VPS9D1 Gene (Protein Coding)

VPS9 Domain Containing 1

GC16M089707
GIFtS:
30
See more...

Aliases for VPS9D1 Gene

Aliases for VPS9D1 Gene

  • VPS9 Domain Containing 1 2 3 5
  • VPS9 Domain-Containing Protein 1 3 4
  • C16orf7 3 4
  • ATP-BL 2 3
  • Chromosome 16 Open Reading Frame 7 2
  • Protein ATP-BL 4
  • VPS9D1 5
  • ATPBL 4

External Ids for VPS9D1 Gene

Previous HGNC Symbols for VPS9D1 Gene

  • C16orf7

Previous GeneCards Identifiers for VPS9D1 Gene

  • GC16M089774

Summaries for VPS9D1 Gene

GeneCards Summary for VPS9D1 Gene

VPS9D1 (VPS9 Domain Containing 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and transporter activity. An important paralog of this gene is GAPVD1.

Gene Wiki entry for VPS9D1 Gene

Additional gene information for VPS9D1 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for VPS9D1 Gene

Genomics for VPS9D1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for VPS9D1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around VPS9D1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for VPS9D1

Genomic Locations for VPS9D1 Gene

Genomic Locations for VPS9D1 Gene
chr16:89,707,133-89,721,231
(GRCh38/hg38)
Size:
14,099 bases
Orientation:
Minus strand
chr16:89,773,541-89,787,394
(GRCh37/hg19)
Size:
13,854 bases
Orientation:
Minus strand

Genomic View for VPS9D1 Gene

Genes around VPS9D1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VPS9D1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VPS9D1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for VPS9D1 Gene

Proteins for VPS9D1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for VPS9D1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2B5-VP9D1_HUMAN
    Recommended name:
    VPS9 domain-containing protein 1
    Protein Accession:
    Q9Y2B5

    Protein attributes for VPS9D1 Gene

    Size:
    631 amino acids
    Molecular mass:
    68956 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA76711.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for VPS9D1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VPS9D1 Gene

Protein Expression for VPS9D1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for VPS9D1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for VPS9D1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for VPS9D1 Gene

Domains & Families for VPS9D1 Gene

Gene Families for VPS9D1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for VPS9D1 Gene

InterPro:
Blocks:
  • FIS bacterial regulatory protein HTH signature
ProtoNet:

Suggested Antigen Peptide Sequences for VPS9D1 Gene

GenScript: Design optimal peptide antigens:
  • Protein ATP-BL (CP007_HUMAN)
genes like me logo Genes that share domains with VPS9D1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for VPS9D1 Gene

Function for VPS9D1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes From GWAS Catalog for VPS9D1 Gene

Gene Ontology (GO) - Molecular Function for VPS9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA --
GO:0005215 transporter activity TAS 10231027
genes like me logo Genes that share ontologies with VPS9D1: view
genes like me logo Genes that share phenotypes with VPS9D1: view

Animal Models for VPS9D1 Gene

MGI Knock Outs for VPS9D1:
  • Vps9d1 Vps9d1<tm1b(KOMP)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS9D1

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for VPS9D1 Gene

Localization for VPS9D1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VPS9D1 gene
Compartment Confidence
nucleus 3
cytosol 3
mitochondrion 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for VPS9D1 Gene

Pathways & Interactions for VPS9D1 Gene

PathCards logo

SuperPathways for VPS9D1 Gene

No Data Available

Interacting Proteins for VPS9D1 Gene

STRING Interaction Network Preview (showing top 1 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: Q9Y2B5-VP9D1_HUMAN ENSP00000374037 for VPS9D1 Gene via UniProtKB STRING IID

GPS-Prot Interaction Network for VPS9D1

Gene Ontology (GO) - Biological Process for VPS9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015986 ATP synthesis coupled proton transport TAS 10231027
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with VPS9D1: view

No data available for Pathways by source and SIGNOR curated interactions for VPS9D1 Gene

Drugs & Compounds for VPS9D1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for VPS9D1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for VPS9D1 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for VPS9D1

Alternative Splicing Database (ASD) splice patterns (SP) for VPS9D1 Gene

No ASD Table

Relevant External Links for VPS9D1 Gene

GeneLoc Exon Structure for
VPS9D1

Expression for VPS9D1 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for VPS9D1 Gene

mRNA expression in normal human tissues for VPS9D1 Gene
mRNA expression by GTEx for VPS9D1 GenemRNA expression by BioGPS for VPS9D1 Gene

mRNA differential expression in normal tissues according to GTEx for VPS9D1 Gene

This gene is overexpressed in Whole Blood (x7.3).

Protein differential expression in normal tissues from HIPED for VPS9D1 Gene

This gene is overexpressed in Fetal Brain (31.4), Frontal cortex (26.7), and Retina (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for VPS9D1 Gene



Protein tissue co-expression partners for VPS9D1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for VPS9D1

SOURCE GeneReport for Unigene cluster for VPS9D1 Gene:

Hs.164410

mRNA Expression by UniProt/SwissProt for VPS9D1 Gene:

Q9Y2B5-VP9D1_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for VPS9D1 Gene

  • Blood(4.1)
genes like me logo Genes that share expression patterns with VPS9D1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for VPS9D1 Gene

Orthologs for VPS9D1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for VPS9D1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia VPS9D1 30 31
  • 92.25 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia VPS9D1 30 31
  • 83.64 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia VPS9D1 30 31
  • 82.78 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Vps9d1 30 17 31
  • 81.34 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Vps9d1 30
  • 80.96 (n)
Oppossum
(Monodelphis domestica)
 Mammalia VPS9D1 31
  • 70 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia VPS9D1 31
  • 69 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves C11H16ORF7 30
  • 68.5 (n)
VPS9D1 31
  • 61 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia VPS9D1 31
  • 64 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia vps9d1 30
  • 58.08 (n)
Str.15453 30
African clawed frog
(Xenopus laevis)
 Amphibia Xl.29400 30
Zebrafish
(Danio rerio)
 Actinopterygii vps9d1 30 31
  • 60 (n)
 OneToOne
idibd5127 30
Species where no ortholog for VPS9D1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for VPS9D1 Gene

ENSEMBL:
Gene Tree for VPS9D1 (if available)
TreeFam:
Gene Tree for VPS9D1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for VPS9D1: view image

Paralogs for VPS9D1 Gene

Paralogs for VPS9D1 Gene

genes like me logo Genes that share paralogs with VPS9D1: view

Variants for VPS9D1 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for VPS9D1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
715687 Benign: not provided 89,711,882(-) A/G NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
768806 Benign: not provided 89,712,511(-) T/C SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for VPS9D1 Gene

Structural Variations from Database of Genomic Variants (DGV) for VPS9D1 Gene

Variant ID Type Subtype PubMed ID
esv2762221 CNV gain+loss 21179565
nsv1057351 CNV loss 25217958
nsv1931 CNV insertion 18451855
nsv428331 CNV gain+loss 18775914
nsv457623 CNV gain 19166990
nsv482951 CNV loss 15286789
nsv509639 CNV insertion 20534489
nsv516241 CNV loss 19592680
nsv573743 CNV gain 21841781
nsv833330 CNV loss 17160897
nsv952079 CNV deletion 24416366

Variation tolerance for VPS9D1 Gene

Residual Variation Intolerance Score: 58.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.07; 50.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VPS9D1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
VPS9D1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VPS9D1 Gene

Disorders for VPS9D1 Gene

Additional Disease Information for VPS9D1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform

No disorders were found for VPS9D1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for VPS9D1 Gene

Publications for VPS9D1 Gene

  1. Isolation and mapping of a putative b subunit of human ATP synthase (ATP-BL) from human leukocytes. (PMID: 10231027) Sugimoto J … Isobe M (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4
  2. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  3. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein MY … Mann M (Cell 2015) 3
  4. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L … Andersson-Svahn H (Molecular & cellular proteomics : MCP 2008) 3
  5. Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes. (PMID: 16368877) Choy KW … Pang CP (Physiological genomics 2006) 3

ExternalLinks

View latest publications for VPS9D1 gene in Mastermind

Products for VPS9D1 Gene

Sources for VPS9D1 Gene