NM_022089.4(ATP13A2):c.2836A>T (p.Ile946Phe) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Jan 1, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000116438.28

Allele description [Variation Report for NM_022089.4(ATP13A2):c.2836A>T (p.Ile946Phe)]

NM_022089.4(ATP13A2):c.2836A>T (p.Ile946Phe)

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.2836A>T (p.Ile946Phe)

HGVS:

NC_000001.11:g.16988161T>A
NG_009054.1:g.28768A>T
NM_001141973.3:c.2821A>T
NM_001141974.3:c.2704A>T
NM_022089.4:c.2836A>TMANE SELECT
NP_001135445.1:p.Ile941Phe
NP_001135446.1:p.Ile902Phe
NP_071372.1:p.Ile946Phe
LRG_834t1:c.2836A>T
LRG_834:g.28768A>T
LRG_834p1:p.Ile946Phe
NC_000001.10:g.17314656T>A
NM_022089.2:c.2836A>T
NM_022089.3:c.2836A>T
Q9NQ11:p.Ile946Phe

Protein change:

I902F

Links:

UniProtKB: Q9NQ11#VAR_058461; dbSNP: rs55708915

NCBI 1000 Genomes Browser:

rs55708915

Molecular consequence:

NM_001141973.3:c.2821A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001141974.3:c.2704A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022089.4:c.2836A>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000150363	Genetic Services Laboratory, University of Chicago	criteria provided, single submitter (ACMG Guidelines, 2007)	Uncertain significance (Feb 7, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001715510	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jan 9, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 19085912, 19705361, 34382491, 25741868
SCV001759516	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Jan 8, 2021)	germline	clinical testing	Citation Link,
SCV004701251	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Jan 1, 2024)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Richards CS, Bale S, Bellissimo DB, Das S, Grody WW, Hegde MR, Lyon E, Ward BE; Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee..

Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae.

PubMed [citation]

PMID:: 18414213

ATP13A2 variability in Parkinson disease.

Vilariño-Güell C, Soto AI, Lincoln SJ, Ben Yahmed S, Kefi M, Heckman MG, Hulihan MM, Chai H, Diehl NN, Amouri R, Rajput A, Mash DC, Dickson DW, Middleton LT, Gibson RA, Hentati F, Farrer MJ.

Hum Mutat. 2009 Mar;30(3):406-10. doi: 10.1002/humu.20877.

PubMed [citation]

PMID:: 19085912
PMCID:: PMC2650009

See all PubMed Citations (5)

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000150363.1

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

#	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

From Mayo Clinic Laboratories, Mayo Clinic, SCV001715510.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (4)

#	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		2	not provided	not provided	not provided

From GeneDx, SCV001759516.1

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

Description

Reported in the heterozygous state in an individual with Parkinson disease; however, a second ATP13A2 variant was not detected and I946F was observed in an unaffected control (Djarmati et al., 2009); This variant is associated with the following publications: (PMID: 19458722, 18075584, 12169656, 19705361, 19085912, 18075585)

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004701251.7

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

#	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		1	not provided	not provided	not provided

Last Updated: Oct 8, 2024

ClinVar

Relating variation to medicine