ATP2C1

ATPase secretory pathway Ca2+ transporting 1, the group of ATPases Ca2+ transporting

Basic information

Region (hg38): 3:130850595-131016712

Previous symbols: [ "BCPM" ]

Links

ENSG00000017260 ∙ NCBI:27032 ∙ OMIM:604384 ∙ HGNC:13211 ∙ Uniprot:P98194 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Hailey-Hailey disease (Strong), mode of inheritance: AD
• Hailey-Hailey disease (Strong), mode of inheritance: AD
• Hailey-Hailey disease (Strong), mode of inheritance: AD
• Hailey-Hailey disease (Supportive), mode of inheritance: AD
• Hailey-Hailey disease (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hailey-Hailey disease	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	4939904; 5093171; 3978039; 2528572; 1554604; 1575528; 10615129; 15545997; 21623880; 21883398; 22124882; 22229453; 22607350; 22788811

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP2C1 gene.

• not provided (17 variants)
• Familial benign pemphigus (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP2C1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			7	8	4	19
missense		2	39		4	45
nonsense	7					7
start loss						0
frameshift	7					7
inframe indel						0
splice donor/acceptor (+/-2bp)	3	3				6
splice region			4	4	4	12
non coding			35	9	60	104
Total	17	5	81	17	68

Highest pathogenic variant AF is 0.00000657

Variants in ATP2C1

This is a list of pathogenic ClinVar variants found in the ATP2C1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-130850713-T-G			Benign (Nov 10, 2018)
3-130850882-T-A		ATP2C1-related disorder	Benign (Mar 19, 2019)
3-130894512-GCTCCCGAGATAGTGGCTGGGCGGGGAA-G			Benign (Nov 01, 2022)
3-130894518-G-A		Familial benign pemphigus	Uncertain significance (Jan 13, 2018)
3-130894533-C-T		Familial benign pemphigus	Uncertain significance (Jan 13, 2018)
3-130894557-C-A		Familial benign pemphigus	Benign (Jan 12, 2018)
3-130894680-G-C		Familial benign pemphigus	Uncertain significance (Jan 17, 2018)
3-130894688-CCT-C		Familial benign pemphigus	Uncertain significance (Jun 14, 2016)
3-130894704-C-T		Familial benign pemphigus	Uncertain significance (Jan 12, 2018)
3-130894706-A-G		Familial benign pemphigus	Uncertain significance (Jan 13, 2018)
3-130894737-T-C		Familial benign pemphigus	Benign (Jan 13, 2018)
3-130894762-G-A		ATP2C1-related disorder	Likely benign (Nov 11, 2019)
3-130894786-CT-C			Likely benign (Jun 04, 2021)
3-130894790-C-G		Familial benign pemphigus • not specified	Benign (Jan 22, 2024)
3-130930437-C-G		Inborn genetic diseases	Uncertain significance (Mar 04, 2024)
3-130930437-C-T		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)
3-130930450-A-C		Inborn genetic diseases	Uncertain significance (Jun 17, 2022)
3-130930450-A-G		Familial benign pemphigus	Uncertain significance (Jan 12, 2018)
3-130930526-AG-A			Pathogenic (Mar 01, 2021)
3-130930533-G-A		Familial benign pemphigus	Benign (Jan 11, 2024)
3-130930702-T-C			Benign (May 10, 2021)
3-130930853-A-G			Benign (Jun 21, 2021)
3-130931782-A-G			Benign (May 10, 2021)
3-130932014-T-C		ATP2C1-related disorder	Likely benign (Nov 25, 2019)
3-130932039-T-C		Familial benign pemphigus	Likely benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP2C1	protein_coding	protein_coding	ENST00000393221	28	166118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000294	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.67	280	514	0.544	0.0000257	6368
Missense in Polyphen		51	167.14	0.30513		2039
Synonymous	0.322	162	167	0.968	0.00000820	1873
Loss of Function	6.43	5	57.7	0.0867	0.00000298	685

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000547	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.0000547	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of the calcium.
• Pathway: Ion channel transport;Purine metabolism;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.209

Intolerance Scores

• loftool: 0.00903
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.904
• hipred: Y
• hipred_score: 0.792
• ghis: 0.597

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.195

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Atp2c1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; embryo phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: calcium ion transport;cellular calcium ion homeostasis;epidermis development;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;actin cytoskeleton reorganization;Golgi calcium ion homeostasis;Golgi calcium ion transport;positive regulation of I-kappaB kinase/NF-kappaB signaling;calcium ion transmembrane transport;manganese ion transmembrane transport;ATP hydrolysis coupled cation transmembrane transport;proton transmembrane transport
• Cellular component: Golgi membrane;Golgi apparatus;trans-Golgi network;membrane;integral component of membrane
• Molecular function: calcium-transporting ATPase activity;ATP binding;proton-exporting ATPase activity, phosphorylative mechanism;manganese-transporting ATPase activity;metal ion binding