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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
ATP2C1
ATPase secretory pathway Ca2+ transporting 1
Chromosome 3 Β· 3q22.1
NCBI Gene: 27032Ensembl: ENSG00000017260.20HGNC: HGNC:13211UniProt: B4E295
156PubMed Papers
21Diseases
0Drugs
53Pathogenic Variants
FUNCTIONAL ROLE
Transporter
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
P-type manganese transporter activitytrans-Golgi networkcalcium ion transportmembraneHailey-Hailey diseaseFamilial benign chronic pemphigusrestless legs syndromemovement disorder
✦AI Summary

ATP2C1 encodes a P-type ATPase that pumps calcium and manganese ions from the cytoplasm into the Golgi apparatus lumen in an ATP-dependent manner 123. The pump operates through a catalytic cycle involving transient phosphorylation that shifts the protein between inward-facing and outward-facing conformational states, facilitating ion translocation across the membrane 24. ATP2C1 maintains Golgi calcium homeostasis, which is essential for protein processing, trafficking, and proper cisternae morphology 53. In keratinocytes specifically, ATP2C1 loads Golgi calcium stores, supporting keratinocyte differentiation and epidermis integrity 65. Heterozygous mutations in ATP2C1 cause Hailey-Hailey disease, a rare autosomal dominant acantholytic dermatosis characterized by compromised keratinocyte adhesion, vesico-bullous lesions in friction areas, and abnormal cytosolic calcium/manganese levels 78. Over 166 pathogenic ATP2C1 mutations have been identified globally, including frameshift and nonsense variants 9. Disease manifestations result from altered junctional protein synthesis and acantholysis, with clinical severity influenced by environmental triggers including humidity, friction, and heat 7. Currently, no cure exists; management involves symptom control through topical and systemic therapies 7.

Sources cited
1
ATP2C1 supplies the Golgi apparatus with Ca2+ and Mn2+ ions essential for protein processing and trafficking
PMID: 12707275
2
ATP2C1 transports ions coupled to ATP hydrolysis via transient phosphorylation and conformational changes
PMID: 16192278
3
ATP2C1 maintains Ca2+ homeostasis in trans-Golgi compartment affecting protein sorting and cisternae morphology
PMID: 20439740
4
ATP2C1 operates through phosphorylation-dependent conformational shifts in the catalytic cycle
PMID: 30923126
5
ATP2C1 localizes to Golgi in keratinocytes and controls Golgi Ca2+ stores; mutations correlate with decreased protein and lower Golgi Ca2+ levels
PMID: 14632183
6
ATP2C1 loads Golgi stores with Ca2+ ions in keratinocytes, contributing to differentiation and epidermis integrity
PMID: 10615129
7
ATP2C1 mutations cause Hailey-Hailey disease with autosomal dominant inheritance, acantholysis, and vesico-bullous lesions; triggered by humidity, friction, heat, and trauma
PMID: 38789364
8
ATP2C1 mutations cause abnormal cytosolic Ca2+/Mn2+ levels and Hailey-Hailey disease pathogenesis
PMID: 28551824
9
Over 166 pathogenic ATP2C1 mutations have been identified worldwide, including frameshift and nonsense mutations
PMID: 29104283
Disease Associationsβ“˜21
Hailey-Hailey diseaseOpen Targets
0.75Strong
Familial benign chronic pemphigusOpen Targets
0.67Moderate
restless legs syndromeOpen Targets
0.42Moderate
movement disorderOpen Targets
0.36Weak
autoimmune disorder of musculoskeletal systemOpen Targets
0.30Weak
cutaneous lupus erythematosusOpen Targets
0.30Weak
systemic lupus erythematosusOpen Targets
0.30Weak
placenta praeviaOpen Targets
0.22Weak
neurodegenerative diseaseOpen Targets
0.21Weak
genetic disorderOpen Targets
0.19Weak
epidermodysplasia verruciformisOpen Targets
0.07Suggestive
Li-Fraumeni syndromeOpen Targets
0.06Suggestive
familial adenomatous polyposis 3Open Targets
0.06Suggestive
familial cylindromatosisOpen Targets
0.06Suggestive
attenuated familial adenomatous polyposisOpen Targets
0.06Suggestive
familial atypical multiple mole melanoma syndromeOpen Targets
0.06Suggestive
head and neck squamous cell carcinomaOpen Targets
0.05Suggestive
myofibromatosis, infantile, 1Open Targets
0.05Suggestive
colorectal cancer, susceptibility to, 12Open Targets
0.05Suggestive
reticulum cell sarcomaOpen Targets
0.05Suggestive
Hailey-Hailey diseaseUniProt
Pathogenic Variants53
NM_001378687.1(ATP2C1):c.2213A>G (p.Asn738Ser)Likely pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 738
NM_001378687.1(ATP2C1):c.1356C>A (p.Tyr452Ter)Pathogenic
not provided|Familial benign pemphigus
β˜…β˜…β˜†β˜†2024β†’ Residue 452
NM_001378687.1(ATP2C1):c.2375_2378del (p.Phe792fs)Pathogenic
Familial benign pemphigus|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 792
NM_001378687.1(ATP2C1):c.2127-1G>ALikely pathogenic
Melanoma|not provided
β˜…β˜†β˜†β˜†2025
NM_001378687.1(ATP2C1):c.2321del (p.Asn774fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 774
NM_001378687.1(ATP2C1):c.2244-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_001378687.1(ATP2C1):c.1741+3A>GPathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_001378687.1(ATP2C1):c.519dup (p.Arg174fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 174
NM_001378687.1(ATP2C1):c.215G>A (p.Trp72Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 72
NM_001378687.1(ATP2C1):c.1402C>T (p.Arg468Ter)Pathogenic
Familial benign pemphigus|not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 468
NM_001378687.1(ATP2C1):c.1553del (p.Gly518fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 518
NM_001378687.1(ATP2C1):c.436_443del (p.Lys146fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 146
NM_001378687.1(ATP2C1):c.836dup (p.Ile280fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 280
NM_001378687.1(ATP2C1):c.2395C>T (p.Arg799Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 799
NM_001378687.1(ATP2C1):c.163C>T (p.Arg55Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 55
NM_001378687.1(ATP2C1):c.688-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_001378687.1(ATP2C1):c.324+1G>TLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_001378687.1(ATP2C1):c.1738A>G (p.Ile580Val)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 580
NM_001378687.1(ATP2C1):c.727G>T (p.Glu243Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 243
NM_001378687.1(ATP2C1):c.2416C>T (p.Arg806Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 806
View on ClinVar β†—
Related Genes
F7Protein interaction90%CFL1Protein interaction87%TMEM165Protein interaction60%ATP2C2Shared pathway50%ATP2A3Shared pathway21%CACNG6Shared pathway18%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
72%
Heart
62%
Lung
45%
Ovary
39%
Liver
25%
Gene Interaction Network
Click a node to explore
ATP2C1F7CFL1TMEM165ATP2C2ATP2A3CACNG6
PROTEIN STRUCTURE
Preparing viewer…
PDB7YAG Β· 3.10 Γ… Β· EM
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.40Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.28 [0.20–0.40]
RankingsWhere ATP2C1 stands among ~20K protein-coding genes
  • #2,878of 20,598
    Most Researched156 Β· top quartile
  • #1,275of 5,498
    Most Pathogenic Variants53 Β· top quartile
  • #2,020of 17,882
    Most Constrained (LOEUF)0.40 Β· top quartile
Genes detectedATP2C1
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
Hailey-Hailey disease: clinical, diagnostic and therapeutic update.
PMID: 38789364
An Bras Dermatol Β· 2024
1.00
2
ATP2C1 gene mutations in Hailey-Hailey disease and possible roles of SPCA1 isoforms in membrane trafficking.
PMID: 27277681
Cell Death Dis Β· 2016
0.90
3
The role of the ATP2C1 gene in Hailey-Hailey disease.
PMID: 28551824
Cell Mol Life Sci Β· 2017
0.80
4
Identification of 2 Novel Mutations in ATP2C1 Gene in Hailey-Hailey Disease and a Literature Review of Variations in a Chinese Han Population.
PMID: 29104283
Med Sci Monit Basic Res Β· 2017
0.70
5
Deciphering glial contributions to CSF1R-related disorder via single-nuclear transcriptomic profiling: a case study.
PMID: 39217398
Acta Neuropathol Commun Β· 2024
0.60