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    ATP10D ATPase phospholipid transporting 10D (putative) [ Homo sapiens (human) ]

    Gene ID: 57205, updated on 27-Nov-2024

    Summary

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    Official Symbol
    ATP10Dprovided by HGNC
    Official Full Name
    ATPase phospholipid transporting 10D (putative)provided by HGNC
    Primary source
    HGNC:HGNC:13549
    See related
    Ensembl:ENSG00000145246 MIM:619815; AllianceGenome:HGNC:13549
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ATPVD
    Summary
    Enables glycosylceramide flippase activity. Predicted to be involved in phospholipid translocation. Located in endoplasmic reticulum; nucleoplasm; and plasma membrane. Part of phospholipid-translocating ATPase complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in placenta (RPKM 7.9), skin (RPKM 7.8) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See ATP10D in Genome Data Viewer
    Location:
    4p12
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (47485275..47593486)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (47452618..47560826)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (47487292..47595503)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15399 Neighboring gene uncharacterized LOC107986277 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21530 Neighboring gene COMM domain containing 8 Neighboring gene Sharpr-MPRA regulatory region 5912 Neighboring gene ribosomal protein L21 pseudogene 52 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15400 Neighboring gene uncharacterized LOC105374444 Neighboring gene corin, serine peptidase Neighboring gene NANOG hESC enhancer GRCh37_chr4:47653202-47653745 Neighboring gene microRNA 8053

    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 gene variant in the Atp10d gene associates with atherosclerotic indices in Japanese elderly population. Kengia JT, et al. Atherosclerosis, 2013 Nov. PMID 24125428
    2. Characterization of a putative type IV aminophospholipid transporter P-type ATPase. Flamant S, et al. Mamm Genome, 2003 Jan. PMID 12532265
    3. Genetic determinants of circulating sphingolipid concentrations in European populations. Hicks AA, et al. PLoS Genet, 2009 Oct. PMID 19798445, Free PMC Article
    4. Yeast and human P4-ATPases transport glycosphingolipids using conserved structural motifs. Roland BP, et al. J Biol Chem, 2019 Feb 8. PMID 30530492, Free PMC Article
    5. Phospholipid Flippase ATP10A Translocates Phosphatidylcholine and Is Involved in Plasma Membrane Dynamics. Naito T, et al. J Biol Chem, 2015 Jun 12. PMID 25947375, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The rs2351791 SNP in the Atp10d gene affects the susceptibility for cardiac and intracranial vascular stenosis in the elderly Japanese population.
      Title: A gene variant in the Atp10d gene associates with atherosclerotic indices in Japanese elderly population.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    3. 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.
    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

    EBI GWAS Catalog

    Description
    Genetic determinants of circulating sphingolipid concentrations in European populations.
    EBI GWAS Catalog
    Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1487

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in monoatomic cation transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 
    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 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    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 VD
    Names
    ATPase, class V, type 10D
    P4-ATPase flippase complex alpha subunit ATP10D
    probable phospholipid-transporting ATPase VD
    type IV aminophospholipid transporting ATPase
    NP_065186.3

    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.

    mRNA and Protein(s)

    1. NM_020453.4 → NP_065186.3  phospholipid-transporting ATPase VD

      See identical proteins and their annotated locations for NP_065186.3

      Status: VALIDATED

      Source sequence(s)
      AC107398, AJ441078, BC131535
      Consensus CDS
      CCDS3476.1
      UniProtKB/Swiss-Prot
      A2RRC8, D6REN2, Q8NC70, Q96SR3, Q9P241
      Related
      ENSP00000273859.3, ENST00000273859.8
      Conserved Domains (6) summary
      TIGR01652
      Location:71 → 1327
      ATPase-Plipid; phospholipid-translocating P-type ATPase, flippase
      pfam00122
      Location:128 → 216
      E1-E2_ATPase; E1-E2 ATPase
      pfam13246
      Location:727 → 807
      Cation_ATPase; Cation transport ATPase (P-type)
      pfam16209
      Location:71 → 122
      PhoLip_ATPase_N; Phospholipid-translocating ATPase N-terminal
      pfam16212
      Location:1082 → 1327
      PhoLip_ATPase_C; Phospholipid-translocating P-type ATPase C-terminal
      cl21460
      Location:1051 → 1082
      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      47485275..47593486
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      47452618..47560826
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P241.3 GenPept UniProtKB/Swiss-Prot:Q9P241

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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