NM_152296.5(ATP1A3):c.385G>A (p.Val129Met) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 2, 2022
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:: RCV002282097.2

Allele description [Variation Report for NM_152296.5(ATP1A3):c.385G>A (p.Val129Met)]

NM_152296.5(ATP1A3):c.385G>A (p.Val129Met)

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.385G>A (p.Val129Met)

HGVS:

NC_000019.10:g.41986202C>T
NG_008015.1:g.13029G>A
NM_001256213.2:c.418G>A
NM_001256214.2:c.424G>A
NM_152296.5:c.385G>AMANE SELECT
NP_001243142.1:p.Val140Met
NP_001243143.1:p.Val142Met
NP_689509.1:p.Val129Met
LRG_1186t1:c.385G>A
LRG_1186:g.13029G>A
LRG_1186p1:p.Val129Met
NC_000019.9:g.42490354C>T
NM_001256214.1:c.424G>A
NM_152296.4:c.385G>A

Protein change:

V129M

Links:

dbSNP: rs1555865401

NCBI 1000 Genomes Browser:

rs1555865401

Molecular consequence:

NM_001256213.2:c.418G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001256214.2:c.424G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152296.5:c.385G>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
SCV002571546	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Sep 2, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002571546

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Sep 2, 2022)

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, SCV002571546.2

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

Description

Reported previously as a de novo variant in a patient with neonatal hypotonia, pervasive developmental disorder, episodes of stiffness when sleeping, severe-injurious behaviors, and childhood-onset schizophrenia (Smedemark-Margulies et al., 2016); Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27626066)

#	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 30, 2023

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