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ATP13A2 ATPase cation transporting 13A2 [ Homo sapiens (human) ]

Gene ID: 23400, updated on 2-Oct-2018

Summary

Official Symbol
ATP13A2provided by HGNC
Official Full Name
ATPase cation transporting 13A2provided by HGNC
Primary source
HGNC:HGNC:30213
See related
Ensembl:ENSG00000159363 MIM:610513; Vega:OTTHUMG00000002293
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CLN12; KRPPD; PARK9; SPG78; HSA9947
Summary
This gene encodes a member of the P5 subfamily of ATPases which transports inorganic cations as well as other substrates. Mutations in this gene are associated with Kufor-Rakeb syndrome (KRS), also referred to as Parkinson disease 9. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Nov 2008]
Expression
Ubiquitous expression in brain (RPKM 19.6), spleen (RPKM 11.2) and 24 other tissues See more
Orthologs

Genomic context

See ATP13A2 in Genome Data Viewer
Location:
1p36.13
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (16985958..17011972, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (17312453..17338467, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ciliary rootlet coiled-coil, rootletin Neighboring gene uncharacterized LOC105376806 Neighboring gene microfibril associated protein 2 Neighboring gene succinate dehydrogenase complex iron sulfur subunit B Neighboring gene peptidyl arginine deiminase 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Parkinson disease 9
MedGen: C1847640 OMIM: 606693 GeneReviews: Parkinson Disease Overview
Compare labs
Spastic paraplegia 78, autosomal recessive
MedGen: C4310662 OMIM: 617225 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ26510

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATPase activity NAS
Non-traceable Author Statement
more info
PubMed 
cation-transporting ATPase activity TAS
Traceable Author Statement
more info
 
cupric ion binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
manganese ion binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
phosphatidic acid binding IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol-3,5-bisphosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
Process Evidence Code Pubs
ATP hydrolysis coupled cation transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
autophagosome organization IDA
Inferred from Direct Assay
more info
PubMed 
cellular calcium ion homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
cellular cation homeostasis TAS
Traceable Author Statement
more info
PubMed 
cellular iron ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to manganese ion IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to manganese ion TAS
Traceable Author Statement
more info
PubMed 
cellular response to oxidative stress IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to oxidative stress TAS
Traceable Author Statement
more info
PubMed 
cellular response to zinc ion TAS
Traceable Author Statement
more info
PubMed 
cellular zinc ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
extracellular exosome biogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
negative regulation of lysosomal protein catabolic process TAS
Traceable Author Statement
more info
PubMed 
negative regulation of neuron death ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
negative regulation of neuron death TAS
Traceable Author Statement
more info
PubMed 
peptidyl-aspartic acid autophosphorylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
polyamine transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of exosomal secretion IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of exosomal secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein autophosphorylation TAS
Traceable Author Statement
more info
PubMed 
regulation of autophagosome size IDA
Inferred from Direct Assay
more info
PubMed 
regulation of autophagy of mitochondrion TAS
Traceable Author Statement
more info
PubMed 
regulation of chaperone-mediated autophagy TAS
Traceable Author Statement
more info
PubMed 
regulation of endopeptidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of glucosylceramidase activity IEA
Inferred from Electronic Annotation
more info
 
regulation of intracellular protein transport NAS
Non-traceable Author Statement
more info
PubMed 
regulation of lysosomal protein catabolic process IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of lysosomal protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of macroautophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of macroautophagy TAS
Traceable Author Statement
more info
PubMed 
regulation of mitochondrion organization IDA
Inferred from Direct Assay
more info
PubMed 
regulation of mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
zinc ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
autophagosome IDA
Inferred from Direct Assay
more info
PubMed 
integral component of lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal lumen TAS
Traceable Author Statement
more info
 
lysosomal membrane HDA PubMed 
lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal membrane TAS
Traceable Author Statement
more info
PubMed 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 
multivesicular body IDA
Inferred from Direct Assay
more info
PubMed 
multivesicular body TAS
Traceable Author Statement
more info
PubMed 
multivesicular body membrane NAS
Non-traceable Author Statement
more info
PubMed 
neuron projection IDA
Inferred from Direct Assay
more info
PubMed 
neuronal cell body IDA
Inferred from Direct Assay
more info
PubMed 
transport vesicle IDA
Inferred from Direct Assay
more info
PubMed 
vesicle IDA
Inferred from Direct Assay
more info
PubMed 
vesicle membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
cation-transporting ATPase 13A2
Names
ATPase 13A2
ATPase type 13A2
probable cation-transporting ATPase 13A2
NP_001135445.1
NP_001135446.1
NP_071372.1
XP_005245867.1
XP_005245868.1
XP_005245869.1
XP_005245872.1
XP_006710575.1
XP_006710576.1
XP_011539430.1
XP_011539431.1
XP_016856333.1
XP_016856334.1
XP_016856335.1
XP_016856336.1
XP_016856337.1
XP_016856338.1
XP_016856339.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009054.1 RefSeqGene

    Range
    5001..30971
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001141973.2NP_001135445.1  cation-transporting ATPase 13A2 isoform 2

    See identical proteins and their annotated locations for NP_001135445.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 2). The transcript contains an upstream ORF that could encode a 103aa protein and may modulate translation from the downstream ORF encoding isoform 2.
    Source sequence(s)
    AK290210, AL354615, BC030267, BC034575, HY024349
    Consensus CDS
    CCDS44073.1
    UniProtKB/Swiss-Prot
    Q9NQ11
    UniProtKB/TrEMBL
    Q8N4D4
    Related
    ENSP00000413307.1, OTTHUMP00000221711, ENST00000452699.5, OTTHUMT00000368161
    Conserved Domains (5) summary
    COG4087
    Location:845894
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391112
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:258493
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39169
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:623659
    Cation_ATPase; Cation transport ATPase (P-type)
  2. NM_001141974.2NP_001135446.1  cation-transporting ATPase 13A2 isoform 3

    See identical proteins and their annotated locations for NP_001135446.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, and lacks two alternate exons in the 3' coding region which results in a frameshift, compared to variant 1. The resulting protein (isoform 3) is shorter and has a distinct C-terminus, compared to isoform 1. The transcript contains an upstream ORF that could encode a 103aa protein and may modulate translation from the downstream ORF encoding isoform 3.
    Source sequence(s)
    AK075310, BC030267, BC034575, HY024349
    Consensus CDS
    CCDS44072.1
    UniProtKB/Swiss-Prot
    Q9NQ11
    UniProtKB/TrEMBL
    Q8N4D4, Q8NBS1
    Related
    ENSP00000341115.5, OTTHUMP00000002400, ENST00000341676.9, OTTHUMT00000006618
    Conserved Domains (5) summary
    COG4087
    Location:806855
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391034
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:258493
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39169
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:623659
    Cation_ATPase; Cation transport ATPase (P-type)
  3. NM_022089.3NP_071372.1  cation-transporting ATPase 13A2 isoform 1

    See identical proteins and their annotated locations for NP_071372.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). The transcript contains an upstream ORF that could encode a 103aa protein and may modulate translation from the downstream ORF encoding isoform 1.
    Source sequence(s)
    AL354615, BC030267, HY024349
    Consensus CDS
    CCDS175.1
    UniProtKB/Swiss-Prot
    Q9NQ11
    Related
    ENSP00000327214.8, OTTHUMP00000002399, ENST00000326735.12, OTTHUMT00000006617
    Conserved Domains (5) summary
    COG4087
    Location:850899
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391117
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:263498
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39174
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:628664
    Cation_ATPase; Cation transport ATPase (P-type)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    16985958..17011972 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006710512.1XP_006710575.1  cation-transporting ATPase 13A2 isoform X4

    Conserved Domains (5) summary
    COG4087
    Location:844893
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391072
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:257492
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39168
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:622658
    Cation_ATPase; Cation transport ATPase (P-type)
  2. XM_017000845.1XP_016856334.1  cation-transporting ATPase 13A2 isoform X8

  3. XM_006710513.1XP_006710576.1  cation-transporting ATPase 13A2 isoform X6

    Conserved Domains (5) summary
    COG4087
    Location:836885
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391064
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:249484
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39169
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:614650
    Cation_ATPase; Cation transport ATPase (P-type)
  4. XM_017000846.1XP_016856335.1  cation-transporting ATPase 13A2 isoform X9

  5. XM_017000849.1XP_016856338.1  cation-transporting ATPase 13A2 isoform X13

  6. XM_005245811.1XP_005245868.1  cation-transporting ATPase 13A2 isoform X2

    Conserved Domains (5) summary
    COG4087
    Location:845894
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391073
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:258493
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39169
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:623659
    Cation_ATPase; Cation transport ATPase (P-type)
  7. XM_017000847.1XP_016856336.1  cation-transporting ATPase 13A2 isoform X10

  8. XM_005245810.1XP_005245867.1  cation-transporting ATPase 13A2 isoform X1

    Conserved Domains (5) summary
    COG4087
    Location:849898
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391077
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:262497
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39114
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:627663
    Cation_ATPase; Cation transport ATPase (P-type)
  9. XM_005245812.1XP_005245869.1  cation-transporting ATPase 13A2 isoform X5

    Conserved Domains (5) summary
    COG4087
    Location:841890
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391069
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:254489
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39174
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:619655
    Cation_ATPase; Cation transport ATPase (P-type)
  10. XM_011541128.1XP_011539430.1  cation-transporting ATPase 13A2 isoform X3

    Conserved Domains (5) summary
    COG4087
    Location:845894
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391073
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:263498
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39174
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:623659
    Cation_ATPase; Cation transport ATPase (P-type)
  11. XM_017000844.1XP_016856333.1  cation-transporting ATPase 13A2 isoform X7

  12. XM_011541129.1XP_011539431.1  cation-transporting ATPase 13A2 isoform X14

    Conserved Domains (5) summary
    COG4087
    Location:781830
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391009
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:263498
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39174
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:559595
    Cation_ATPase; Cation transport ATPase (P-type)
  13. XM_017000850.1XP_016856339.1  cation-transporting ATPase 13A2 isoform X15

  14. XM_005245815.1XP_005245872.1  cation-transporting ATPase 13A2 isoform X11

    Conserved Domains (5) summary
    COG4087
    Location:811860
    COG4087; Soluble P-type ATPase [General function prediction only]
    TIGR01657
    Location:391039
    P-ATPase-V; P-type ATPase of unknown pump specificity (type V)
    pfam00122
    Location:263498
    E1-E2_ATPase; E1-E2 ATPase
    pfam12409
    Location:39174
    P5-ATPase; P5-type ATPase cation transporter
    pfam13246
    Location:628664
    Cation_ATPase; Cation transport ATPase (P-type)
  15. XM_017000848.1XP_016856337.1  cation-transporting ATPase 13A2 isoform X12

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