Gene Gene information from NCBI Gene database.
Entrez ID 23400
Gene name ATPase cation transporting 13A2
Gene symbol ATP13A2
Synonyms (NCBI Gene)
CLN12HSA9947KRPPDPARK9SPG78
Chromosome 1
Chromosome location 1p36.13
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 v
SNPs SNP information provided by dbSNP.
34
SNP ID Visualize variation Clinical significance Consequence
rs55943100 C>G Conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant
rs112549590 T>C Conflicting-interpretations-of-pathogenicity Intron variant
rs115985012 G>A Conflicting-interpretations-of-pathogenicity, likely-benign Synonymous variant, intron variant, coding sequence variant
rs121918227 C>G Pathogenic Missense variant, coding sequence variant
rs138546275 C>T Conflicting-interpretations-of-pathogenicity Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
3
miRTarBase ID miRNA Experiments Reference
MIRT041277 hsa-miR-193b-3p CLASH 23622248
MIRT039758 hsa-miR-615-3p CLASH 23622248
MIRT806646 hsa-miR-2681 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
100
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0000421 Component Autophagosome membrane IEA
GO:0005515 Function Protein binding IPI 22645275, 27278822
GO:0005524 Function ATP binding IEA
GO:0005764 Component Lysosome IDA 16964263, 21542062, 24603074, 25392495
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
610513 30213 ENSG00000159363
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9NQ11
Protein name Polyamine-transporting ATPase 13A2 (EC 7.6.2.-)
Protein function ATPase which acts as a lysosomal polyamine exporter with high affinity for spermine (PubMed:31996848). Also stimulates cellular uptake of polyamines and protects against polyamine toxicity (PubMed:31996848). Plays a role in intracellular cation
PDB 7FJM , 7FJP , 7FJQ , 7M5V , 7M5X , 7M5Y , 7N70 , 7N72 , 7N73 , 7N74 , 7N75 , 7N76 , 7N77 , 7N78 , 7VPI , 7VPJ , 7VPK , 7VPL , 8IEK , 8IEL , 8IEM , 8IEN , 8IEO , 8IER , 8IES
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF12409 P5-ATPase 31 176 P5-type ATPase cation transporter Family
PF00122 E1-E2_ATPase 290 491 Family
PF00702 Hydrolase 507 788 Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in brain; protein levels are markedly increased in brain from subjects with Parkinson disease and subjects with dementia with Lewy bodies. Detected in pyramidal neurons located throughout the cingulate cortex (at protein leve
Sequence
MSADSSPLVGSTPTGYGTLTIGTSIDPLSSSVSSVRLSGYCGSPWRVIGYHVVVWMMAGI
PLLLFRWKPLWGVRLRLRPCNLAHAETLVIEIRDKEDSSWQLFTVQVQTEAIGEGSLEPS
PQSQAEDGRSQAAVGAVPEGAWKDTAQLHKSEEAVSVGQKRVLRYYLFQGQRYIWI
ETQQ
AFYQVSLLDHGRSCDDVHRSRHGLSLQDQMVRKAIYGPNVISIPVKSYPQLLVDEALNPY
YGFQAFSIALWLADHYYWYALCIFLISSISICLSLYKTRKQSQTLRDMVKLSMRVCVCRP
GGEEEWVDSSELVPGDCLVLPQEGGLMPCDAALVAGECMVNESSLTGESIPVLKTALPEG
LGPYCAETHRRHTLFCGTLILQARAYVGPHVLAVVTRTGFCTAKGGLVSSILHPRPINFK
FYKHSMKFVAALSVLALLGTIYSIFILYRNRVPLNEIVIRALDLVTVVVPPALPAAMTVC
TLYAQSRLRRQ
GIFCIHPLRINLGGKLQLVCFDKTGTLTEDGLDVMGVVPLKGQAFLPLV
PEPRRLPVGPLLRALATCHALSRLQDTPVGDPMDLKMVESTGWVLEEEPAADSAFGTQVL
AVMRPPLWEPQLQAMEEPPVPVSVLHRFPFSSALQRMSVVVAWPGATQPEAYVKGSPELV
AGLCNPETVPTDFAQMLQSYTAAGYRVVALASKPLPTVPSLEAAQQLTRDTVEGDLSLLG
LLVMRNLLKPQTTPVIQALRRTRIRAVMVTGDNLQTAVTVARGCGMVAPQEHLIIVHATH
PERGQPAS
LEFLPMESPTAVNGVKDPDQAASYTVEPDPRSRHLALSGPTFGIIVKHFPKL
LPKVLVQGTVFARMAPEQKTELVCELQKLQYCVGMCGDGANDCGALKAADVGISLSQAEA
SVVSPFTSSMASIECVPMVIREGRCSLDTSFSVFKYMALYSLTQFISVLILYTINTNLGD
LQFLAIDLVITTTVAVLMSRTGPALVLGRVRPPGALLSVPVLSSLLLQMVLVTGVQLGGY
FLTLAQPWFVPLNRTVAAPDNLPNYENTVVFSLSSFQYLILAAAVSKGAPFRRPLYTNVP
FLVALALLSSVLVGLVLVPGLLQGPLALRNITDTGFKLLLLGLVTLNFVGAFMLESVLDQ
CLPACLRRLRPKRASKKRFKQLERELAEQPWPPLPAGPLR
Sequence length 1180
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Ion transport by P-type ATPases
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
1895
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
ATP13A2-related disorder Pathogenic rs2523962293 RCV004550586
Autosomal recessive spastic paraplegia type 78 Likely pathogenic; Pathogenic rs776448394, rs2076751251, rs1557666781, rs2100768788, rs2076949269, rs2077109424, rs2101042002, rs2100785804, rs771581490, rs1377055875, rs2100783138, rs1483668823, rs786205056, rs121918227, rs758150853
View all (38 more)
RCV001863238
RCV001333123
RCV001388838
RCV001388839
RCV003771646
RCV005863478
RCV001808130
RCV001809240
RCV002038991
RCV001871476
RCV002014056
RCV001952943
RCV001851532
RCV001851533
RCV003098114
RCV002509909
RCV003079000
RCV002599306
RCV003115622
RCV002711920
RCV002819487
RCV002819521
RCV002834461
RCV002847354
RCV002847403
RCV002866471
RCV002913788
RCV002899793
RCV002943346
RCV003023466
RCV003037983
RCV003778207
RCV004556871
RCV003782265
RCV003783169
RCV003788419
RCV003803387
RCV003817903
RCV000415542
RCV000415585
RCV000415515
RCV000415546
RCV000415578
RCV001201356
RCV000762864
RCV002532645
RCV003767821
RCV000702718
RCV000818226
RCV001066185
RCV001059802
RCV001095688
RCV001095707
RCV001262240
Kufor-Rakeb syndrome Likely pathogenic; Pathogenic rs776448394, rs1557666781, rs2100768788, rs2076949269, rs771581490, rs1377055875, rs2100783138, rs1483668823, rs786205056, rs2100817106, rs121918227, rs758150853, rs2523637901, rs1389678247, rs2523608853
View all (39 more)
RCV001331222
RCV001388838
RCV001388839
RCV003771646
RCV002038991
RCV001871476
RCV002014056
RCV001952943
RCV000001278
RCV000001279
RCV000001280
RCV003098114
RCV002467405
RCV003079000
RCV002599306
RCV003115622
RCV002711920
RCV002819487
RCV002819521
RCV002834461
RCV002847354
RCV002847403
RCV002866471
RCV002913788
RCV002899793
RCV002943346
RCV003023466
RCV003037983
RCV003234628
RCV003314298
RCV003340702
RCV003778207
RCV003782265
RCV003783169
RCV003788419
RCV003803387
RCV003817903
RCV002502449
RCV004767251
RCV004767252
RCV000023818
RCV000023819
RCV000541447
RCV000762864
RCV002532645
RCV003767821
RCV000702718
RCV000818226
RCV000056335
RCV000056336
RCV001066185
RCV001059802
RCV001095688
RCV001095707
RCV002480876
Neurodegeneration with brain iron accumulation Likely pathogenic; Pathogenic rs121918227, rs2522710840, rs1334843918, rs1412349209, rs2523268622, rs765632065, rs758014228 RCV004766975
RCV002510343
RCV003111604
RCV003226841
RCV004701061
RCV001844194
RCV001269095
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Acute myeloid leukemia Likely benign; Benign; Uncertain significance rs140087527, rs61739752, rs55979991, rs74058364 RCV005919098
RCV005887956
RCV005896783
RCV005912126
ATPase cation transporting 13A2 related juvenile neuronal ceroid lipofuscinosis Conflicting classifications of pathogenicity rs55708915 RCV003483485
Cervical cancer Benign; Likely benign rs61739752, rs56367069, rs55979991 RCV005887958
RCV005887966
RCV005896785
Cholangiocarcinoma Benign rs2076604 RCV005922087
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Alcohol Related Disorders Associate 20669327
Amyotrophic Lateral Sclerosis Associate 40424855
Ataxia Associate 22285144, 31588715
Basal Ganglia Diseases Associate 31944623
Carcinoma Non Small Cell Lung Associate 26245297
Cataract Age Related Nuclear Associate 32337810
Cognition Disorders Associate 20853184, 22117566
Dementia Associate 21665991, 22885599, 24334770
Drug Related Side Effects and Adverse Reactions Associate 19345671, 22847264, 23628791, 24742361, 26134396
Drug Related Side Effects and Adverse Reactions Inhibit 24252509