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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	27032
Gene name	ATPase secretory pathway Ca2+ transporting 1
Gene symbol	ATP2C1
Synonyms (NCBI Gene)	ATP2C1ABCPMHHDPMR1SPCA1hSPCA1
Chromosome	3
Chromosome location	3q22.1
Summary	The protein encoded by this gene belongs to the family of P-type cation transport ATPases. This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium ions. Defects in this gene cause Hailey-Hailey disease, an aut

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SNP ID	Visualize variation	Clinical significance	Consequence
rs137853012	G>A	Pathogenic	Missense variant, coding sequence variant
rs137853013	C>G,T	Pathogenic	Stop gained, missense variant, coding sequence variant
rs137853014	G>T	Pathogenic	Missense variant, coding sequence variant
rs137853015	T>C	Pathogenic	Missense variant, coding sequence variant
rs776982434	C>G,T	Pathogenic	Coding sequence variant, missense variant, stop gained, genic upstream transcript variant
rs963144528	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1048609704	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1057517706	TTGT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1057518594	->A	Pathogenic	Frameshift variant, coding sequence variant
rs1057520634	C>T	Pathogenic	Stop gained, coding sequence variant
rs1131691355	->AA	Pathogenic	Frameshift variant, coding sequence variant
rs1553767857	G>-	Pathogenic	Frameshift variant, genic upstream transcript variant, coding sequence variant
rs1553775581	T>-	Pathogenic	Frameshift variant, coding sequence variant
rs1559971447	->CCTC	Pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant
rs1559982055	G>A	Pathogenic	Splice acceptor variant
rs1560033613	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1576976863	GT>-	Pathogenic	Frameshift variant, coding sequence variant

153

Show/Hide all (153)

miRTarBase ID	miRNA	Experiments	Reference
MIRT040808	hsa-miR-18a-3p	CLASH	23622248
MIRT807876	hsa-miR-3120-3p	CLIP-seq
MIRT807877	hsa-miR-3910	CLIP-seq
MIRT807878	hsa-miR-4708-3p	CLIP-seq
MIRT807879	hsa-miR-4729	CLIP-seq
MIRT807880	hsa-miR-4786-3p	CLIP-seq
MIRT807881	hsa-miR-4789-5p	CLIP-seq
MIRT807882	hsa-miR-1914	CLIP-seq
MIRT807883	hsa-miR-3545-5p	CLIP-seq
MIRT807884	hsa-miR-3660	CLIP-seq
MIRT807885	hsa-miR-4526	CLIP-seq
MIRT807886	hsa-miR-4645-3p	CLIP-seq
MIRT807887	hsa-miR-4793-5p	CLIP-seq
MIRT807888	hsa-miR-186	CLIP-seq
MIRT807889	hsa-miR-3664-5p	CLIP-seq
MIRT807890	hsa-miR-3692	CLIP-seq
MIRT807891	hsa-miR-451b	CLIP-seq
MIRT807892	hsa-miR-4696	CLIP-seq
MIRT807893	hsa-miR-4714-5p	CLIP-seq
MIRT807894	hsa-miR-545	CLIP-seq
MIRT807895	hsa-miR-634	CLIP-seq
MIRT807896	hsa-miR-101	CLIP-seq
MIRT807897	hsa-miR-144	CLIP-seq
MIRT807898	hsa-miR-183	CLIP-seq
MIRT807899	hsa-miR-330-3p	CLIP-seq
MIRT807900	hsa-miR-4323	CLIP-seq
MIRT807901	hsa-miR-4758-3p	CLIP-seq
MIRT807902	hsa-miR-4797-3p	CLIP-seq
MIRT807903	hsa-miR-517b	CLIP-seq
MIRT807904	hsa-miR-548p	CLIP-seq
MIRT807905	hsa-miR-802	CLIP-seq
MIRT1938625	hsa-miR-4799-5p	CLIP-seq
MIRT1938626	hsa-miR-1343	CLIP-seq
MIRT1938627	hsa-miR-203	CLIP-seq
MIRT1938628	hsa-miR-3662	CLIP-seq
MIRT1938629	hsa-miR-4646-5p	CLIP-seq
MIRT1938630	hsa-miR-4705	CLIP-seq
MIRT1938631	hsa-miR-4719	CLIP-seq
MIRT1938632	hsa-miR-483-3p	CLIP-seq
MIRT1938633	hsa-miR-513a-3p	CLIP-seq
MIRT1938634	hsa-miR-532-5p	CLIP-seq
MIRT1938635	hsa-miR-561	CLIP-seq
MIRT1938625	hsa-miR-4799-5p	CLIP-seq
MIRT2177870	hsa-miR-3122	CLIP-seq
MIRT2177871	hsa-miR-3913-5p	CLIP-seq
MIRT1938626	hsa-miR-1343	CLIP-seq
MIRT1938629	hsa-miR-4646-5p	CLIP-seq
MIRT1938625	hsa-miR-4799-5p	CLIP-seq
MIRT1938632	hsa-miR-483-3p	CLIP-seq
MIRT2481231	hsa-miR-1202	CLIP-seq
MIRT2481232	hsa-miR-1206	CLIP-seq
MIRT2481233	hsa-miR-1264	CLIP-seq
MIRT1938626	hsa-miR-1343	CLIP-seq
MIRT807888	hsa-miR-186	CLIP-seq
MIRT807882	hsa-miR-1914	CLIP-seq
MIRT2481234	hsa-miR-19a	CLIP-seq
MIRT2481235	hsa-miR-19b	CLIP-seq
MIRT1938627	hsa-miR-203	CLIP-seq
MIRT2481236	hsa-miR-214	CLIP-seq
MIRT2481237	hsa-miR-3121-3p	CLIP-seq
MIRT2481238	hsa-miR-3143	CLIP-seq
MIRT2481239	hsa-miR-3157-3p	CLIP-seq
MIRT2481240	hsa-miR-3157-5p	CLIP-seq
MIRT2481241	hsa-miR-3160-3p	CLIP-seq
MIRT2481242	hsa-miR-3194-5p	CLIP-seq
MIRT2481243	hsa-miR-3200-5p	CLIP-seq
MIRT2481244	hsa-miR-323-3p	CLIP-seq
MIRT2481245	hsa-miR-3545-3p	CLIP-seq
MIRT807883	hsa-miR-3545-5p	CLIP-seq
MIRT2481246	hsa-miR-3613-3p	CLIP-seq
MIRT2481247	hsa-miR-3619-5p	CLIP-seq
MIRT1938628	hsa-miR-3662	CLIP-seq
MIRT2481248	hsa-miR-371-5p	CLIP-seq
MIRT2481249	hsa-miR-371b-5p	CLIP-seq
MIRT2481250	hsa-miR-3926	CLIP-seq
MIRT2481251	hsa-miR-3972	CLIP-seq
MIRT2481252	hsa-miR-409-3p	CLIP-seq
MIRT2481253	hsa-miR-4303	CLIP-seq
MIRT807900	hsa-miR-4323	CLIP-seq
MIRT2481254	hsa-miR-4487	CLIP-seq
MIRT2481255	hsa-miR-4530	CLIP-seq
MIRT2481256	hsa-miR-4635	CLIP-seq
MIRT807886	hsa-miR-4645-3p	CLIP-seq
MIRT1938629	hsa-miR-4646-5p	CLIP-seq
MIRT2481257	hsa-miR-4668-3p	CLIP-seq
MIRT2481258	hsa-miR-4717-3p	CLIP-seq
MIRT2481259	hsa-miR-4717-5p	CLIP-seq
MIRT807901	hsa-miR-4758-3p	CLIP-seq
MIRT2481260	hsa-miR-4762-5p	CLIP-seq
MIRT807887	hsa-miR-4793-5p	CLIP-seq
MIRT807902	hsa-miR-4797-3p	CLIP-seq
MIRT1938625	hsa-miR-4799-5p	CLIP-seq
MIRT1938632	hsa-miR-483-3p	CLIP-seq
MIRT1938633	hsa-miR-513a-3p	CLIP-seq
MIRT2481261	hsa-miR-513c	CLIP-seq
MIRT2481262	hsa-miR-514b-5p	CLIP-seq
MIRT1938634	hsa-miR-532-5p	CLIP-seq
MIRT2481263	hsa-miR-543	CLIP-seq
MIRT2481264	hsa-miR-548ae	CLIP-seq
MIRT2481265	hsa-miR-548aj	CLIP-seq
MIRT2481266	hsa-miR-548am	CLIP-seq
MIRT2481267	hsa-miR-548x	CLIP-seq
MIRT2481268	hsa-miR-558	CLIP-seq
MIRT2481269	hsa-miR-562	CLIP-seq
MIRT2481270	hsa-miR-579	CLIP-seq
MIRT2481271	hsa-miR-599	CLIP-seq
MIRT2481272	hsa-miR-645	CLIP-seq
MIRT2481273	hsa-miR-657	CLIP-seq
MIRT2481274	hsa-miR-761	CLIP-seq
MIRT807905	hsa-miR-802	CLIP-seq
MIRT2481275	hsa-miR-874	CLIP-seq
MIRT2481276	hsa-miR-888	CLIP-seq
MIRT2481277	hsa-miR-938	CLIP-seq
MIRT1938625	hsa-miR-4799-5p	CLIP-seq
MIRT1938626	hsa-miR-1343	CLIP-seq
MIRT807888	hsa-miR-186	CLIP-seq
MIRT807882	hsa-miR-1914	CLIP-seq
MIRT2481234	hsa-miR-19a	CLIP-seq
MIRT2481235	hsa-miR-19b	CLIP-seq
MIRT1938627	hsa-miR-203	CLIP-seq
MIRT2481237	hsa-miR-3121-3p	CLIP-seq
MIRT2675694	hsa-miR-3145-3p	CLIP-seq
MIRT2481241	hsa-miR-3160-3p	CLIP-seq
MIRT2481243	hsa-miR-3200-5p	CLIP-seq
MIRT2481244	hsa-miR-323-3p	CLIP-seq
MIRT807883	hsa-miR-3545-5p	CLIP-seq
MIRT2481246	hsa-miR-3613-3p	CLIP-seq
MIRT1938628	hsa-miR-3662	CLIP-seq
MIRT2481250	hsa-miR-3926	CLIP-seq
MIRT2481253	hsa-miR-4303	CLIP-seq
MIRT2675695	hsa-miR-4446-5p	CLIP-seq
MIRT2481254	hsa-miR-4487	CLIP-seq
MIRT807886	hsa-miR-4645-3p	CLIP-seq
MIRT1938629	hsa-miR-4646-5p	CLIP-seq
MIRT2481257	hsa-miR-4668-3p	CLIP-seq
MIRT2481258	hsa-miR-4717-3p	CLIP-seq
MIRT2481259	hsa-miR-4717-5p	CLIP-seq
MIRT2675696	hsa-miR-4755-5p	CLIP-seq
MIRT807887	hsa-miR-4793-5p	CLIP-seq
MIRT807902	hsa-miR-4797-3p	CLIP-seq
MIRT1938625	hsa-miR-4799-5p	CLIP-seq
MIRT1938632	hsa-miR-483-3p	CLIP-seq
MIRT1938633	hsa-miR-513a-3p	CLIP-seq
MIRT1938634	hsa-miR-532-5p	CLIP-seq
MIRT2481264	hsa-miR-548ae	CLIP-seq
MIRT2481265	hsa-miR-548aj	CLIP-seq
MIRT2481266	hsa-miR-548am	CLIP-seq
MIRT2481267	hsa-miR-548x	CLIP-seq
MIRT2481268	hsa-miR-558	CLIP-seq
MIRT2481271	hsa-miR-599	CLIP-seq
MIRT2481272	hsa-miR-645	CLIP-seq
MIRT807905	hsa-miR-802	CLIP-seq
MIRT2481276	hsa-miR-888	CLIP-seq

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Transcription factor	Regulation	Reference
SP1	Activation	15955096
YY1	Activation	15955096

Show/Hide all (57)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IBA
GO:0000139	Component	Golgi membrane	IDA	12804581, 21187401
GO:0000139	Component	Golgi membrane	TAS
GO:0000166	Function	Nucleotide binding	IEA
GO:0005388	Function	P-type calcium transporter activity	IBA
GO:0005388	Function	P-type calcium transporter activity	IDA	16192278
GO:0005388	Function	P-type calcium transporter activity	IDA	12707275, 12810057, 16192278
GO:0005388	Function	P-type calcium transporter activity	IEA
GO:0005388	Function	P-type calcium transporter activity	IMP	10615129
GO:0005509	Function	Calcium ion binding	IDA	12707275, 16192278
GO:0005524	Function	ATP binding	IDA	12707275, 16192278
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005794	Component	Golgi apparatus	IDA	11741891, 12707275
GO:0005794	Component	Golgi apparatus	IEA
GO:0005802	Component	Trans-Golgi network	IDA	14632183
GO:0005886	Component	Plasma membrane	IBA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006816	Process	Calcium ion transport	IDA	12707275, 12810057, 16192278
GO:0006816	Process	Calcium ion transport	IEA
GO:0006816	Process	Calcium ion transport	IMP	10615129
GO:0006828	Process	Manganese ion transport	IBA
GO:0006828	Process	Manganese ion transport	IDA	12707275
GO:0006874	Process	Intracellular calcium ion homeostasis	IBA
GO:0006874	Process	Intracellular calcium ion homeostasis	IDA	12707275, 12810057
GO:0006874	Process	Intracellular calcium ion homeostasis	IEA
GO:0006874	Process	Intracellular calcium ion homeostasis	IMP	10615129
GO:0008544	Process	Epidermis development	IMP	10615129
GO:0012505	Component	Endomembrane system	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	NAS	10615129
GO:0016339	Process	Calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	IMP	14632182
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0030026	Process	Intracellular manganese ion homeostasis	IDA	12707275
GO:0030036	Process	Actin cytoskeleton organization	IMP	14632182
GO:0030145	Function	Manganese ion binding	IDA	12707275
GO:0032468	Process	Golgi calcium ion homeostasis	IEA
GO:0032468	Process	Golgi calcium ion homeostasis	IMP	14632183, 20439740
GO:0032468	Process	Golgi calcium ion homeostasis	ISS
GO:0032472	Process	Golgi calcium ion transport	IMP	14632183
GO:0032580	Component	Golgi cisterna membrane	IEA
GO:0032580	Component	Golgi cisterna membrane	ISS
GO:0033106	Component	Cis-Golgi network membrane	IEA
GO:0033106	Component	Cis-Golgi network membrane	ISS
GO:0042998	Process	Positive regulation of Golgi to plasma membrane protein transport	IEA
GO:0042998	Process	Positive regulation of Golgi to plasma membrane protein transport	IMP	20439740
GO:0042998	Process	Positive regulation of Golgi to plasma membrane protein transport	ISS
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	HMP	12761501
GO:0046872	Function	Metal ion binding	IEA
GO:0070588	Process	Calcium ion transmembrane transport	IBA
GO:0070588	Process	Calcium ion transmembrane transport	IEA
GO:0071421	Process	Manganese ion transmembrane transport	IEA
GO:0098629	Process	Trans-Golgi network membrane organization	IMP	20439740
GO:0140613	Function	P-type manganese transporter activity	IDA	21187401
GO:0140613	Function	P-type manganese transporter activity	IEA

MIM	HGNC	e!Ensembl
604384	13211	ENSG00000017260

P98194

Protein name

Calcium-transporting ATPase type 2C member 1 (ATPase 2C1) (EC 7.2.2.10) (ATP-dependent Ca(2+) pump PMR1) (Ca(2+)/Mn(2+)-ATPase 2C1) (Secretory pathway Ca(2+)-transporting ATPase type 1) (SPCA1)

Protein function

ATP-driven pump that supplies the Golgi apparatus with Ca(2+) and Mn(2+) ions, both essential cofactors for processing and trafficking of newly synthesized proteins in the secretory pathway (PubMed:12707275, PubMed:16192278, PubMed:20439740, Pub

PDB

7YAG , 7YAH , 7YAI , 7YAJ , 7YAM , 8IWP , 8IWR , 8IWS , 8IWT , 8IWU , 8IWW

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00690	Cation_ATPase_N	26 → 94	Cation transporter/ATPase, N-terminus	Domain
PF00122	E1-E2_ATPase	133 → 328		Family
PF00702	Hydrolase	344 → 656		Domain
PF00689	Cation_ATPase_C	726 → 898	Cation transporting ATPase, C-terminus	Family

Tissue specificity

TISSUE SPECIFICITY: Found in most tissues except colon, thymus, spleen and leukocytes (PubMed:15831496). Expressed in keratinocytes (at protein level) (PubMed:14632183, PubMed:15831496). {ECO:0000269|PubMed:14632183, ECO:0000269|PubMed:15831496}.

Sequence

MKVARFQKIPNGENETMIPVLTSKKASELPVSEVASILQADLQNGLNKCEVSHRRAFHGW
NEFDISEDEPLWKKYISQFKNPLIMLLLASAVISVLMHQFDDAVSITVAILIVVTVAFVQ
EYRSEKSLEELSKLVPPECHCVREGKLEHTLARDLVPGDTVCLSVGDRVPADLRLFEAVD
LSIDESSLTGETTPCSKVTAPQPAATNGDLASRSNIAFMGTLVRCGKAKGVVIGTGENSE
FGEVFKMMQAEEAPKTPLQKSMDLLGKQLSFYSFGIIGIIMLVGWLLGKDILEMFTISVS
LAVAAIPEGLPIVVTVTLALGVMRMVKKRAIVKKLPIVETLGCCNVICSDKTGTLTKNEM
TVTHIFTSDGLHAEVTGVGYNQFGEVIVDGDVVHGFYNPAVSRIVEAGCVCNDAVIRNNT
LMGKPTEGALIALAMKMGLDGLQQDYIRKAEYPFSSEQKWMAVKCVHRTQQDRPEICFMK
GAYEQVIKYCTTYQSKGQTLTLTQQQRDVYQQEKARMGSAGLRVLALASGPELGQLTFLG
LVGIIDPPRTGVKEAVTTLIASGVSIKMITGDSQETAVAIASRLGLYSKTSQSVSGEEID
AMDVQQLSQIVPKVAVFYRASPRHKMKIIKSLQKNGSVVAMTGDGVNDAVALKAADIGVA
MGQTGTDVCKEAADMILVDDDFQTIMSAIEEGKGIYNNIKNFVRFQLSTSIAALTLISLA
TLMNFPNPLNAMQILWINIIMDGPPAQSLGVEPVDKDVIRKPPRNWKDSILTKNLILKIL
VSSIIIVCGTLFVFWRELRDNVITPRDTTMTFTCFVFFDMFNALSSRSQTKSVFEIGLCS
NRMFCYAVLGSIMGQLLVIYFPPLQKVFQTESLSILDLLFLLGLTSSVCIVAEIIKKVER
SREKIQKHVSSTSSSFLEV

Sequence length

919

Interactions

View interactions

	Reactome
			Ion transport by P-type ATPases

108

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Familial benign pemphigus	Pathogenic; Likely pathogenic	rs1559982055, rs2531541423, rs2531541261, rs997949050, rs1559971447, rs137853012, rs137853013, rs137853014, rs1560033613, rs137853015, rs748204512, rs2531133399, rs1057517706	RCV001845026 RCV002510485 RCV002510486 RCV002510487 RCV000005923 RCV000005924 RCV000005925 RCV000005927 RCV000005928 RCV000005929 RCV000005930 RCV000005931 RCV005034582 RCV000005926

Show/Hide Unknown Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Adrenocortical carcinoma, hereditary	Benign	rs16835513	RCV005897595
ATP2C1-related disorder	Benign; Uncertain significance; Likely benign	rs72987807, rs117316812, rs16835513, rs773854095, rs554783338, rs774114512, rs754745816, rs760722622, rs61731516, rs143199078	RCV003895809 RCV003903640 RCV003972447 RCV003923991 RCV003909691 RCV003952034 RCV003949199 RCV003937387 RCV003922700 RCV003970855
Cervical cancer	Benign; Uncertain significance	rs79928051, rs115940289	RCV005920108 RCV005913898
Cholangiocarcinoma	Benign	rs16835513	RCV005897599
Malignant lymphoma, large B-cell, diffuse	Benign	rs16835513	RCV005897597
Ovarian serous cystadenocarcinoma	Benign	rs79540389	RCV005915660
Uterine carcinosarcoma	Benign	rs16835513	RCV005897598
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	rs79540389, rs79928051, rs115940289	RCV005915661 RCV005920109 RCV005913899
Uveal melanoma	Benign	rs16835513	RCV005897596

Show/Hide Text Mining Associations (16)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Breast Neoplasms	Associate	20837466, 31783287
Calcinosis	Stimulate	28618103
Carcinoma Squamous Cell	Stimulate	18618715
Chronic Pain	Associate	33926923
Darier Disease	Associate	11886536, 18060195
Diabetes Mellitus	Associate	38014829
Diabetes Mellitus Type 1	Associate	38014829
Erythema	Associate	11886536
Grover's disease	Associate	31605620
Heart Diseases	Associate	39241028
Inflammation	Associate	39217398
Lung Neoplasms	Associate	28487954, 34761591
Pemphigus	Associate	23505434
Pemphigus Benign Familial	Associate	11886536, 15677451, 18060195, 25837627, 31605620, 38014829, 39241028
Tooth Erosion	Associate	11886536
Uterine Cervical Neoplasms	Associate	18618715

ATP2C1 (ATPase secretory pathway Ca2+ transporting 1)