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    ATP10A ATPase phospholipid transporting 10A (putative) [ Homo sapiens (human) ]

    Gene ID: 57194, updated on 27-Nov-2024

    Summary

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    Official Symbol
    ATP10Aprovided by HGNC
    Official Full Name
    ATPase phospholipid transporting 10A (putative)provided by HGNC
    Primary source
    HGNC:HGNC:13542
    See related
    Ensembl:ENSG00000206190 MIM:605855; AllianceGenome:HGNC:13542
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ATPVA; ATPVC; ATP10C
    Summary
    The protein encoded by this gene belongs to the family of P-type cation transport ATPases, and to the subfamily of aminophospholipid-transporting ATPases. The aminophospholipid translocases transport phosphatidylserine and phosphatidylethanolamine from one side of a bilayer to another. This gene is maternally expressed. It maps within the most common interval of deletion responsible for Angelman syndrome, also known as 'happy puppet syndrome'. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in adrenal (RPKM 2.8), lung (RPKM 2.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATP10A in Genome Data Viewer
    Location:
    15q12
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (25672237..25865088, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (23410024..23605753, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (25923859..26108474, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2250 Neighboring gene uncharacterized LOC107984789 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:25808594-25809158 Neighboring gene uncharacterized LOC124903448 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:25888031-25888974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:25895885-25896385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:25917854-25918562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:25918563-25919270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:25940327-25940827 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:25941814-25942360 Neighboring gene RNA, 5S ribosomal pseudogene 390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:26014919-26015420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9163 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:26047665-26048164 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:26047324-26047457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:26056572-26057072 Neighboring gene uncharacterized LOC107984770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:26082467-26082968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:26082969-26083468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:26090222-26091063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9165 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6265 Neighboring gene microRNA 4715 Neighboring gene ATP10A divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:26143028-26143528 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:26143529-26144029 Neighboring gene long intergenic non-protein coding RNA 2346 Neighboring gene MRPS18C pseudogene 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. A previously unrecognised phenotype characterised by obesity, muscular hypotonia, and ability to speak in patients with Angelman syndrome caused by an imprinting defect. Gillessen-Kaesbach G, et al. Eur J Hum Genet, 1999 Sep. PMID 10482951
    2. Phospholipid-flipping activity of P4-ATPase drives membrane curvature. Takada N, et al. EMBO J, 2018 May 2. PMID 29599178, Free PMC Article
    3. A novel maternally expressed gene, ATP10C, encodes a putative aminophospholipid translocase associated with Angelman syndrome. Meguro M, et al. Nat Genet, 2001 May. PMID 11326269
    4. Gender influences monoallelic expression of ATP10A in human brain. Hogart A, et al. Hum Genet, 2008 Oct. PMID 18726118, Free PMC Article
    5. Association study of the 15q11-q13 maternal expression domain in Japanese autistic patients. Kato C, et al. Am J Med Genet B Neuropsychiatr Genet, 2008 Oct 5. PMID 18186074

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. results suggest that enhanced PC flipping activity due to exogenous ATP10A expression alters the lipid composition at the plasma membrane
      Title: Phospholipid Flippase ATP10A Translocates Phosphatidylcholine and Is Involved in Plasma Membrane Dynamics.
    2. has been proven that hypocaloric diets induce changes in the DNA methylation pattern in PBMCs (CpG18 of ATP10A and CpG 21 of WT1) and that some of these markers could be used as early indicators of response to metabolic effects of weight-loss programs
      Title: A dual epigenomic approach for the search of obesity biomarkers: DNA methylation in relation to diet-induced weight loss.
    3. ATP10A gene is imprinted, with preferential expression from the maternal allele in human brain.
      Title: The human aminophospholipid-transporting ATPase gene ATP10C maps adjacent to UBE3A and exhibits similar imprinted expression.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. In the analysis of a four-marker haplotype located in ATP10C, a statistically significant difference was observed in the frequency of one haplotype between male autism patients and controls
      Title: Association study of the 15q11-q13 maternal expression domain in Japanese autistic patients.
    6. monoallelic expression of human ATP10A is variable in the population and is influenced by both gender and common genetic variation
      Title: Gender influences monoallelic expression of ATP10A in human brain.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Role of UBE3A and ATP10A genes in autism susceptibility region 15q11-q13 in an Italian population: a positive replication for UBE3A.
    8. report the generation of the complete genomic structure
      Title: An aminophospholipid translocase associated with body fat and type 2 diabetes phenotypes.
    Submit: New GeneRIF Correction

    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
    Haploinsufficency

    No evidence available (Last evaluated 2012-04-24)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-04-24)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    EBI GWAS Catalog
    Genome-wide detection of allele specific copy number variation associated with insulin resistance in African Americans from the HyperGEN study.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0566

    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 ATPase-coupled intramembrane lipid transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATPase-coupled intramembrane lipid transporter activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables ATPase-coupled intramembrane lipid transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables glycosylceramide flippase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylcholine flippase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylcholine floppase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in monoatomic ion transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    involved_in phospholipid translocation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phospholipid translocation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of membrane tubulation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell shape NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of phospholipid-translocating ATPase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of phospholipid-translocating ATPase complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    phospholipid-transporting ATPase VA
    Names
    ATPase type IV, phospholipid transporting (P-type)
    ATPase, Class V, type 10C
    ATPase, class V, type 10A
    P4-ATPase flippase complex alpha subunit ATP10A
    aminophospholipid translocase VA
    probable phospholipid-transporting ATPase VA
    NP_077816.1
    XP_005268318.1
    XP_011520128.1
    XP_011520130.1
    XP_011520131.1
    XP_016877926.1
    XP_047288846.1
    XP_047288847.1
    XP_047288848.1
    XP_054234475.1
    XP_054234476.1
    XP_054234477.1
    XP_054234478.1
    XP_054234479.1
    XP_054234480.1
    XP_054234481.1

    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.

    Genomic

    1. NG_009282.1 RefSeqGene

      Range
      4876..189491
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_024490.4 → NP_077816.1  phospholipid-transporting ATPase VA

      See identical proteins and their annotated locations for NP_077816.1

      Status: REVIEWED

      Source sequence(s)
      AC016266, AC023449, AC109512
      Consensus CDS
      CCDS32178.1
      UniProtKB/Swiss-Prot
      O60312, Q4G0S9, Q969I4
      Related
      ENSP00000450480.2, ENST00000555815.7
      Conserved Domains (5) summary
      TIGR01652
      Location:61 → 1309
      ATPase-Plipid; phospholipid-translocating P-type ATPase, flippase
      pfam13246
      Location:697 → 782
      Cation_ATPase; Cation transport ATPase (P-type)
      pfam16209
      Location:49 → 108
      PhoLip_ATPase_N; Phospholipid-translocating ATPase N-terminal
      pfam16212
      Location:1057 → 1302
      PhoLip_ATPase_C; Phospholipid-translocating P-type ATPase C-terminal
      cl21460
      Location:1026 → 1057
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    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

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      25672237..25865088 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521828.3 → XP_011520130.1  phospholipid-transporting ATPase VA isoform X2

      Conserved Domains (5) summary
      TIGR01652
      Location:61 → 1309
      ATPase-Plipid; phospholipid-translocating P-type ATPase, flippase
      pfam13246
      Location:697 → 782
      Cation_ATPase; Cation transport ATPase (P-type)
      pfam16209
      Location:49 → 108
      PhoLip_ATPase_N; Phospholipid-translocating ATPase N-terminal
      pfam16212
      Location:1057 → 1302
      PhoLip_ATPase_C; Phospholipid-translocating P-type ATPase C-terminal
      cl21460
      Location:1026 → 1057
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    2. XM_005268261.5 → XP_005268318.1  phospholipid-transporting ATPase VA isoform X1

      See identical proteins and their annotated locations for XP_005268318.1

      UniProtKB/Swiss-Prot
      O60312, Q4G0S9, Q969I4
      Conserved Domains (5) summary
      TIGR01652
      Location:61 → 1309
      ATPase-Plipid; phospholipid-translocating P-type ATPase, flippase
      pfam13246
      Location:697 → 782
      Cation_ATPase; Cation transport ATPase (P-type)
      pfam16209
      Location:49 → 108
      PhoLip_ATPase_N; Phospholipid-translocating ATPase N-terminal
      pfam16212
      Location:1057 → 1302
      PhoLip_ATPase_C; Phospholipid-translocating P-type ATPase C-terminal
      cl21460
      Location:1026 → 1057
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    3. XM_011521826.3 → XP_011520128.1  phospholipid-transporting ATPase VA isoform X1

      See identical proteins and their annotated locations for XP_011520128.1

      UniProtKB/Swiss-Prot
      O60312, Q4G0S9, Q969I4
      Related
      ENSP00000349325.6, ENST00000356865.11
      Conserved Domains (5) summary
      TIGR01652
      Location:61 → 1309
      ATPase-Plipid; phospholipid-translocating P-type ATPase, flippase
      pfam13246
      Location:697 → 782
      Cation_ATPase; Cation transport ATPase (P-type)
      pfam16209
      Location:49 → 108
      PhoLip_ATPase_N; Phospholipid-translocating ATPase N-terminal
      pfam16212
      Location:1057 → 1302
      PhoLip_ATPase_C; Phospholipid-translocating P-type ATPase C-terminal
      cl21460
      Location:1026 → 1057
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    4. XM_047432891.1 → XP_047288847.1  phospholipid-transporting ATPase VA isoform X3

    5. XM_047432890.1 → XP_047288846.1  phospholipid-transporting ATPase VA isoform X3

    6. XM_017022437.2 → XP_016877926.1  phospholipid-transporting ATPase VA isoform X3

      Conserved Domains (5) summary
      COG0474
      Location:56 → 995
      MgtA; Magnesium-transporting ATPase (P-type) [Inorganic ion transport and metabolism]
      TIGR01484
      Location:562 → 743
      HAD-SF-IIB; HAD-superfamily hydrolase, subfamily IIB
      pfam13246
      Location:392 → 477
      Cation_ATPase; Cation transport ATPase (P-type)
      pfam16212
      Location:752 → 997
      PhoLip_ATPase_C; Phospholipid-translocating P-type ATPase C-terminal
      cl21460
      Location:721 → 752
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    7. XM_047432892.1 → XP_047288848.1  phospholipid-transporting ATPase VA isoform X3

    8. XM_011521829.3 → XP_011520131.1  phospholipid-transporting ATPase VA isoform X3

      Conserved Domains (5) summary
      COG0474
      Location:56 → 995
      MgtA; Magnesium-transporting ATPase (P-type) [Inorganic ion transport and metabolism]
      TIGR01484
      Location:562 → 743
      HAD-SF-IIB; HAD-superfamily hydrolase, subfamily IIB
      pfam13246
      Location:392 → 477
      Cation_ATPase; Cation transport ATPase (P-type)
      pfam16212
      Location:752 → 997
      PhoLip_ATPase_C; Phospholipid-translocating P-type ATPase C-terminal
      cl21460
      Location:721 → 752
      HAD_like; Haloacid Dehalogenase-like Hydrolases

    RNA

    1. XR_001751368.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      23410024..23605753 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378502.1 → XP_054234477.1  phospholipid-transporting ATPase VA isoform X2

    2. XM_054378501.1 → XP_054234476.1  phospholipid-transporting ATPase VA isoform X1

      UniProtKB/Swiss-Prot
      O60312, Q4G0S9, Q969I4

    3. XM_054378500.1 → XP_054234475.1  phospholipid-transporting ATPase VA isoform X1

      UniProtKB/Swiss-Prot
      O60312, Q4G0S9, Q969I4

    4. XM_054378504.1 → XP_054234479.1  phospholipid-transporting ATPase VA isoform X3

    5. XM_054378503.1 → XP_054234478.1  phospholipid-transporting ATPase VA isoform X3

    6. XM_054378506.1 → XP_054234481.1  phospholipid-transporting ATPase VA isoform X3

    7. XM_054378505.1 → XP_054234480.1  phospholipid-transporting ATPase VA isoform X3

    RNA

    1. XR_008488999.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60312.2 GenPept UniProtKB/Swiss-Prot:O60312

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