3):c.2146AAG[1] (p.Lys717del)]

NM_152296.5(ATP1A3):c.2146AAG[1] (p.Lys717del)

Gene:
ATP1A3:ATPase Na+/K+ transporting subunit alpha 3 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
19q13.2
Genomic location:
Preferred name:
NM_152296.5(ATP1A3):c.2146AAG[1] (p.Lys717del)
HGVS:
  • NC_000019.10:g.41975742TTC[1]
  • NG_008015.1:g.23485AAG[1]
  • NM_001256213.2:c.2179AAG[1]
  • NM_001256214.2:c.2185AAG[1]
  • NM_152296.5:c.2146AAG[1]MANE SELECT
  • NP_001243142.1:p.Lys728del
  • NP_001243143.1:p.Lys730del
  • NP_689509.1:p.Lys717del
  • LRG_1186t1:c.2146AAG[1]
  • LRG_1186:g.23485AAG[1]
  • LRG_1186p1:p.Lys717del
  • NC_000019.9:g.42479894TTC[1]
  • NM_152296.4:c.2149_2151delAAG
Protein change:
K717del
Links:
dbSNP: rs1064795403
NCBI 1000 Genomes Browser:
rs1064795403
Molecular consequence:
  • NM_001256213.2:c.2179AAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001256214.2:c.2185AAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_152296.5:c.2146AAG[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000571169GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Jul 29, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000571169.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The c.2149_2151delAAG variant in the ATP1A3 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The c.2149_2151delAAG variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.2149_2151delAAG variant results in an in-frame deletion and is predicted to cause loss of a Lysine residue at codon 717, denoted Lys717del. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, we interpret the c.2149_2151delAAG as a likely pathogenic variant.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Apr 23, 2022