ATP2C2 ATPase secretory pathway Ca2+ transporting 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ATP2C2provided by HGNC
Official Full Name: ATPase secretory pathway Ca2+ transporting 2provided by HGNC
Primary source: HGNC:HGNC:29103
See related: Ensembl:ENSG00000064270 MIM:613082; AllianceGenome:HGNC:29103
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SPCA2
Summary: Enables P-type calcium transporter activity and P-type manganese transporter activity. Predicted to be involved in calcium ion transmembrane transport; intracellular calcium ion homeostasis; and manganese ion transport. Predicted to act upstream of or within mammary gland epithelium development; positive regulation of calcium ion import; and protein localization to plasma membrane. Predicted to be located in trans-Golgi network membrane. Predicted to be active in Golgi membrane; endoplasmic reticulum; and plasma membrane. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in colon (RPKM 16.5), skin (RPKM 9.9) and 12 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q24.1

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (84368538..84464187)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (90434936..90530568)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (84402144..84497793)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures.
Title: A rare missense variant in the ATP2C2 gene is associated with language impairment and related measures.
Secretory pathway Ca(2+)-ATPase SPCA2 regulates mitochondrial respiration and DNA damage response through store-independent calcium entry.
Title: Secretory pathway Ca(2+)-ATPase SPCA2 regulates mitochondrial respiration and DNA damage response through store-independent calcium entry.
ATP2C2 Has Potential to Define Tumor Microenvironment in Breast Cancer.
Title: ATP2C2 Has Potential to Define Tumor Microenvironment in Breast Cancer.
Original association of ion transporters mediates the ECM-induced breast cancer cell survival: Kv10.1-Orai1-SPCA2 partnership.
Title: Original association of ion transporters mediates the ECM-induced breast cancer cell survival: Kv10.1-Orai1-SPCA2 partnership.
SPCA2C influences Ca(2+) homeostasis through multiple mechanisms, some of which are independent of Orai1, suggesting novel and possibly cell-specific Ca(2+) regulation.
Title: The pancreas-specific form of secretory pathway calcium ATPase 2 regulates multiple pathways involved in calcium homeostasis.
Low SPCA2 expression is associated with Epithelial-Mesenchymal Transition in Breast Cancer.
Title: A Ca(2+)-ATPase Regulates E-cadherin Biogenesis and Epithelial-Mesenchymal Transition in Breast Cancer Cells.
The genome-wide association meta-analysis identified five single nucleotide polymorphisms (SNPs) on chromosome 16 within ATP2C2 that associated with age of first cannabis use.
Title: Genome-wide association meta-analysis of age at first cannabis use.
In total, four independent SNPs within DYX1C1 and ATP2C2 were found to be associated with MMR stronger than expected from multiple testing. To explore potential pathomechanisms, we annotated these variants with functional data including tissue-specific expression analysis and eQTLs.
Title: ATP2C2 and DYX1C1 are putative modulators of dyslexia-related MMR.
The Secretory Pathway Ca(2+) -ATPases SPCA1 and SPCA2 are strongly induced under osteogenic conditions that elicit microcalcifications. SPCA gene expression is significantly elevated in breast cancer subtypes that are associated with microcalcifications.
Title: Secretory pathway Ca(2+) -ATPases promote in vitro microcalcifications in breast cancer cells.
The extract was found to comprise mainly primary fatty acid amides (PFAAs) by NMR analysis. Individual PFAAs, especially oleamide and linoleamide, almost completely inhibited hSPCA2 activity with IC50 values of 7.5 muM and 3.8 muM, respectively.
Title: Identification of novel inhibitors of human SPCA2.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2018-09-17) ClinGen Genome Curation Page Haploinsufficency No evidence available (Last evaluated 2018-09-17) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association analysis of blood biomarkers in chronic obstructive pulmonary disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D16S2951 (e-PCR)
- UniSTS:54851

SHGC-60885 (e-PCR)
- UniSTS:67914

RH65309 (e-PCR)
- UniSTS:87900

STS-N48584 (e-PCR)
- UniSTS:14264

RH36547 (e-PCR)
- UniSTS:185

SGC31818 (e-PCR)
- UniSTS:99832

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables P-type calcium transporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables P-type calcium transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables P-type manganese transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in calcium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular calcium ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info
involved_in mammary gland epithelium development	IEA Inferred from Electronic Annotation more info
involved_in manganese ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in manganese ion transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of calcium ion import	IEA Inferred from Electronic Annotation more info
involved_in protein localization to plasma membrane	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in Golgi membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic side of plasma membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in trans-Golgi network membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: calcium-transporting ATPase type 2C member 2

Names: ATPase 2C2; ATPase, Ca++ transporting, type 2C, member 2; Ca(2+)/Mn(2+)-ATPase 2C2; secretory pathway Ca(2+)-ATPase 2; secretory pathway Ca(2+)-transporting ATPase type 2; secretory pathway calcium ATPase 2

NP_001273456.2

EC 7.2.2.10

NP_001278383.1

EC 7.2.2.10

NP_055676.3

EC 7.2.2.10

XP_011521788.1

EC 7.2.2.10

XP_011521789.1

EC 7.2.2.10

XP_047290950.1

EC 7.2.2.10

XP_054170532.1

EC 7.2.2.10

XP_054170533.1

EC 7.2.2.10

XP_054170534.1

EC 7.2.2.10

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001286527.3 → NP_001273456.2 calcium-transporting ATPase type 2C member 2 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC022165, AY791884, BX648333

Consensus CDS

CCDS67088.1

UniProtKB/TrEMBL

B7ZA13

Related

ENSP00000397925.2, ENST00000416219.6

Conserved Domains (6) summary

TIGR01522
Location:55 → 960

ATPase-IIA2_Ca; golgi membrane calcium-translocating P-type ATPase

COG4087
Location:625 → 709

COG4087; Soluble P-type ATPase [General function prediction only]

pfam00122
Location:149 → 368

E1-E2_ATPase; E1-E2 ATPase

pfam00689
Location:756 → 957

Cation_ATPase_C; Cation transporting ATPase, C-terminus

pfam00690
Location:63 → 125

Cation_ATPase_N; Cation transporter/ATPase, N-terminus

pfam13246
Location:441 → 523

Cation_ATPase; Cation transport ATPase (P-type)
NM_001291454.2 → NP_001278383.1 calcium-transporting ATPase type 2C member 2 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, contains multiple differences in the coding region, and initiates translation at an alternate downstream start codon, compared to variant 1. The resulting isoform (3) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AK091051, AY791884, BX648333

UniProtKB/TrEMBL

B3KR57

Related

ENST00000420010.6

Conserved Domains (5) summary

COG4087
Location:474 → 558

COG4087; Soluble P-type ATPase [General function prediction only]

TIGR01116
Location:23 → 777

ATPase-IIA1_Ca; sarco/endoplasmic reticulum calcium-translocating P-type ATPase

pfam00122
Location:23 → 217

E1-E2_ATPase; E1-E2 ATPase

pfam00689
Location:605 → 777

Cation_ATPase_C; Cation transporting ATPase, C-terminus

pfam13246
Location:290 → 372

Cation_ATPase; Cation transport ATPase (P-type)
NM_014861.4 → NP_055676.3 calcium-transporting ATPase type 2C member 2 isoform 2

See identical proteins and their annotated locations for NP_055676.3

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The resulting isoform (2) is shorter than isoform 1.

Source sequence(s)

AY791884, BX648333

Consensus CDS

CCDS42207.1

UniProtKB/Swiss-Prot

B4DU76, E7ES94, O75185, Q5HYC3, Q5S053, Q68CQ2

UniProtKB/TrEMBL

B7ZA13

Related

ENSP00000262429.4, ENST00000262429.9

Conserved Domains (1) summary

cd02085
Location:85 → 927

P-type_ATPase_SPCA; golgi-associated secretory pathway Ca(2+) transport ATPases, similar to human ATPase secretory pathway Ca(2+) transporting 1/hSPCA1 and Saccharomyces cerevisiae Ca(2+)/Mn(2+)-transporting P-type ATPase, Pmr1p

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

84368538..84464187

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011523486.3 → XP_011521788.1 calcium-transporting ATPase type 2C member 2 isoform X1

UniProtKB/TrEMBL

B7ZA13

Conserved Domains (6) summary

TIGR01522
Location:32 → 937

ATPase-IIA2_Ca; golgi membrane calcium-translocating P-type ATPase

COG4087
Location:602 → 686

COG4087; Soluble P-type ATPase [General function prediction only]

pfam00122
Location:126 → 345

E1-E2_ATPase; E1-E2 ATPase

pfam00689
Location:733 → 934

Cation_ATPase_C; Cation transporting ATPase, C-terminus

pfam00690
Location:40 → 102

Cation_ATPase_N; Cation transporter/ATPase, N-terminus

pfam13246
Location:418 → 500

Cation_ATPase; Cation transport ATPase (P-type)
XM_047434994.1 → XP_047290950.1 calcium-transporting ATPase type 2C member 2 isoform X2

UniProtKB/TrEMBL

B7ZA13
XM_011523487.3 → XP_011521789.1 calcium-transporting ATPase type 2C member 2 isoform X3

Conserved Domains (3) summary

COG4087
Location:282 → 366

COG4087; Soluble P-type ATPase [General function prediction only]

pfam00689
Location:413 → 614

Cation_ATPase_C; Cation transporting ATPase, C-terminus

pfam13246
Location:98 → 180

Cation_ATPase; Cation transport ATPase (P-type)

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

90434936..90530568

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054314557.1 → XP_054170532.1 calcium-transporting ATPase type 2C member 2 isoform X1

UniProtKB/TrEMBL

B7ZA13
XM_054314558.1 → XP_054170533.1 calcium-transporting ATPase type 2C member 2 isoform X2

UniProtKB/TrEMBL

B7ZA13
XM_054314559.1 → XP_054170534.1 calcium-transporting ATPase type 2C member 2 isoform X3