Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	23400
Gene name Gene Name - the full gene name approved by the HGNC.	ATPase cation transporting 13A2
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	ATP13A2
Synonyms (NCBI Gene) Gene synonyms aliases	CLN12, HSA9947, KRPPD, PARK9, SPG78
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p36.13
Summary Summary of gene provided in NCBI Entrez Gene.	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

Show/Hide all(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
rs144557304	C>A,T	Likely-benign, uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs144701072	C>T	Pathogenic	Coding sequence variant, missense variant
rs144708504	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs145515028	G>A	Conflicting-interpretations-of-pathogenicity, not-provided	Coding sequence variant, missense variant
rs149372969	G>A,C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs150519745	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs199624796	G>A	Pathogenic	Missense variant, coding sequence variant
rs200587951	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant
rs369863178	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant, missense variant, coding sequence variant
rs372993383	C>G,T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs373607247	C>A,G,T	Pathogenic, uncertain-significance	Coding sequence variant, missense variant, stop gained
rs377253172	C>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, coding sequence variant, intron variant
rs587776890	AA>-	Pathogenic	Coding sequence variant, frameshift variant
rs587777053	A>C	Pathogenic	Coding sequence variant, missense variant
rs749798211	CTGGGGAAGCAGG>-	Uncertain-significance, pathogenic	Splice acceptor variant, coding sequence variant, intron variant
rs758014228	A>C	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Splice donor variant, intron variant
rs759020707	T>A,G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs762033589	->CT	Pathogenic	Frameshift variant, coding sequence variant
rs765632065	G>-	Pathogenic-likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs773246271	G>A	Pathogenic	Stop gained, coding sequence variant
rs786205056	C>T	Pathogenic	Intron variant
rs866035312	G>A	Pathogenic	Coding sequence variant, intron variant, stop gained
rs1057519289	G>A	Pathogenic	Stop gained, missense variant, coding sequence variant
rs1057519290	AGA>-	Pathogenic	Inframe deletion, coding sequence variant
rs1057519291	G>A	Pathogenic	Missense variant, intron variant, coding sequence variant
rs1057519292	G>A	Pathogenic	Stop gained, coding sequence variant
rs1057519293	G>A	Pathogenic	Stop gained, coding sequence variant
rs1303653650	G>A	Pathogenic	Coding sequence variant, stop gained
rs1570759415	GA>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all(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

Show/Hide all(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
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	HDA	17897319
GO:0005765	Component	Lysosomal membrane	IDA	23499937, 26134396, 29505581
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005765	Component	Lysosomal membrane	TAS	25548531
GO:0005768	Component	Endosome	IEA
GO:0005770	Component	Late endosome	IDA	25392495
GO:0005771	Component	Multivesicular body	IDA	24603074, 25392495
GO:0005771	Component	Multivesicular body	TAS	25548531
GO:0005776	Component	Autophagosome	IDA	24603074
GO:0006874	Process	Intracellular calcium ion homeostasis	IBA
GO:0006874	Process	Intracellular calcium ion homeostasis	IDA	22186024
GO:0006879	Process	Intracellular iron ion homeostasis	IMP	26818499
GO:0006882	Process	Intracellular zinc ion homeostasis	IEA
GO:0006882	Process	Intracellular zinc ion homeostasis	IMP	24334770, 24603074
GO:0006914	Process	Autophagy	IEA
GO:0006914	Process	Autophagy	IMP	27278822
GO:0007041	Process	Lysosomal transport	IMP	31996848
GO:0008270	Function	Zinc ion binding	ISS	22361905, 23202360
GO:0008289	Function	Lipid binding	IEA
GO:0010628	Process	Positive regulation of gene expression	IMP	27278822
GO:0010821	Process	Regulation of mitochondrion organization	IBA
GO:0010821	Process	Regulation of mitochondrion organization	IDA	22186024
GO:0010821	Process	Regulation of mitochondrion organization	IEA
GO:0010821	Process	Regulation of mitochondrion organization	IMP	22198378
GO:0012506	Component	Vesicle membrane	IEA
GO:0015203	Function	Polyamine transmembrane transporter activity	IBA
GO:0015203	Function	Polyamine transmembrane transporter activity	IDA	31996848
GO:0015417	Function	ABC-type polyamine transporter activity	IEA
GO:0015662	Function	P-type ion transporter activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	16964263
GO:0016241	Process	Regulation of macroautophagy	IMP	22198378
GO:0016241	Process	Regulation of macroautophagy	TAS	22885599
GO:0016243	Process	Regulation of autophagosome size	IBA
GO:0016243	Process	Regulation of autophagosome size	IDA	22186024
GO:0016243	Process	Regulation of autophagosome size	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0016887	Function	ATP hydrolysis activity	NAS	24252804
GO:0019829	Function	ATPase-coupled monoatomic cation transmembrane transporter activity	IBA
GO:0019829	Function	ATPase-coupled monoatomic cation transmembrane transporter activity	IEA
GO:0019829	Function	ATPase-coupled monoatomic cation transmembrane transporter activity	TAS
GO:0030003	Process	Intracellular monoatomic cation homeostasis	TAS	25548531
GO:0030133	Component	Transport vesicle	IDA	22186024
GO:0030145	Function	Manganese ion binding	ISS	22361905, 23202360
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031902	Component	Late endosome membrane	IBA
GO:0031902	Component	Late endosome membrane	IDA	29505581
GO:0031902	Component	Late endosome membrane	IEA
GO:0031982	Component	Vesicle	IDA	24603074
GO:0032585	Component	Multivesicular body membrane	IEA
GO:0032585	Component	Multivesicular body membrane	NAS	24603074
GO:0033157	Process	Regulation of intracellular protein transport	NAS	24334770
GO:0034220	Process	Monoatomic ion transmembrane transport	TAS
GO:0034599	Process	Cellular response to oxidative stress	IEA
GO:0034599	Process	Cellular response to oxidative stress	IMP	26134396
GO:0034599	Process	Cellular response to oxidative stress	TAS	26392192
GO:0043005	Component	Neuron projection	IDA	22186024
GO:0043005	Component	Neuron projection	IEA
GO:0043025	Component	Neuronal cell body	IDA	22186024
GO:0043025	Component	Neuronal cell body	IEA
GO:0043202	Component	Lysosomal lumen	TAS
GO:0043523	Process	Regulation of neuron apoptotic process	ISS	23499937
GO:0046872	Function	Metal ion binding	IEA
GO:0050714	Process	Positive regulation of protein secretion	IMP	25392495
GO:0055088	Process	Lipid homeostasis	IMP	31132336
GO:0061462	Process	Protein localization to lysosome	IEA
GO:0061462	Process	Protein localization to lysosome	IMP	30538141
GO:0061909	Process	Autophagosome-lysosome fusion	IBA
GO:0061909	Process	Autophagosome-lysosome fusion	IEA
GO:0061909	Process	Autophagosome-lysosome fusion	IMP	30538141
GO:0070300	Function	Phosphatidic acid binding	IDA	26134396
GO:0071287	Process	Cellular response to manganese ion	IMP	22285144
GO:0071287	Process	Cellular response to manganese ion	TAS	23628791, 26392192
GO:0071294	Process	Cellular response to zinc ion	TAS	26392192
GO:0080025	Function	Phosphatidylinositol-3,5-bisphosphate binding	IDA	26134396
GO:0097734	Process	Extracellular exosome biogenesis	IMP	25392495
GO:0098655	Process	Monoatomic cation transmembrane transport	IEA
GO:0140358	Function	P-type transmembrane transporter activity	IEA
GO:1900180	Process	Regulation of protein localization to nucleus	IEA
GO:1900180	Process	Regulation of protein localization to nucleus	IMP	27278822
GO:1902047	Process	Polyamine transmembrane transport	IBA
GO:1902047	Process	Polyamine transmembrane transport	IDA	23205587
GO:1903135	Function	Cupric ion binding	ISS	23202360
GO:1903146	Process	Regulation of autophagy of mitochondrion	TAS	25548531
GO:1903543	Process	Positive regulation of exosomal secretion	IDA	24603074
GO:1903543	Process	Positive regulation of exosomal secretion	IEA
GO:1903543	Process	Positive regulation of exosomal secretion	IMP	25392495
GO:1903710	Process	Spermine transmembrane transport	IMP	31996848
GO:1904714	Process	Regulation of chaperone-mediated autophagy	TAS	22885599
GO:1905037	Process	Autophagosome organization	IDA	22186024
GO:1905165	Process	Regulation of lysosomal protein catabolic process	IEA
GO:1905165	Process	Regulation of lysosomal protein catabolic process	IGI	24334770
GO:1905165	Process	Regulation of lysosomal protein catabolic process	IMP	23499937
GO:1905166	Process	Negative regulation of lysosomal protein catabolic process	TAS	22885599

MIM	HGNC	e!Ensembl
610513	30213	ENSG00000159363

Protein

UniProt ID

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
PQSQAEDGRSQAAVGAVPEGAWKDTAQLHKSEEAVSVGQKRVLRYYLFQGQRYIWIETQQ
AFYQVSLLDHGRSCDDVHRSRHGLSLQDQMVRKAIYGPNVISIPVKSYPQLLVDEALNPY
YGFQAFSIALWLADHYYWYALCIFLISSISICLSLYKTRKQSQTLRDMVKLSMRVCVCRP
GGEEEWVDSSELVPGDCLVLPQEGGLMPCDAALVAGECMVNESSLTGESIPVLKTALPEG
LGPYCAETHRRHTLFCGTLILQARAYVGPHVLAVVTRTGFCTAKGGLVSSILHPRPINFK
FYKHSMKFVAALSVLALLGTIYSIFILYRNRVPLNEIVIRALDLVTVVVPPALPAAMTVC
TLYAQSRLRRQGIFCIHPLRINLGGKLQLVCFDKTGTLTEDGLDVMGVVPLKGQAFLPLV
PEPRRLPVGPLLRALATCHALSRLQDTPVGDPMDLKMVESTGWVLEEEPAADSAFGTQVL
AVMRPPLWEPQLQAMEEPPVPVSVLHRFPFSSALQRMSVVVAWPGATQPEAYVKGSPELV
AGLCNPETVPTDFAQMLQSYTAAGYRVVALASKPLPTVPSLEAAQQLTRDTVEGDLSLLG
LLVMRNLLKPQTTPVIQALRRTRIRAVMVTGDNLQTAVTVARGCGMVAPQEHLIIVHATH
PERGQPASLEFLPMESPTAVNGVKDPDQAASYTVEPDPRSRHLALSGPTFGIIVKHFPKL
LPKVLVQGTVFARMAPEQKTELVCELQKLQYCVGMCGDGANDCGALKAADVGISLSQAEA
SVVSPFTSSMASIECVPMVIREGRCSLDTSFSVFKYMALYSLTQFISVLILYTINTNLGD
LQFLAIDLVITTTVAVLMSRTGPALVLGRVRPPGALLSVPVLSSLLLQMVLVTGVQLGGY
FLTLAQPWFVPLNRTVAAPDNLPNYENTVVFSLSSFQYLILAAAVSKGAPFRRPLYTNVP
FLVALALLSSVLVGLVLVPGLLQGPLALRNITDTGFKLLLLGLVTLNFVGAFMLESVLDQ
CLPACLRRLRPKRASKKRFKQLERELAEQPWPPLPAGPLR

Sequence length

1180

Interactions

View interactions

	Reactome
			Ion transport by P-type ATPases

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Kufor-Rakeb Syndrome	kufor-rakeb syndrome	rs587776890, rs765632065, rs587777053, rs144701072, rs1057519289, rs786205056, rs2100817106, rs121918227, rs1057519292, rs762033589, rs1057519293	N/A
Spastic Paraplegia	autosomal recessive spastic paraplegia type 78	rs765632065, rs1057519289, rs773246271, rs1057519290, rs1057519291, rs1057519292, rs1057519293	N/A
neurodegeneration with brain iron accumulation	Neurodegeneration with brain iron accumulation	rs765632065, rs758014228, rs121918227	N/A

Show/Hide Text Mining Associations (50)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
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
Dystonia	Associate	20669327
Dystonia Dopa responsive	Associate	20669327
Frontotemporal Dementia	Associate	34382491
Genetic Diseases Inborn	Associate	20669327
Heredodegenerative Disorders Nervous System	Associate	20853184
Intellectual Disability	Associate	30250217
Intrauterine Growth Retardation Metaphyseal Dysplasia Adrenal Hypoplasia Congenita And Genital Anomalies	Associate	27217339
Iron Deficiencies	Associate	24361204
Kufor Rakeb syndrome	Associate	19085912, 19345671, 20853184, 21665991, 22117566, 22388936, 22743658, 22885599, 23522931, 24334770, 26134396, 27165006, 29966207, 31132336, 31588715 View all (5 more)
Leukemia Myeloid Acute	Associate	38022627
Lewy Body Disease	Associate	22647602, 22885599
Lewy Body Disease	Inhibit	24252509
Lung Neoplasms	Associate	26245297
Lysosomal Storage Diseases	Associate	22647602, 22885599, 24252509, 24334770, 31132336, 33799982
Meige Syndrome	Associate	22743658
Mental Disorders	Associate	31944623
Mitochondrial Diseases	Associate	24399444, 26134396
Motor Neuron Disease	Associate	40424855
Muscle Weakness	Associate	20669327, 28821231
Neoplasms	Associate	26245297
Neurodegenerative Diseases	Associate	22743658, 22847264, 27278822, 33799982, 34715014
Neuroferritinopathy	Associate	22743658, 35180557
Neuronal Ceroid Lipofuscinoses	Associate	22388936, 22847264, 27217339, 31132336, 31588715
Neurotoxicity Syndromes	Associate	22285144
Pallidopyramidal syndrome	Associate	20669327, 20853184, 24361204
Pantothenate Kinase Associated Neurodegeneration	Associate	22743658, 28821231, 39419454
Paraplegia	Associate	27217339, 31944623
Parkinson Disease	Associate	19085912, 22388936, 22457822, 22623900, 22647602, 22885599, 24252509, 24399444, 24742361, 25374329, 26134396, 26245297, 27217339, 27278822, 29966207 View all (17 more)
Parkinson Disease	Stimulate	35173238
Parkinson Disease Secondary	Associate	19087301, 19097176, 19345671, 20669327, 20853184, 21665991, 22285144, 22388936, 22457822, 22885599, 23628791, 24334770, 27278822, 28131822, 30237140, 31132336, 31588715, 33799982 View all (3 more)
Parkinsonian Disorders	Associate	19097176, 20853184, 21665991, 22117566, 22623900, 22647602, 22743658, 22847264
Parkinsonism Dystonia Infantile	Associate	22743658
Polyneuropathies	Associate	31588715
Seizures	Associate	31944623
Spastic Paraplegia Hereditary	Associate	20669327, 27165006, 31132336, 31588715, 31944623
Stroke	Associate	36065636
Supranuclear Palsy Progressive	Associate	20853184
Synucleinopathies	Associate	31097622, 33046546
Wallerian degeneration of the pyramidal tract	Associate	22885599
Zinc Deficiency Neonatal due to Low Breast Milk Zinc	Associate	24399444

ATP13A2 (ATPase cation transporting 13A2)