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VPS9D1 VPS9 domain containing 1 [ Homo sapiens (human) ]

Gene ID: 9605, updated on 3-Apr-2024

Summary

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Official Symbol
VPS9D1provided by HGNC
Official Full Name
VPS9 domain containing 1provided by HGNC
Primary source
HGNC:HGNC:13526
See related
Ensembl:ENSG00000075399 MIM:619292; AllianceGenome:HGNC:13526
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
ATPBL; ATP-BL; C16orf7
Summary
Enables identical protein binding activity. Predicted to be involved in ATP synthesis coupled proton transport. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 5.5), appendix (RPKM 5.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q24.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (89707134..89720898, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (95791896..95805664, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (89773542..89787306, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7919 Neighboring gene long intergenic non-protein coding RNA 2166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89765851-89766716 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7921 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7920 Neighboring gene cyclin dependent kinase 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11418 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89772795-89773295 Neighboring gene spermatogenesis associated 2 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89777095-89777658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11419 Neighboring gene VPS9D1 antisense RNA 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7923 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:89795065-89795636 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46690 Neighboring gene zinc finger protein 276 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46706 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46704 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46707/46708 Neighboring gene MPRA-validated peak2667 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46713 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46714 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46718 Neighboring gene FA complementation group A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11421 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:89846248-89846785 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89872952-89873474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7925 Neighboring gene Sharpr-MPRA regulatory region 3988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11422 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46779 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7927 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:89900233-89901432 Neighboring gene uncharacterized LOC124903760 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89903444-89904066 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:89904067-89904688 Neighboring gene spire type actin nucleation factor 2

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. Isolation and mapping of a putative b subunit of human ATP synthase (ATP-BL) from human leukocytes. Sugimoto J, et al. DNA Res, 1999 Feb 26. PMID 10231027
  2. Vps9d1 regulates tubular endosome formation through specific activation of Rab22A. Nakashima S, et al. J Cell Sci, 2023 Mar 15. PMID 36762583
  3. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. Choy KW, et al. Physiol Genomics, 2006 Mar 13. PMID 16368877
  4. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512
  5. Toward a confocal subcellular atlas of the human proteome. Barbe L, et al. Mol Cell Proteomics, 2008 Mar. PMID 18029348

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Vps9d1 regulates tubular endosome formation through specific activation of Rab22A.
    Title: Vps9d1 regulates tubular endosome formation through specific activation of Rab22A.
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

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IEA
Inferred from Electronic Annotation
more info
  
enables guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables small GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in proton motive force-driven ATP synthesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in endocytic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
VPS9 domain-containing protein 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.

mRNA and Protein(s)

  1. NM_004913.3 → NP_004904.2  VPS9 domain-containing protein 1

    See identical proteins and their annotated locations for NP_004904.2

    Status: VALIDATED

    Source sequence(s)
    AB018551, AC010538, AI458261, BC052626, BM920493, BY795348, CA428853
    Consensus CDS
    CCDS42220.1
    UniProtKB/Swiss-Prot
    Q9Y2B5
    UniProtKB/TrEMBL
    H3BM58
    Related
    ENSP00000374037.3, ENST00000389386.8
    Conserved Domains (1) summary
    pfam02204
    Location:509 → 624
    VPS9; Vacuolar sorting protein 9 (VPS9) domain

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    89707134..89720898 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047434932.1 → XP_047290888.1  VPS9 domain-containing protein 1 isoform X5

  2. XM_011523476.4 → XP_011521778.1  VPS9 domain-containing protein 1 isoform X4

    UniProtKB/TrEMBL
    H3BM58
    Conserved Domains (1) summary
    pfam02204
    Location:509 → 624
    VPS9; Vacuolar sorting protein 9 (VPS9) domain

  3. XM_047434931.1 → XP_047290887.1  VPS9 domain-containing protein 1 isoform X2

  4. XM_047434936.1 → XP_047290892.1  VPS9 domain-containing protein 1 isoform X9

  5. XM_005256329.6 → XP_005256386.1  VPS9 domain-containing protein 1 isoform X3

    UniProtKB/TrEMBL
    H3BM58
    Conserved Domains (1) summary
    pfam02204
    Location:510 → 625
    VPS9; Vacuolar sorting protein 9 (VPS9) domain

  6. XM_047434935.1 → XP_047290891.1  VPS9 domain-containing protein 1 isoform X8

  7. XM_047434930.1 → XP_047290886.1  VPS9 domain-containing protein 1 isoform X1

  8. XM_047434937.1 → XP_047290893.1  VPS9 domain-containing protein 1 isoform X10

    Related
    ENSP00000454244.1, ENST00000561976.5

  9. XM_047434933.1 → XP_047290889.1  VPS9 domain-containing protein 1 isoform X6

  10. XM_047434934.1 → XP_047290890.1  VPS9 domain-containing protein 1 isoform X7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    95791896..95805664 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054314449.1 → XP_054170424.1  VPS9 domain-containing protein 1 isoform X5

  2. XM_054314448.1 → XP_054170423.1  VPS9 domain-containing protein 1 isoform X4

  3. XM_054314446.1 → XP_054170421.1  VPS9 domain-containing protein 1 isoform X2

  4. XM_054314453.1 → XP_054170428.1  VPS9 domain-containing protein 1 isoform X9

  5. XM_054314447.1 → XP_054170422.1  VPS9 domain-containing protein 1 isoform X3

  6. XM_054314451.1 → XP_054170426.1  VPS9 domain-containing protein 1 isoform X8

  7. XM_054314445.1 → XP_054170420.1  VPS9 domain-containing protein 1 isoform X1

  8. XM_054314450.1 → XP_054170425.1  VPS9 domain-containing protein 1 isoform X6

  9. XM_054314452.1 → XP_054170427.1  VPS9 domain-containing protein 1 isoform X7

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2B5.2 GenPept UniProtKB/Swiss-Prot:Q9Y2B5

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