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

Gene ID: 57205, updated on 5-Mar-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. Is integral component of plasma membrane. Part of phospholipid-translocating ATPase complex. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
4p12
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (47485275..47593486)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (47452618..47560826)
105.20220307 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)

Genotypes

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_2023_10

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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