ATP2C2 (ATPase secretory pathway Ca2+ transporting 2)

Gene

• Entrez ID: 9914
• Gene name: ATPase secretory pathway Ca2+ transporting 2
• Gene symbol: ATP2C2
• Synonyms (NCBI Gene): SPCA2
• Chromosome: 16
• Chromosome location: 16q24.1

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs78887288	G>A	Conflicting-interpretations-of-pathogenicity	Upstream transcript variant, genic upstream transcript variant, coding sequence variant, missense variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT807906	hsa-miR-2114	CLIP-seq
MIRT807907	hsa-miR-548n	CLIP-seq
MIRT807908	hsa-miR-548t	CLIP-seq
MIRT2384621	hsa-miR-1184	CLIP-seq
MIRT2384622	hsa-miR-1301	CLIP-seq
MIRT2384623	hsa-miR-3074-5p	CLIP-seq
MIRT2384624	hsa-miR-3124-3p	CLIP-seq
MIRT2384625	hsa-miR-3685	CLIP-seq
MIRT2384626	hsa-miR-384	CLIP-seq
MIRT2384627	hsa-miR-4660	CLIP-seq
MIRT2384628	hsa-miR-5047	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IBA
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	15677451, 15831496
GO:0005388	Function	P-type calcium transporter activity	IEA
GO:0005515	Function	Protein binding	IPI	20887894
GO:0005524	Function	ATP binding	IEA
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005794	Component	Golgi apparatus	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006816	Process	Calcium ion transport	IEA
GO:0006828	Process	Manganese ion transport	IBA
GO:0006874	Process	Intracellular calcium ion homeostasis	IBA
GO:0009898	Component	Cytoplasmic side of plasma membrane	IEA
GO:0016020	Component	Membrane	IEA
GO:0016323	Component	Basolateral plasma membrane	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0032588	Component	Trans-Golgi network membrane	IEA
GO:0032588	Component	Trans-Golgi network membrane	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	IEA
GO:0061180	Process	Mammary gland epithelium development	IEA
GO:0070588	Process	Calcium ion transmembrane transport	IBA
GO:0071421	Process	Manganese ion transmembrane transport	IEA
GO:0072659	Process	Protein localization to plasma membrane	IEA
GO:0090280	Process	Positive regulation of calcium ion import	IEA
GO:0140613	Function	P-type manganese transporter activity	IDA	15831496
GO:0140613	Function	P-type manganese transporter activity	IEA

Other IDs

• MIM: 613082
• HGNC: 29103
• e!Ensembl: ENSG00000064270

Protein

• UniProt ID: O75185
• Protein name: Calcium-transporting ATPase type 2C member 2 (ATPase 2C2) (EC 7.2.2.10) (Ca(2+)/Mn(2+)-ATPase 2C2) (Secretory pathway Ca(2+)-transporting ATPase type 2) (SPCA2)
• 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:15677451, PubMed:15831496, PubMed:16332677, Pub
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00690	Cation_ATPase_N	58 → 125	Cation transporter/ATPase, N-terminus	Domain
  PF00122	E1-E2_ATPase	164 → 357		Family
  PF00702	Hydrolase	373 → 686		Domain
  PF00689	Cation_ATPase_C	756 → 929	Cation transporting ATPase, C-terminus	Family

• Tissue specificity: TISSUE SPECIFICITY: Highly expressed in the gastrointestinal and respiratory tracts, prostate, thyroid, salivary, and mammary glands (PubMed:15831496). Expressed in colon epithelial cells (at protein level). Expressed in brain and testis (at protein level
• Sequence:

  MVEGRVSEFLKKLGFSGGGRQYQALEKDEEEALIDEQSELKAIEKEKKVTALPPKEACKC
  QKEDLARAFCVDLHTGLSEFSVTQRRLAHGWNEFVADNSEPVWKKYLDQFKNPLILLLLG
  SALVSVLTKEYEDAVSIATAVLVVVTVAFIQEYRSEKSLEELTKLVPPECNCLREGKLQH
  LLARELVPGDVVSLSIGDRIPADIRLTEVTDLLVDESSFTGEAEPCSKTDSPLTGGGDLT
  TLSNIVFMGTLVQYGRGQGVVIGTGESSQFGEVFKMMQAEETPKTPLQKSMDRLGKQLTL
  FSFGIIGLIMLIGWSQGKQLLSMFTIGVSLAVAAIPEGLPIVVMVTLVLGVLRMAKKRVI
  VKKLPIVETLGCCSVLCSDKTGTLTANEMTVTQLVTSDGLRAEVSGVGYDGQGTVCLLPS
  KEVIKEFSNVSVGKLVEAGCVANNAVIRKNAVMGQPTEGALMALAMKMDLSDIKNSYIRK
  KEIPFSSEQKWMAVKCSLKTEDQEDIYFMKGALEEVIRYCTMYNNGGIPLPLTPQQRSFC
  LQEEKRMGSLGLRVLALASGPELGRLTFLGLVGIIDPPRVGVKEAVQVLSESGVSVKMIT
  GDALETALAIGRNIGLCNGKLQAMSGEEVDSVEKGELADRVGKVSVFFRTSPKHKLKIIK
  ALQESGAIVAMTGDGVNDAVALKSADIGIAMGQTGTDVSKEAANMILVDDDFSAIMNAVE
  EGKGIFYNIKNFVRFQLSTSISALSLITLSTVFNLPSPLNAMQILWINIIMDGPPAQSLG
  VEPVDKDAFRQPPRSVRDTILSRALILKILMSAAIIISGTLFIFWKEMPEDRASTPRTTT
  MTFTCFVFFDLFNALTCRSQTKLIFEIGFLRNHMFLYSVLGSILGQLAVIYIPPLQRVFQ
  TENLGALDLLFLTGLASSVFILSELLKLCEKYCCSPKRVQMHPEDV

• Sequence length: 946

Pathways

Reactome:

Ion transport by P-type ATPases

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATP2C2-related disorder	Benign; Likely benign; Uncertain significance; Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	GWASDB_DG	18839057		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Attention deficit hyperactivity disorder	Attention Deficit Hyperactivity Disorder	GWASCAT_DG	18839057		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Breast Carcinoma	Breast Carcinoma	BEFREE	27692665		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	30718673, 30923126, 31783287, 33936088, 35063802	Associate	★☆☆☆☆ Found in Text Mining only
Calcinosis	Calcinosis	Pubtator	28618103	Stimulate	★☆☆☆☆ Found in Text Mining only
Chronic Obstructive Airway Disease	Chronic Obstructive Pulmonary Disease	GWASCAT_DG	23144326		★☆☆☆☆ Found in Text Mining only
Dyslexia	Dyslexia	BEFREE	21165691, 25448322		★☆☆☆☆ Found in Text Mining only
Dyslexia	Dyslexia	Pubtator	29201552, 33864365	Associate	★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	36899615	Associate	★☆☆☆☆ Found in Text Mining only
Language Disorders	Language Disorders	BEFREE	19646677, 21457949, 23228431, 25448322		★☆☆☆☆ Found in Text Mining only
Language Disorders	Language development disorders	Pubtator	19646677, 33864365	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	27692665		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	31076498		★☆☆☆☆ Found in Text Mining only
Pancreatitis	Pancreatitis	BEFREE	27017909		★☆☆☆☆ Found in Text Mining only
Parkinson Disease Secondary	Secondary parkinson disease	Pubtator	15677451	Associate	★☆☆☆☆ Found in Text Mining only
Pemphigus Benign Familial	Benign familial pemphigus	Pubtator	15677451, 30923126	Associate	★☆☆☆☆ Found in Text Mining only
Specific Language Disorder	Specific language disorder	Pubtator	19646677	Associate	★☆☆☆☆ Found in Text Mining only
Specific language impairment	Specific Language Impairment	BEFREE	19646677, 25296922		★☆☆☆☆ Found in Text Mining only
Thyroid Neoplasms	Thyroid cancer	Pubtator	32849296	Associate	★☆☆☆☆ Found in Text Mining only