Aliases for GAPVD1 Gene

Aliases for GAPVD1 Gene

  • GTPase Activating Protein And VPS9 Domains 1 2 3 5
  • GTPase-Activating Protein And VPS9 Domain-Containing Protein 1 3 4
  • Rab5-Activating Protein 6 3 4
  • GAPex-5 3 4
  • GAPEX5 3 4
  • RAP6 3 4
  • Rab5 Exchange Factor 3
  • KIAA1521 4

External Ids for GAPVD1 Gene

Previous GeneCards Identifiers for GAPVD1 Gene

  • GC09P125104
  • GC09P127063
  • GC09P128024
  • GC09P097636
  • GC09P125261

Summaries for GAPVD1 Gene

GeneCards Summary for GAPVD1 Gene

GAPVD1 (GTPase Activating Protein And VPS9 Domains 1) is a Protein Coding gene. Diseases associated with GAPVD1 include Familial Idiopathic Steroid-Resistant Nephrotic Syndrome With Focal Segmental Hyalinosis. Among its related pathways are Vesicle-mediated transport and Clathrin-mediated endocytosis. Gene Ontology (GO) annotations related to this gene include GTPase activator activity and GTPase activating protein binding. An important paralog of this gene is RIN3.

UniProtKB/Swiss-Prot Summary for GAPVD1 Gene

  • Acts both as a GTPase-activating protein (GAP) and a guanine nucleotide exchange factor (GEF), and participates in various processes such as endocytosis, insulin receptor internalization or LC2A4/GLUT4 trafficking. Acts as a GEF for the Ras-related protein RAB31 by exchanging bound GDP for free GTP, leading to regulate LC2A4/GLUT4 trafficking. In the absence of insulin, it maintains RAB31 in an active state and promotes a futile cycle between LC2A4/GLUT4 storage vesicles and early endosomes, retaining LC2A4/GLUT4 inside the cells. Upon insulin stimulation, it is translocated to the plasma membrane, releasing LC2A4/GLUT4 from intracellular storage vesicles. Also involved in EGFR trafficking and degradation, possibly by promoting EGFR ubiquitination and subsequent degradation by the proteasome. Has GEF activity for Rab5 and GAP activity for Ras.

Gene Wiki entry for GAPVD1 Gene

Additional gene information for GAPVD1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GAPVD1 Gene

Genomics for GAPVD1 Gene

GeneHancer (GH) Regulatory Elements for GAPVD1 Gene

Promoters and enhancers for GAPVD1 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 GAPVD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GAPVD1 gene promoter:
  • AP-1
  • ATF-2
  • ATF6
  • CREB
  • Egr-4
  • MRF-2
  • Nkx2-5
  • Olf-1
  • STAT5A

Genomic Locations for GAPVD1 Gene

Genomic Locations for GAPVD1 Gene
chr9:125,241,663-125,367,207
(GRCh38/hg38)
Size:
125,545 bases
Orientation:
Plus strand
chr9:128,024,073-128,129,486
(GRCh37/hg19)
Size:
105,414 bases
Orientation:
Plus strand

Genomic View for GAPVD1 Gene

Genes around GAPVD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GAPVD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GAPVD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GAPVD1 Gene

Proteins for GAPVD1 Gene

  • Protein details for GAPVD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14C86-GAPD1_HUMAN
    Recommended name:
    GTPase-activating protein and VPS9 domain-containing protein 1
    Protein Accession:
    Q14C86
    Secondary Accessions:
    • A8MYK3
    • B0QZ62
    • B0QZ63
    • B0QZ64
    • Q14C76
    • Q2Q1W1
    • Q8ND92
    • Q8WU86
    • Q96CZ4
    • Q9NXQ1
    • Q9P207
    • Q9Y4N0

    Protein attributes for GAPVD1 Gene

    Size:
    1478 amino acids
    Molecular mass:
    164980 Da
    Quaternary structure:
    • Interacts with TRIP10/CIP4 (By similarity). Interacts with RAB5A.
    SequenceCaution:
    • Sequence=AAH21119.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH21119.1; Type=Frameshift; Positions=742; Evidence={ECO:0000305}; Sequence=BAA90959.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA90959.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA96045.3; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for GAPVD1 Gene

neXtProt entry for GAPVD1 Gene

Post-translational modifications for GAPVD1 Gene

  • Ubiquitination at Lys24, Lys49, and Lys1327
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GAPVD1 Gene

Domains & Families for GAPVD1 Gene

Gene Families for GAPVD1 Gene

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

Protein Domains for GAPVD1 Gene

Suggested Antigen Peptide Sequences for GAPVD1 Gene

GenScript: Design optimal peptide antigens:
  • GTPase activating protein and VPS9 domains 1 (B0QZ65_HUMAN)
  • GTPase activating protein and VPS9 domains 1 (B0QZ66_HUMAN)
  • GTPase activating protein and VPS9 domains 1 (B0QZ67_HUMAN)
  • cDNA FLJ11471 fis, clone HEMBA1001675, highly similar to Mus musculus GTPase activating protein and VPS9 domains 1 (Gapvd1), mRNA (B3KMM3_HUMAN)
  • cDNA FLJ52111, highly similar to Homo sapiens GTPase activating protein and VPS9 domains 1 (GAPVD1), mRNA (B4DGD8_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q14C86

UniProtKB/Swiss-Prot:

GAPD1_HUMAN :
  • Belongs to the GAPVD1 family.
Family:
  • Belongs to the GAPVD1 family.
genes like me logo Genes that share domains with GAPVD1: view

Function for GAPVD1 Gene

Molecular function for GAPVD1 Gene

UniProtKB/Swiss-Prot Function:
Acts both as a GTPase-activating protein (GAP) and a guanine nucleotide exchange factor (GEF), and participates in various processes such as endocytosis, insulin receptor internalization or LC2A4/GLUT4 trafficking. Acts as a GEF for the Ras-related protein RAB31 by exchanging bound GDP for free GTP, leading to regulate LC2A4/GLUT4 trafficking. In the absence of insulin, it maintains RAB31 in an active state and promotes a futile cycle between LC2A4/GLUT4 storage vesicles and early endosomes, retaining LC2A4/GLUT4 inside the cells. Upon insulin stimulation, it is translocated to the plasma membrane, releasing LC2A4/GLUT4 from intracellular storage vesicles. Also involved in EGFR trafficking and degradation, possibly by promoting EGFR ubiquitination and subsequent degradation by the proteasome. Has GEF activity for Rab5 and GAP activity for Ras.

Phenotypes From GWAS Catalog for GAPVD1 Gene

Gene Ontology (GO) - Molecular Function for GAPVD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IMP 16410077
GO:0005096 GTPase activator activity IEA --
GO:0032794 GTPase activating protein binding IMP 16410077
GO:0045296 cadherin binding HDA 25468996
genes like me logo Genes that share ontologies with GAPVD1: view
genes like me logo Genes that share phenotypes with GAPVD1: view

Animal Model Products

CRISPR Products

miRNA for GAPVD1 Gene

miRTarBase miRNAs that target GAPVD1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GAPVD1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GAPVD1 Gene

Localization for GAPVD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GAPVD1 Gene

Membrane; Peripheral membrane protein. Endosome. Note=Recruited to the plasma membrane by TRIP10/CIP4 in response to insulin.

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 GAPVD1 gene
Compartment Confidence
cytosol 5
endosome 4
plasma membrane 3
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for GAPVD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005829 cytosol TAS,IDA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with GAPVD1: view

Pathways & Interactions for GAPVD1 Gene

genes like me logo Genes that share pathways with GAPVD1: view

Pathways by source for GAPVD1 Gene

Gene Ontology (GO) - Biological Process for GAPVD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006897 endocytosis IEA --
GO:0007165 signal transduction IEA --
GO:0043087 regulation of GTPase activity IEA --
GO:0043547 positive regulation of GTPase activity IEA --
GO:0051223 regulation of protein transport IMP 16410077
genes like me logo Genes that share ontologies with GAPVD1: view

No data available for SIGNOR curated interactions for GAPVD1 Gene

Drugs & Compounds for GAPVD1 Gene

(5) Drugs for GAPVD1 Gene - From: PharmGKB and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Interferon beta-1a Approved, Investigational Pharma 212
Interferon beta-1b Approved Pharma 90
Guanosine diphosphate Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with GAPVD1: view

Transcripts for GAPVD1 Gene

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GAPVD1

Alternative Splicing Database (ASD) splice patterns (SP) for GAPVD1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18a · 18b ^ 19 ^ 20 ^
SP1: - - - -
SP2: - -
SP3:
SP4: - -
SP5:
SP6:
SP7:
SP8:

ExUns: 21a · 21b · 21c · 21d ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25a · 25b
SP1: - -
SP2: - -
SP3:
SP4:
SP5: - -
SP6:
SP7: - -
SP8:

Relevant External Links for GAPVD1 Gene

GeneLoc Exon Structure for
GAPVD1
ECgene alternative splicing isoforms for
GAPVD1

Expression for GAPVD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GAPVD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for GAPVD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (16.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GAPVD1 Gene



Protein tissue co-expression partners for GAPVD1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of GAPVD1 Gene:

GAPVD1

SOURCE GeneReport for Unigene cluster for GAPVD1 Gene:

Hs.495134

Evidence on tissue expression from TISSUES for GAPVD1 Gene

  • Nervous system(4.5)
  • Intestine(4.2)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with GAPVD1: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GAPVD1 Gene

Orthologs for GAPVD1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for GAPVD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GAPVD1 32
  • 99.77 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GAPVD1 33
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia GAPVD1 33 32
  • 94.16 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia GAPVD1 33
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia GAPVD1 33 32
  • 91.86 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gapvd1 17 33 32
  • 90.49 (n)
rat
(Rattus norvegicus)
Mammalia Gapvd1 32
  • 89.54 (n)
chicken
(Gallus gallus)
Aves GAPVD1 33 32
  • 82.56 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GAPVD1 33
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gapvd1 32
  • 74.62 (n)
Str.1904 32
African clawed frog
(Xenopus laevis)
Amphibia Xl.9260 32
zebrafish
(Danio rerio)
Actinopterygii GAPVD1 (1 of 2) 33
  • 76 (a)
OneToMany
gapvd1 33 32
  • 71.3 (n)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG1657 33
  • 23 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea rme-6 33
  • 23 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VPS9 33
  • 16 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1494 33
  • 32 (a)
OneToOne
Cin.3895 32
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3895 32
Species where no ortholog for GAPVD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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 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)

Evolution for GAPVD1 Gene

ENSEMBL:
Gene Tree for GAPVD1 (if available)
TreeFam:
Gene Tree for GAPVD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GAPVD1: view image

Paralogs for GAPVD1 Gene

Paralogs for GAPVD1 Gene

genes like me logo Genes that share paralogs with GAPVD1: view

Variants for GAPVD1 Gene

Sequence variations from dbSNP and Humsavar for GAPVD1 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000002956 -- 125,290,030(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000052618 -- 125,274,384(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000054595 -- 125,349,842(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000067452 -- 125,295,370(+) T/G genic_upstream_transcript_variant, intron_variant
rs1000081800 -- 125,343,899(+) T/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for GAPVD1 Gene

Variant ID Type Subtype PubMed ID
esv1528230 CNV insertion 17803354
esv2599223 CNV insertion 19546169
esv2739042 CNV deletion 23290073
nsv1046626 CNV gain 25217958
nsv831722 CNV gain 17160897
nsv968753 CNV duplication 23825009

Variation tolerance for GAPVD1 Gene

Residual Variation Intolerance Score: 2.04% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.89; 48.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GAPVD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GAPVD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GAPVD1 Gene

Disorders for GAPVD1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for GAPVD1 Gene - From: Orphanet

Disorder Aliases PubMed IDs
familial idiopathic steroid-resistant nephrotic syndrome with focal segmental hyalinosis
  • familial idiopathic steroid-resistant nephrotic syndrome with focal segmental glomerulosclerosis
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for GAPVD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GAPVD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GAPVD1 Gene

Publications for GAPVD1 Gene

  1. Rab5-activating protein 6, a novel endosomal protein with a role in endocytosis. (PMID: 16410077) Hunker CM … Barbieri MA (Biochemical and biophysical research communications 2006) 3 4 23 56
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56
  3. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 56
  4. Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing. (PMID: 30890647) Viita T … Vartiainen MK (Journal of cell science 2019) 3 56
  5. Quantitative mapping of RNA-mediated nuclear estrogen receptor β interactome in human breast cancer cells. (PMID: 29509190) Giurato G … Tarallo R (Scientific data 2018) 3 56

Products for GAPVD1 Gene

Sources for GAPVD1 Gene