ATP2C2

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

Basic information

Region (hg38): 16:84368526-84464187

Links

ENSG00000064270 ∙ NCBI:9914 ∙ OMIM:613082 ∙ HGNC:29103 ∙ Uniprot:O75185 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP2C2 gene.

• Inborn genetic diseases (96 variants)
• not provided (58 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP2C2 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				15	9	24
missense			93	7	9	109
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region			1	3	3	7
non coding				3	4	7
Total	0	0	93	25	23

Variants in ATP2C2

This is a list of pathogenic ClinVar variants found in the ATP2C2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-84368623-A-G		not specified	Uncertain significance (Jun 07, 2023)
16-84368656-G-A		not specified	Uncertain significance (Feb 06, 2023)
16-84368670-G-A		not specified	Uncertain significance (Oct 02, 2023)
16-84368680-A-G		ATP2C2-related disorder	Likely benign (Dec 27, 2022)
16-84368710-C-G		not specified	Uncertain significance (Aug 17, 2021)
16-84398553-C-T		ATP2C2-related disorder	Likely benign (Jun 06, 2019)
16-84398569-C-T		not specified	Uncertain significance (Jun 02, 2023)
16-84398570-G-C		ATP2C2-related disorder	Likely benign (Apr 08, 2019)
16-84405153-A-T		not specified	Conflicting classifications of pathogenicity (Jan 18, 2024)
16-84405187-C-G		ATP2C2-related disorder	Likely benign (Aug 29, 2019)
16-84405214-C-T		ATP2C2-related disorder	Likely benign (Mar 20, 2019)
16-84405215-G-A		not specified	Uncertain significance (Jan 03, 2022)
16-84405221-G-A			Conflicting classifications of pathogenicity (Mar 01, 2023)
16-84408400-T-G			Likely benign (Jun 06, 2018)
16-84408455-C-A			Likely benign (Mar 01, 2023)
16-84408489-G-A			Benign (Dec 31, 2019)
16-84410590-T-C		not specified	Uncertain significance (Jul 08, 2022)
16-84410598-A-T		not specified	Uncertain significance (Mar 24, 2023)
16-84410600-C-G		ATP2C2-related disorder	Benign (Apr 25, 2019)
16-84410600-C-T			Likely benign (Aug 16, 2018)
16-84410733-G-C		not specified	Uncertain significance (Nov 21, 2023)
16-84410753-C-T		not specified	Uncertain significance (Jan 30, 2024)
16-84415491-A-G		not specified	Uncertain significance (Sep 12, 2023)
16-84415502-C-G		not specified	Uncertain significance (Mar 14, 2023)
16-84415518-G-A		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP2C2	protein_coding	protein_coding	ENST00000262429	27	95661

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.02e-60	5.09e-14	122278	22	2541	124841	0.0103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-5.59	950	573	1.66	0.0000357	6136
Missense in Polyphen		469	276.56	1.6958		2851
Synonymous	-8.50	423	251	1.68	0.0000183	1887
Loss of Function	-3.44	75	49.0	1.53	0.00000243	578

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00981	0.00978
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.00237	0.00234
Finnish	0.0265	0.0263
European (Non-Finnish)	0.0117	0.0116
Middle Eastern	0.00237	0.00234
South Asian	0.00949	0.00936
Other	0.0114	0.0114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of calcium. {ECO:0000250}.
• Pathway: Vitamin D Receptor Pathway;Ion channel transport;Transport of small molecules;Ion transport by P-type ATPases (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.113
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.6

Haploinsufficiency Scores

• pHI: 0.145
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.189

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Atp2c2

Gene ontology

• Biological process: cellular calcium ion homeostasis;calcium ion transmembrane transport;manganese ion transmembrane transport;ATP hydrolysis coupled cation transmembrane transport;proton transmembrane transport
• Cellular component: Golgi membrane;integral component of membrane
• Molecular function: calcium-transporting ATPase activity;protein binding;ATP binding;proton-exporting ATPase activity, phosphorylative mechanism;manganese-transporting ATPase activity;metal ion binding