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

Gene Gene information from NCBI Gene database. Gene SNPs Other IDs Associated diseases
Entrez ID	487
Gene name	ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1
Gene symbol	ATP2A1
Synonyms (NCBI Gene)	ATP2ASERCA1
Chromosome	16
Chromosome location	16p11.2
Summary	This gene encodes one of the SERCA Ca(2+)-ATPases, which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of muscle cells. This enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to

Show/Hide all (21)

SNP ID	Visualize variation	Clinical significance	Consequence
rs111266804	G>A,C	Likely-pathogenic	Splice donor variant
rs113803159	C>G	Conflicting-interpretations-of-pathogenicity, likely-benign	Synonymous variant, coding sequence variant
rs117350233	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs121918113	C>T	Pathogenic	Coding sequence variant, stop gained
rs121918114	C>A	Pathogenic	Coding sequence variant, stop gained
rs121918115	C>G,T	Uncertain-significance, pathogenic	Coding sequence variant, missense variant
rs398124554	C>-	Uncertain-significance, pathogenic	Frameshift variant, coding sequence variant
rs398124555	->T	Uncertain-significance, pathogenic	Frameshift variant, coding sequence variant
rs551660089	G>A	Likely-pathogenic, pathogenic	Splice donor variant
rs748241465	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs751365374	C>-,CC,CCC	Pathogenic-likely-pathogenic, likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs755227074	G>A	Likely-pathogenic	Splice donor variant
rs895911431	C>T	Pathogenic	Stop gained, coding sequence variant
rs897301304	C>T	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs972494690	G>A,T	Pathogenic	Coding sequence variant, stop gained, missense variant
rs1409892710	T>G	Pathogenic	Stop gained, coding sequence variant
rs1421005631	CT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1555515558	TGTGGCTGCCAT>ACGGCATA	Pathogenic	Frameshift variant, coding sequence variant
rs1555516994	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1567479853	A>T	Likely-pathogenic	Splice acceptor variant
rs1596682330	GGT>TGG	Likely-pathogenic	Splice donor variant, coding sequence variant

Show/Hide all (3)

miRTarBase ID	miRNA	Experiments
MIRT807203	hsa-miR-4312	CLIP-seq
MIRT807204	hsa-miR-4660	CLIP-seq
MIRT807205	hsa-miR-646	CLIP-seq

Show/Hide all (67)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005388	Function	P-type calcium transporter activity	IBA
GO:0005388	Function	P-type calcium transporter activity	IDA	1329967, 8729696
GO:0005388	Function	P-type calcium transporter activity	IEA
GO:0005388	Function	P-type calcium transporter activity	ISS
GO:0005388	Function	P-type calcium transporter activity	TAS
GO:0005509	Function	Calcium ion binding	IEA
GO:0005509	Function	Calcium ion binding	IMP	9405806
GO:0005509	Function	Calcium ion binding	ISS
GO:0005515	Function	Protein binding	IPI	9295312, 28890335
GO:0005524	Function	ATP binding	IEA
GO:0005524	Function	ATP binding	ISS
GO:0005739	Component	Mitochondrion	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	11402072
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0005793	Component	Endoplasmic reticulum-Golgi intermediate compartment	ISS
GO:0006811	Process	Monoatomic ion transport	IEA
GO:0006816	Process	Calcium ion transport	IDA	11402072
GO:0006816	Process	Calcium ion transport	IEA
GO:0006816	Process	Calcium ion transport	IMP	9405806
GO:0006874	Process	Intracellular calcium ion homeostasis	IBA
GO:0006874	Process	Intracellular calcium ion homeostasis	IEA
GO:0006942	Process	Regulation of striated muscle contraction	IMP	9405806
GO:0008637	Process	Apoptotic mitochondrial changes	IMP	19061639
GO:0016020	Component	Membrane	IBA
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	ISS
GO:0016020	Component	Membrane	NAS	9405806
GO:0016529	Component	Sarcoplasmic reticulum	IEA
GO:0016529	Component	Sarcoplasmic reticulum	ISS
GO:0016529	Component	Sarcoplasmic reticulum	NAS	8841193
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0030899	Function	Calcium-dependent ATPase activity	ISS
GO:0031095	Component	Platelet dense tubular network membrane	IEA
GO:0031095	Component	Platelet dense tubular network membrane	TAS
GO:0031448	Process	Positive regulation of fast-twitch skeletal muscle fiber contraction	IDA	12479237
GO:0031673	Component	H zone	IDA	1329967
GO:0031674	Component	I band	IDA	1329967
GO:0032470	Process	Positive regulation of endoplasmic reticulum calcium ion concentration	IMP	11402072
GO:0032471	Process	Negative regulation of endoplasmic reticulum calcium ion concentration	IMP	11402072, 19061639
GO:0033017	Component	Sarcoplasmic reticulum membrane	IC	8040329
GO:0033017	Component	Sarcoplasmic reticulum membrane	IEA
GO:0033017	Component	Sarcoplasmic reticulum membrane	ISS
GO:0033017	Component	Sarcoplasmic reticulum membrane	TAS	11402072
GO:0034220	Process	Monoatomic ion transmembrane transport	TAS
GO:0034704	Component	Calcium channel complex	IC	11402072
GO:0034976	Process	Response to endoplasmic reticulum stress	IMP	19061639
GO:0042803	Function	Protein homodimerization activity	IPI	11402072
GO:0045988	Process	Negative regulation of striated muscle contraction	IMP	10914677
GO:0046872	Function	Metal ion binding	IEA
GO:0048471	Component	Perinuclear region of cytoplasm	ISS
GO:0051561	Process	Positive regulation of mitochondrial calcium ion concentration	IMP	19061639
GO:0051659	Process	Maintenance of mitochondrion location	IMP	19061639
GO:0070059	Process	Intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	IEA
GO:0070059	Process	Intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	IMP	19061639
GO:0070509	Process	Calcium ion import	IMP	8040329
GO:0070588	Process	Calcium ion transmembrane transport	IBA
GO:0070588	Process	Calcium ion transmembrane transport	IEA
GO:0090076	Process	Relaxation of skeletal muscle	IDA	8841193
GO:0106134	Process	Positive regulation of cardiac muscle cell contraction	ISS
GO:1901896	Process	Positive regulation of ATPase-coupled calcium transmembrane transporter activity	ISS
GO:1902082	Process	Positive regulation of calcium ion import into sarcoplasmic reticulum	ISS
GO:1903779	Process	Regulation of cardiac conduction	IEA
GO:1903779	Process	Regulation of cardiac conduction	TAS
GO:1990036	Process	Calcium ion import into sarcoplasmic reticulum	ISS

MIM	HGNC	e!Ensembl
108730	811	ENSG00000196296

O14983

Protein name

Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (SERCA1) (SR Ca(2+)-ATPase 1) (EC 7.2.2.10) (Calcium pump 1) (Calcium-transporting ATPase sarcoplasmic reticulum type, fast twitch skeletal muscle isoform) (Endoplasmic reticulum class 1/2 Ca(2+) ATPase)

Protein function

Key regulator of striated muscle performance by acting as the major Ca(2+) ATPase responsible for the reuptake of cytosolic Ca(2+) into the sarcoplasmic reticulum. Catalyzes the hydrolysis of ATP coupled with the translocation of calcium from th

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00690	Cation_ATPase_N	4 → 72	Cation transporter/ATPase, N-terminus	Domain
PF00122	E1-E2_ATPase	121 → 329		Family
PF13246	Cation_ATPase	418 → 528		Family
PF00689	Cation_ATPase_C	784 → 987	Cation transporting ATPase, C-terminus	Family

Tissue specificity

TISSUE SPECIFICITY: Skeletal muscle, fast twitch muscle (type II) fibers. {ECO:0000269|PubMed:8825625}.

Sequence

MEAAHAKTTEECLAYFGVSETTGLTPDQVKRNLEKYGLNELPAEEGKTLWELVIEQFEDL
LVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALK
EYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILAIKSTTLRVDQSIL
TGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVGTEIGKIRDQMA
ATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWFRGAIYYFKIAV
ALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQ
MSVCKMFIIDKVDGDICLLNEFSITGSTYAPEGEVLKNDKPVRPGQYDGLVELATICALC
NDSSLDFNEAKGVYEKVGEATETALTTLVEKMNVFNTDVRSLSKVERANACNSVIRQLMK
KEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPLTGP
VKEKIMAVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSARFLEYETDLTFVGVVGML
DPPRKEVTGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDD
LPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAM
GSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAA
LGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAI
GGYVGAATVGAAAWWFLYAEDGPHVNYSQLTHFMQCTEDNTHFEGIDCEVFEAPEPMTMA
LSVLVTIEMCNALNSLSENQSLLRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLR
ALDLTQWLMVLKISLPVIGLDEILKFVARNYLEDPEDERRK

Sequence length

1001

Interactions

View interactions

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)

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
ATP2A1-related disorder	Likely pathogenic; Pathogenic	rs1964095605, rs141559558, rs1421005631, rs751365374	RCV003408056 RCV003900067 RCV003409731 RCV003392382	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Brody myopathy	Pathogenic; Likely pathogenic	rs1433893346, rs760995377, rs1187948767, rs745337023, rs368234110, rs756940046, rs1963456518, rs2152215136, rs2152196826, rs2152196866, rs569683468, rs752371826, rs2152213646, rs559067146, rs2152204111 View all (35 more)	RCV001333623 RCV001785135 RCV001785142 RCV001785150 RCV001785173 View all (50 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Familial cancer of breast	Likely pathogenic; Pathogenic	rs551660089	RCV005898133	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTHMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BRODY DISEASE	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGESTIVE HEART FAILURE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEART FAILURE	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOGONADISM	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (36)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
B-Cell Lymphomas	B-Cell Lymphoma	BEFREE	30086823		★★★★★ ★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	34684111	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Brody myopathy	Brody Myopathy	BEFREE	10914677, 12763865, 15083169, 15469975, 18786632, 20533403, 22704959, 23911890, 8825625, 8841193, 9367679		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brody myopathy	Brody Myopathy	UNIPROT_DG	10914677		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brody myopathy	Brody Myopathy	CLINVAR_DG	10914677, 23911890, 8841193		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brody myopathy	Brody Myopathy	ORPHANET_DG	10914677		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brody myopathy	Brody Myopathy	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brody myopathy	Brody myopathy	Pubtator	32040565, 40323132, 8825625	Associate	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brody myopathy	Brody Myopathy	GENOMICS_ENGLAND_DG	8841193, 9367679		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Brody myopathy	Brody Myopathy	CTD_human_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	37510286	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Familial Idiopathic	Cardiomyopathy	BEFREE	28612341		★★★★★ ★☆☆☆☆ Found in Text Mining only
Central Core Myopathy (disorder)	Myopathy	BEFREE	9873004		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congestive heart failure	Congestive Heart Failure	CTD_human_DG	19776660		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cryptorchidism	Cryptorchidism	LHGDN	16933204		★★★★★ ★☆☆☆☆ Found in Text Mining only
Dermatologic disorders	Dermatologic Disorders	BEFREE	12763865		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	28483572		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	28483572		★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	28694205	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dyslipidemias	Dyslipidemias	Pubtator	28694205	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease Type V	Glycogen Storage Disease	BEFREE	22347505		★★★★★ ★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease Type V	Glycogen storage disease	Pubtator	22347505, 35563042	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Heart failure	Heart Failure	CTD_human_DG	19776660		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Heart Failure, Right-Sided	Heart Failure	CTD_human_DG	19776660		★★★★★ ★☆☆☆☆ Found in Text Mining only
Left-Sided Heart Failure	Heart Failure	CTD_human_DG	19776660		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Hyperthermia	Malignant hyperthermia	Pubtator	32040565	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	37227248	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Myocardial Failure	Myocardial Infarction	CTD_human_DG	19776660		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myofibrillar Myopathy	Myofibrillar myopathy	BEFREE	8845717		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myopathy	Myopathy	BEFREE	22704959, 23911890		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myotonic Dystrophy	Myotonic dystrophy	Pubtator	20071745, 22758909, 29947794, 36631509	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
MYOTONIC DYSTROPHY 1	Myotonic dystrophy	BEFREE	15972723		★★★★★ ★☆☆☆☆ Found in Text Mining only
Oropharyngeal Neoplasms	Oropharyngeal neoplasm	Pubtator	32415241	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	35133336	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	15718407	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Septicemia	Septicemia	BEFREE	28765908		★★★★★ ★☆☆☆☆ Found in Text Mining only

ATP2A1 (ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1)