GeneBe

ATP2C2

protein-coding

ATPase secretory pathway Ca2+ transporting 2, the group of ATPases Ca2+ transporting

Gene 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, Jul 2025]

MANE transcript

NM_014861.4

Inheritance

AD

ClinVar variants

U:297B:69

Top phenotype

ATP2C2-related disorder

gnomAD constraint

pLI —, LoF o/e 1.53

Max pathogenic AF

—

Genomic locus

chr16:84,368,527-84,464,187

External References & Databases

Ensembl (ENSG00000064270)NCBI Gene (9914)OMIM (613082)HGNC:29103GenCCUniProt (O75185)AlphaFoldClinVar (ATP2C2)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~95.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

speech disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0004730

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ATP2C2 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 300
not providedTotal: 57
ATP2C2-related disorderTotal: 43

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014861.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
26
clinvar
10
clinvar
 38
missense
290
clinvar
22
clinvar
10
clinvar
 322
nonsense
1
clinvar
 1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
4
clinvar
1
clinvar
 5
Total002974821366
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 46 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_014861.4RefSeqNP_055676.327MANE Select
ENST00000262429.9EnsemblENSP00000262429.427MANE Select
NM_001286527.3RefSeqNP_001273456.228Standard
NM_001291454.2RefSeqNP_001278383.123Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Vitamin D Receptor Pathway
  • Ion channel transport
  • Transport of small molecules
  • Ion transport by P-type ATPases

Biological Process

  • cellular calcium ion homeostasis
  • calcium ion transmembrane transport
  • manganese ion transmembrane transport
  • ATP hydrolysis coupled cation transmembrane transport
  • proton transmembrane transport

Molecular Function

  • calcium-transporting ATPase activity
  • protein binding
  • ATP binding
  • proton-exporting ATPase activity, phosphorylative mechanism
  • manganese-transporting ATPase activity

Cellular Component

  • Golgi membrane
  • integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000262429
Coding exons
27
Length
95661
Individuals with no LoFs
122278
Homozygous LoFs
22
Heterozygous LoFs
2541
Defined
124841
p
0.0103
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-5.599505731.660.00003576136
Missense (PolyPhen)469276.561.69582851
Synonymous-8.504232511.680.00001831887
Loss of Function-3.447549.01.530.00000243578

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00280.0028notable
Latino/Admixed American0.00700.0070notable
Ashkenazi Jewish0.00110.0011notable
East Asian0.00240.0023notable
Finnish0.0270.026notable
European (Non-Finnish)0.0120.012notable
South Asian0.00950.0094notable
Other0.0110.011notable

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium. {ECO:0000250}.;

Recessive Scores

pRec
0.105

Intolerance Scores

LoFtool
0.113
RVIS EVS
-0.35
RVIS percentile EVS
29.6

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.189

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerHighMediumHigh
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