NM_152296.5(ATP1A3):c.1825G>A (p.Asp609Asn) AND Dystonia 12

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 24, 2020
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:: RCV001321417.7

Allele description [Variation Report for NM_152296.5(ATP1A3):c.1825G>A (p.Asp609Asn)]

NM_152296.5(ATP1A3):c.1825G>A (p.Asp609Asn)

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.1825G>A (p.Asp609Asn)

HGVS:

NC_000019.10:g.41978054C>T
NG_008015.1:g.21177G>A
NM_001256213.2:c.1858G>A
NM_001256214.2:c.1864G>A
NM_152296.5:c.1825G>AMANE SELECT
NP_001243142.1:p.Asp620Asn
NP_001243143.1:p.Asp622Asn
NP_689509.1:p.Asp609Asn
LRG_1186t1:c.1825G>A
LRG_1186:g.21177G>A
LRG_1186p1:p.Asp609Asn
NC_000019.9:g.42482206C>T

Protein change:

D609N

Links:

dbSNP: rs2075190697

NCBI 1000 Genomes Browser:

rs2075190697

Molecular consequence:

NM_001256213.2:c.1858G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001256214.2:c.1864G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152296.5:c.1825G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Dystonia 12 (DYT12)
Synonyms:: DYT-ATP1A3; Rapid-Onset Dystonia-Parkinsonism
Identifiers:: MONDO: MONDO:0007496; MedGen: C1868681; Orphanet: 71517; OMIM: 128235

Recent activity

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Cecropterus dobra voucher NVG-11182
Cecropterus dobra voucher NVG-11182

biosample
Cecropterus nevada nevada voucher LACM:NVG-14114A10
Cecropterus nevada nevada voucher LACM:NVG-14114A10

biosample
cytochrome c oxidase subunit I, partial (mitochondrion) [Ceratodictyon sp.]
cytochrome c oxidase subunit I, partial (mitochondrion) [Ceratodictyon sp.]
gi|2422684310|gb|WBN91020.1|

Protein
radial spoke head 14 homolog [Homo sapiens]
radial spoke head 14 homolog [Homo sapiens]
gi|7657530|ref|NP_055248.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001512244	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 24, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001512244

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 24, 2020)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001512244.4

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

Description

This variant is not present in population databases (ExAC no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt ATP1A3 protein function. This variant has not been reported in the literature in individuals with ATP1A3-related conditions. This sequence change replaces aspartic acid with asparagine at codon 609 of the ATP1A3 protein (p.Asp609Asn). The aspartic acid residue is highly conserved and there is a small physicochemical difference between aspartic acid and asparagine.

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

Last Updated: Sep 29, 2024

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