NM_022089.4(ATP13A2):c.1309C>G (p.Leu437Val) AND Inborn genetic diseases

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 26, 2018
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:: RCV002314040.9

Allele description [Variation Report for NM_022089.4(ATP13A2):c.1309C>G (p.Leu437Val)]

NM_022089.4(ATP13A2):c.1309C>G (p.Leu437Val)

Gene:

ATP13A2:ATPase cation transporting 13A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p36.13

Genomic location:

Preferred name:

NM_022089.4(ATP13A2):c.1309C>G (p.Leu437Val)

Other names:

p.Leu437Val

HGVS:

NC_000001.11:g.16996298G>C
NG_009054.1:g.20631C>G
NM_001141973.3:c.1294C>G
NM_001141974.3:c.1294C>G
NM_022089.4:c.1309C>GMANE SELECT
NP_001135445.1:p.Leu432Val
NP_001135446.1:p.Leu432Val
NP_071372.1:p.Leu437Val
LRG_834t1:c.1309C>G
LRG_834:g.20631C>G
LRG_834p1:p.Leu437Val
NC_000001.10:g.17322793G>C
NM_022089.2:c.1309C>G
NM_022089.3:c.1309C>G

Protein change:

L432V

Links:

dbSNP: rs149372969

NCBI 1000 Genomes Browser:

rs149372969

Molecular consequence:

NM_001141973.3:c.1294C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001141974.3:c.1294C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_022089.4:c.1309C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000848888	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 26, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000848888

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 26, 2018)

germline

clinical testing

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

Citation Link

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

Parkinson's disease, genetic variability and the Faroe Islands.

Petersen MS, Guella I, Bech S, Gustavsson E, Farrer MJ.

Parkinsonism Relat Disord. 2015 Jan;21(1):75-8. doi: 10.1016/j.parkreldis.2014.10.027. Epub 2014 Nov 4.

PubMed [citation]

PMID:: 25466404

Details of each submission

From Ambry Genetics, SCV000848888.5

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

Description

The p.L437V variant (also known as c.1309C>G), located in coding exon 14 of the ATP13A2 gene, results from a C to G substitution at nucleotide position 1309. The leucine at codon 437 is replaced by valine, an amino acid with highly similar properties. In one study, this p.L437V alteration (resulting from c.1311G>C) was detected in six individuals from the Faroe Islands with Parkinson disease (PD), none of whom carried a second alteration in the ATP13A2 gene. Of these six individuals, one had disease onset at age 28, and also carried alterations of unknown significance in LRRK2 and CNAJC13 (Petersen MS et al. Parkinsonism Relat. Disord., 2015 Jan;21:75-8). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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