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.	492
Gene name Gene Name - the full gene name approved by the HGNC.	ATPase plasma membrane Ca2+ transporting 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	ATP2B3
Synonyms (NCBI Gene) Gene synonyms aliases	CFAP39, CLA2, OPCA, PMCA3, PMCA3a, SCAX1
Disease Acronyms (UniProt) Disease acronyms from UniProt database	SCAX1
Chromosome Chromosome number	X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	Xq28
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene belongs to the family of P-type primary ion transport ATPases characterized by the formation of an aspartyl phosphate intermediate during the reaction cycle. These enzymes remove bivalent calcium ions from eukaryotic cells

Show/Hide all(8)

SNP ID	Visualize variation	Clinical significance	Consequence
rs150989590	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, coding sequence variant
rs368215361	C>G,T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs397514619	G>A	Likely-pathogenic, pathogenic	Non coding transcript variant, missense variant, coding sequence variant
rs724160009	GCTGGT>-	Pathogenic	Non coding transcript variant, inframe deletion, coding sequence variant
rs724160011	CTGGTC>-	Pathogenic	Non coding transcript variant, inframe deletion, coding sequence variant
rs724160012	TCGTGG>-	Pathogenic	Non coding transcript variant, inframe deletion, coding sequence variant
rs782596945	G>A,T	Pathogenic	Synonymous variant, genic downstream transcript variant, missense variant, 3 prime UTR variant, coding sequence variant, non coding transcript variant
rs1603040061	C>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant

Show/Hide all(54)

miRTarBase ID	miRNA	Experiments	Reference
MIRT645896	hsa-miR-5193	HITS-CLIP	23824327
MIRT645897	hsa-miR-660-3p	HITS-CLIP	23824327
MIRT645895	hsa-miR-877-3p	HITS-CLIP	23824327
MIRT645894	hsa-miR-1236-3p	HITS-CLIP	23824327
MIRT645893	hsa-miR-3909	HITS-CLIP	23824327
MIRT645892	hsa-miR-6852-3p	HITS-CLIP	23824327
MIRT645891	hsa-miR-4691-5p	HITS-CLIP	23824327
MIRT645889	hsa-miR-6792-3p	HITS-CLIP	23824327
MIRT645890	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT645888	hsa-miR-6881-3p	HITS-CLIP	23824327
MIRT645887	hsa-miR-676-3p	HITS-CLIP	23824327
MIRT645886	hsa-miR-670-3p	HITS-CLIP	23824327
MIRT645885	hsa-miR-1238-3p	HITS-CLIP	23824327
MIRT645884	hsa-miR-2355-3p	HITS-CLIP	23824327
MIRT645896	hsa-miR-5193	HITS-CLIP	23824327
MIRT645897	hsa-miR-660-3p	HITS-CLIP	23824327
MIRT645895	hsa-miR-877-3p	HITS-CLIP	23824327
MIRT645894	hsa-miR-1236-3p	HITS-CLIP	23824327
MIRT645893	hsa-miR-3909	HITS-CLIP	23824327
MIRT645892	hsa-miR-6852-3p	HITS-CLIP	23824327
MIRT645891	hsa-miR-4691-5p	HITS-CLIP	23824327
MIRT645889	hsa-miR-6792-3p	HITS-CLIP	23824327
MIRT645890	hsa-miR-6749-3p	HITS-CLIP	23824327
MIRT645888	hsa-miR-6881-3p	HITS-CLIP	23824327
MIRT645887	hsa-miR-676-3p	HITS-CLIP	23824327
MIRT645886	hsa-miR-670-3p	HITS-CLIP	23824327
MIRT645885	hsa-miR-1238-3p	HITS-CLIP	23824327
MIRT645884	hsa-miR-2355-3p	HITS-CLIP	23824327
MIRT807664	hsa-miR-3144-3p	CLIP-seq
MIRT807665	hsa-miR-3187-3p	CLIP-seq
MIRT807666	hsa-miR-4435	CLIP-seq
MIRT807667	hsa-miR-455-5p	CLIP-seq
MIRT807668	hsa-miR-4643	CLIP-seq
MIRT807669	hsa-miR-4701-5p	CLIP-seq
MIRT807670	hsa-miR-4733-3p	CLIP-seq
MIRT807671	hsa-miR-548s	CLIP-seq
MIRT807672	hsa-miR-588	CLIP-seq
MIRT807673	hsa-miR-764	CLIP-seq
MIRT807674	hsa-miR-875-5p	CLIP-seq
MIRT807675	hsa-miR-296-5p	CLIP-seq
MIRT807676	hsa-miR-3918	CLIP-seq
MIRT2177846	hsa-miR-105	CLIP-seq
MIRT2177847	hsa-miR-1266	CLIP-seq
MIRT2177848	hsa-miR-3667-3p	CLIP-seq
MIRT2177849	hsa-miR-3682-5p	CLIP-seq
MIRT2177850	hsa-miR-4279	CLIP-seq
MIRT2177851	hsa-miR-4518	CLIP-seq
MIRT807667	hsa-miR-455-5p	CLIP-seq
MIRT2177852	hsa-miR-4659a-3p	CLIP-seq
MIRT2177853	hsa-miR-4659b-3p	CLIP-seq
MIRT2177854	hsa-miR-4778-3p	CLIP-seq
MIRT2177855	hsa-miR-767-3p	CLIP-seq
MIRT2177856	hsa-miR-942	CLIP-seq
MIRT2384618	hsa-miR-3121-5p	CLIP-seq

Show/Hide all(27)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005388	Function	Calcium transmembrane transporter activity, phosphorylative mechanism	IBA	21873635
GO:0005515	Function	Protein binding	IPI	18029012
GO:0005516	Function	Calmodulin binding	IEA
GO:0005524	Function	ATP binding	IEA
GO:0005886	Component	Plasma membrane	IDA	18029012
GO:0005886	Component	Plasma membrane	TAS
GO:0005887	Component	Integral component of plasma membrane	IBA	21873635
GO:0006874	Process	Cellular calcium ion homeostasis	IBA	21873635
GO:0015085	Function	Calcium ion transmembrane transporter activity	IDA	18029012
GO:0019829	Function	ATPase-coupled cation transmembrane transporter activity	IBA	21873635
GO:0030165	Function	PDZ domain binding	IBA	21873635
GO:0034220	Process	Ion transmembrane transport	TAS
GO:0043231	Component	Intracellular membrane-bounded organelle	IBA	21873635
GO:0046872	Function	Metal ion binding	IEA
GO:0051480	Process	Regulation of cytosolic calcium ion concentration	IBA	21873635
GO:0051480	Process	Regulation of cytosolic calcium ion concentration	IDA	18029012
GO:0098793	Component	Presynapse	IEA
GO:0098978	Component	Glutamatergic synapse	IDA	18029012
GO:0098978	Component	Glutamatergic synapse	IMP	18029012
GO:0098982	Component	GABA-ergic synapse	IDA	18029012
GO:0098982	Component	GABA-ergic synapse	IMP	18029012
GO:0099509	Process	Regulation of presynaptic cytosolic calcium ion concentration	IEA
GO:1903561	Component	Extracellular vesicle	HDA	24769233
GO:1903779	Process	Regulation of cardiac conduction	TAS
GO:1905056	Function	Calcium-transporting ATPase activity involved in regulation of presynaptic cytosolic calcium ion concentration	IDA	18029012
GO:1905056	Function	Calcium-transporting ATPase activity involved in regulation of presynaptic cytosolic calcium ion concentration	IMP	18029012
GO:1990034	Process	Calcium ion export across plasma membrane	IDA	18029012

MIM	HGNC	e!Ensembl
300014	816	ENSG00000067842

Protein

UniProt ID

Q16720

Protein name

Plasma membrane calcium-transporting ATPase 3 (PMCA3) (EC 7.2.2.10) (Plasma membrane calcium ATPase isoform 3) (Plasma membrane calcium pump isoform 3)

Protein function

ATP-driven Ca(2+) ion pump involved in the maintenance of basal intracellular Ca(2+) levels at the presynaptic terminals (PubMed:18029012, PubMed:22912398, PubMed:25953895, PubMed:27035656). Uses ATP as an energy source to transport cytosolic Ca

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00690	Cation_ATPase_N	51 → 121	Cation transporter/ATPase, N-terminus	Domain
PF00122	E1-E2_ATPase	190 → 306		Family
PF00122	E1-E2_ATPase	341 → 451		Family
PF13246	Cation_ATPase	516 → 612		Family
PF00689	Cation_ATPase_C	876 → 1058	Cation transporting ATPase, C-terminus	Family
PF12424	ATP_Ca_trans_C	1100 → 1146	Plasma membrane calcium transporter ATPase C terminal	Family

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in the cerebellum (PubMed:8187550). Expressed in adrenal glands (PubMed:27035656). {ECO:0000269|PubMed:27035656, ECO:0000269|PubMed:8187550}.

Sequence

MGDMANSSIEFHPKPQQQRDVPQAGGFGCTLAELRTLMELRGAEALQKIEEAYGDVSGLC
RRLKTSPTEGLADNTNDLEKRRQIYGQNFIPPKQPKTFLQLVWEALQDVTLIILEVAAIV
SLGLSFYAPPGEESEACGNVSGGAEDEGEAEAGWIEGAAILLSVICVVLVTAFNDWSKEK
QFRGLQSRIEQEQKFTVIRNGQLLQVPVAALVVGDIAQVKYGDLLPADGVLIQANDLKID
ESSLTGESDHVRKSADKDPMLLSGTHVMEGSGRMVVTAVGVNSQTGIIFTLLGAGGEEEE
KKDKKGKQQDGAMESSQTKAKKQDGAVAMEMQPLKSAEGGEMEEREKKKANAPKKEKSVL
QGKLTKLAVQIGKAGLVMSAITVIILVLYFVIETFVVEGRTWLAECTPVYVQYFVKFFII
GVTVLVVAVPEGLPLAVTISLAYSVKKMMKDNNLVRHLDACETMGNATAICSDKTGTLTT
NRMTVVQSYLGDTHYKEIPAPSALTPKILDLLVHAISINSAYTTKILPPEKEGALPRQVG
NKTECALLGFVLDLKRDFQPVREQIPEDKLYKVYTFNSVRKSMSTVIRMPDGGFRLFSKG
ASEILLKKCTNILNSNGELRGFRPRDRDDMVRKIIEPMACDGLRTICIAYRDFSAGQEPD
WDNENEVVGDLTCIAVVGIEDPVRPEVPEAIRKCQRAGITVRMVTGDNINTARAIAAKCG
IIQPGEDFLCLEGKEFNRRIRNEKGEIEQERLDKVWPKLRVLARSSPTDKHTLVKGIIDS
TTGEQRQVVAVTGDGTNDGPALKKADVGFAMGIAGTDVAKEASDIILTDDNFTSIVKAVM
WGRNVYDSISKFLQFQLTVNVVAVIVAFTGACITQDSPLKAVQMLWVNLIMDTFASLALA
TEPPTESLLLRKPYGRDKPLISRTMMKNILGHAVYQLAIIFTLLFVGELFFDIDSGRNAP
LHSPPSEHYTIIFNTFVMMQLFNEINARKIHGERNVFDGIFSNPIFCTIVLGTFGIQIVI
VQFGGKPFSCSPLSTEQWLWCLFVGVGELVWGQVIATIPTSQLKCLKEAGHGPGKDEMTD
EELAEGEEEIDHAERELRRGQILWFRGLNRIQTQIRVVKAFRSSLYEGLEKPESKTSIHN
FMATPEFLINDYTHNIPLIDDTDVDENEERLRAPPPPSPNQNNNAIDSGIYLTTHVTKSA
TSSVFSSSPGSPLHSVETSL

Sequence length

1220

Interactions

View interactions

	KEGG		Reactome
	Calcium signaling pathway cGMP-PKG signaling pathway cAMP signaling pathway Adrenergic signaling in cardiomyocytes Aldosterone synthesis and secretion Endocrine and other factor-regulated calcium reabsorption Salivary secretion Pancreatic secretion Mineral absorption		Reduction of cytosolic Ca++ levels Ion homeostasis Ion transport by P-type ATPases

Show/Hide Causal Diseases (8)

Disease term	Disease name	dbSNP ID	References
Causal
Hyperaldosteronism	NON RARE IN EUROPE: Aldosterone-producing adenoma, Hyperaldosteronism	rs28934586, rs104894068, rs387906778, rs386352319, rs587777437, rs587777438, rs587777439, rs786205050, rs771507094, rs1085307938, rs1553853557, rs1553856214, rs1293789661, rs1553857113, rs758379595	23416519
Aldosterone-producing adrenal cortex adenoma	Aldosterone-Producing Adrenal Cortex Adenoma	rs724160008, rs11540945, rs724160010, rs724160009, rs724160011, rs724160012
Cerebellar ataxia, x-linked	X-linked non progressive cerebellar ataxia	rs397514619, rs782596945
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291 View all (32 more)
Hypertension	Hypertensive disease	rs13306026	23416519
Hypotonia	Neonatal Hypotonia	rs141138948, rs397517172, rs869312824, rs1583169151
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Spinocerebellar ataxia, x-linked	SPINOCEREBELLAR ATAXIA, X-LINKED 1	rs797044558	22912398

Show/Hide Unknown Diseases (1)

Disease term	Disease name	Evidence	References	Source
Unknown
Cerebellar Ataxia, X-Linked	X-linked non progressive cerebellar ataxia			GenCC

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text Mining
ACTH Secreting Pituitary Adenoma	Associate	26743443
Adenoma	Associate	31000732
Adrenocortical Adenoma	Associate	31789380
Aphasia Broca	Associate	28807751
Ataxia	Associate	27632770, 28807751, 36207321
Cerebellar Ataxia	Associate	22912398, 25953895, 27632770, 28807751, 36207321
Congenital disorder of glycosylation type 1A	Associate	28807751
Cushing Syndrome	Associate	26743443
Developmental Disabilities	Associate	25953895
Fetal akinesia syndrome X linked	Associate	31680123
Genetic Diseases Inborn	Associate	25953895
Hearing Loss	Associate	36207321
Hearing Loss Unilateral	Associate	40302475
Hyperaldosteronism	Associate	24082052, 24866132, 25906099, 26066391, 26252618, 26351028, 26743443, 26807823, 27729216, 30085035, 30739536, 31000732, 32002807, 32516371, 33677921, 33796077, 40302475 View all (2 more)
Hypersensitivity Delayed	Associate	36207321
Muscle Hypotonia	Associate	25953895, 28807751
Neoplasms	Associate	26252618, 31000732
Neurologic Manifestations	Associate	25953895
Nystagmus Pathologic	Associate	28807751

ATP2B3 (ATPase plasma membrane Ca2+ transporting 3)