NM_152296.5(ATP1A3):c.662G>A (p.Cys221Tyr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 23, 2017
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:: RCV000480352.1

Allele description [Variation Report for NM_152296.5(ATP1A3):c.662G>A (p.Cys221Tyr)]

NM_152296.5(ATP1A3):c.662G>A (p.Cys221Tyr)

Gene:

ATP1A3:ATPase Na+/K+ transporting subunit alpha 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.2

Genomic location:

Preferred name:

NM_152296.5(ATP1A3):c.662G>A (p.Cys221Tyr)

HGVS:

NC_000019.10:g.41985368C>T
NG_008015.1:g.13863G>A
NM_001256213.2:c.695G>A
NM_001256214.2:c.701G>A
NM_152296.5:c.662G>AMANE SELECT
NP_001243142.1:p.Cys232Tyr
NP_001243143.1:p.Cys234Tyr
NP_689509.1:p.Cys221Tyr
LRG_1186t1:c.662G>A
LRG_1186:g.13863G>A
LRG_1186p1:p.Cys221Tyr
NC_000019.9:g.42489520C>T
NM_152296.4:c.662G>A

Protein change:

C221Y

Links:

dbSNP: rs782125149

NCBI 1000 Genomes Browser:

rs782125149

Molecular consequence:

NM_001256213.2:c.695G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001256214.2:c.701G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152296.5:c.662G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000574258	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Mar 23, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000574258

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Mar 23, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000574258.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The C221Y variant in the ATP1A3 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The C221Y variant is observed in 1/16512 (0.006%) alleles from individuals of South Asian background in the ExAC dataset (Lek et al., 2016). The C221Y variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals, and in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret C221Y as a variant of uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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