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Aliases for HPS6 Gene

Aliases for HPS6 Gene

  • HPS6, Biogenesis Of Lysosomal Organelles Complex 2 Subunit 3 2 3 5
  • Ruby-Eye Protein Homolog 3 4
  • Hermansky-Pudlak Syndrome-6 Protein (HPS6) 3
  • Hermansky-Pudlak Syndrome 6 Protein 3
  • Hermansky-Pudlak Syndrome 6 2
  • BLOC2S3 3
  • Ru 4

External Ids for HPS6 Gene

Previous GeneCards Identifiers for HPS6 Gene

  • GC10P103058
  • GC10P103956
  • GC10P103489
  • GC10P103815
  • GC10P097457

Summaries for HPS6 Gene

Entrez Gene Summary for HPS6 Gene

  • This intronless gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. This protein interacts with Hermansky-Pudlak syndrome 5 protein. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 6. [provided by RefSeq, Jul 2008]

GeneCards Summary for HPS6 Gene

HPS6 (HPS6, Biogenesis Of Lysosomal Organelles Complex 2 Subunit 3) is a Protein Coding gene. Diseases associated with HPS6 include Hermansky-Pudlak Syndrome 6 and Hermansky-Pudlak Syndrome Without Pulmonary Fibrosis. Gene Ontology (GO) annotations related to this gene include Rab GTPase binding and GTP-dependent protein binding.

UniProtKB/Swiss-Prot for HPS6 Gene

  • May regulate the synthesis and function of lysosomes and of highly specialized organelles, such as melanosomes and platelet dense granules (PubMed:17041891). Acts as cargo adapter for the dynein-dynactin motor complex to mediate the transport of lysosomes from the cell periphery to the perinuclear region. Facilitates retrograde lysosomal trafficking by linking the motor complex to lysosomes, and perinuclear positioning of lysosomes is crucial for the delivery of endocytic cargos to lysosomes, for lysosome maturation and functioning (PubMed:25189619).

Gene Wiki entry for HPS6 Gene

Additional gene information for HPS6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPS6 Gene

Genomics for HPS6 Gene

GeneHancer (GH) Regulatory Elements for HPS6 Gene

Promoters and enhancers for HPS6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10I102064 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 564.5 +0.3 280 2.5 HDGF FOXA2 ARNT ARID4B SIN3A ZNF2 YY1 POLR2B ZNF766 ZNF416 HPS6 SUFU LDB1 KCNIP2 GC10P102070
GH10I101828 Promoter/Enhancer 2 FANTOM5 Ensembl ENCODE dbSUPER 53.4 -234.4 -234384 4.4 HDGF PKNOX1 CLOCK SMAD1 ARNT SIN3A ZNF2 ZBTB7B ZNF766 ZNF302 PPRC1 LDB1 GBF1 LZTS2 MRPL43 HPS6 NOLC1 SUFU ENSG00000272572 KCNIP2-AS1
GH10I101814 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 28.2 -248.3 -248258 5.9 HDGF PKNOX1 CLOCK FOXA2 SMAD1 MLX ARNT ARID4B NEUROD1 SIN3A KCNIP2-AS1 MGEA5 PPRC1 HPS6 LDB1 GBF1 MRPL43 TWNK SUFU NPM3
GH10I102431 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE 25.1 +368.8 368830 5.5 HDGF FOXA2 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SLC30A9 POLR2B CUEDC2 HPS6 PPRC1 LDB1 PDCD11 TAF5 SUFU GBF1 PCGF6 RPARP-AS1
GH10I102150 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 25.8 +87.0 87014 3.4 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 POLR2B NOLC1 HPS6 PPRC1 LDB1 GBF1 POLL ELOVL3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HPS6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HPS6 gene promoter:

Genomic Locations for HPS6 Gene

Genomic Locations for HPS6 Gene
chr10:102,065,367-102,068,038
(GRCh38/hg38)
Size:
2,672 bases
Orientation:
Plus strand
chr10:103,825,124-103,827,795
(GRCh37/hg19)

Genomic View for HPS6 Gene

Genes around HPS6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPS6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPS6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HPS6 Gene

Proteins for HPS6 Gene

  • Protein details for HPS6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86YV9-HPS6_HUMAN
    Recommended name:
    Hermansky-Pudlak syndrome 6 protein
    Protein Accession:
    Q86YV9
    Secondary Accessions:
    • Q5VV69
    • Q9H685

    Protein attributes for HPS6 Gene

    Size:
    775 amino acids
    Molecular mass:
    82975 Da
    Quaternary structure:
    • Component of the biogenesis of lysosome-related organelles complex-2 (or BLOC2) composed of HPS3, HPS5 and HPS6. Interacts with HPS5 and HPS3 (PubMed:15030569, PubMed:25189619). Interacts with biogenesis of lysosome-related organelles complex-1 (BLOC1). Interacts with AP-3 complex (PubMed:16837549). Interacts with MNAT1 (Probable). Interacts with DCTN1 and dynein intermediate chain (PubMed:25189619).
    SequenceCaution:
    • Sequence=BAB15378.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for HPS6 Gene

Post-translational modifications for HPS6 Gene

  • Ubiquitination at isoforms=239, posLast=469469, isoforms=534, isoforms=646, and posLast=672672

Other Protein References for HPS6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HPS6 Gene

Domains & Families for HPS6 Gene

Gene Families for HPS6 Gene

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

Protein Domains for HPS6 Gene

Suggested Antigen Peptide Sequences for HPS6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HPS6: view

No data available for UniProtKB/Swiss-Prot for HPS6 Gene

Function for HPS6 Gene

Molecular function for HPS6 Gene

UniProtKB/Swiss-Prot Function:
May regulate the synthesis and function of lysosomes and of highly specialized organelles, such as melanosomes and platelet dense granules (PubMed:17041891). Acts as cargo adapter for the dynein-dynactin motor complex to mediate the transport of lysosomes from the cell periphery to the perinuclear region. Facilitates retrograde lysosomal trafficking by linking the motor complex to lysosomes, and perinuclear positioning of lysosomes is crucial for the delivery of endocytic cargos to lysosomes, for lysosome maturation and functioning (PubMed:25189619).

Phenotypes From GWAS Catalog for HPS6 Gene

Gene Ontology (GO) - Molecular Function for HPS6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25189619
GO:0017137 Rab GTPase binding IPI 22511774
GO:0030742 GTP-dependent protein binding IPI 22511774
genes like me logo Genes that share ontologies with HPS6: view
genes like me logo Genes that share phenotypes with HPS6: view

Human Phenotype Ontology for HPS6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for HPS6 Gene

miRTarBase miRNAs that target HPS6

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for HPS6 Gene

Localization for HPS6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HPS6 Gene

Microsome membrane. Cytoplasm, cytosol. Early endosome membrane. Lysosome membrane.

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 HPS6 gene
Compartment Confidence
cytosol 5
lysosome 5
endosome 4
mitochondrion 3
endoplasmic reticulum 3
plasma membrane 1

Gene Ontology (GO) - Cellular Components for HPS6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005764 lysosome IEA --
GO:0005765 lysosomal membrane IEA,IDA 25189619
GO:0005768 endosome IEA --
GO:0005783 endoplasmic reticulum IEA --
genes like me logo Genes that share ontologies with HPS6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HPS6 Gene

Pathways & Interactions for HPS6 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HPS6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006996 organelle organization IEA --
GO:0007596 blood coagulation IEA --
GO:0030318 melanocyte differentiation IEA --
GO:0032418 lysosome localization IEA,IMP 25189619
GO:0043473 pigmentation IEA --
genes like me logo Genes that share ontologies with HPS6: view

No data available for Pathways by source and SIGNOR curated interactions for HPS6 Gene

Drugs & Compounds for HPS6 Gene

No Compound Related Data Available

Transcripts for HPS6 Gene

mRNA/cDNA for HPS6 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(121) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HPS6 Gene

Hermansky-Pudlak syndrome 6:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HPS6 Gene

No ASD Table

Relevant External Links for HPS6 Gene

GeneLoc Exon Structure for
HPS6
ECgene alternative splicing isoforms for
HPS6

Expression for HPS6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HPS6 Gene

Protein differential expression in normal tissues from HIPED for HPS6 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (17.8), Testis (11.2), and Adrenal (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HPS6 Gene



Protein tissue co-expression partners for HPS6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HPS6 Gene:

HPS6

SOURCE GeneReport for Unigene cluster for HPS6 Gene:

Hs.125133

mRNA Expression by UniProt/SwissProt for HPS6 Gene:

Q86YV9-HPS6_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for HPS6 Gene

  • Skin(4.3)
  • Kidney(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HPS6 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • integumentary
  • nervous
Organs:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • face
  • head
  • nose
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with HPS6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for HPS6 Gene

Orthologs for HPS6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HPS6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia HPS6 33 34
  • 99.23 (n)
dog
(Canis familiaris)
Mammalia HPS6 33 34
  • 87.6 (n)
cow
(Bos Taurus)
Mammalia HPS6 33 34
  • 86.92 (n)
mouse
(Mus musculus)
Mammalia Hps6 33 16 34
  • 82.63 (n)
rat
(Rattus norvegicus)
Mammalia Hps6 33
  • 81.19 (n)
chicken
(Gallus gallus)
Aves HPS6 33 34
  • 55.92 (n)
lizard
(Anolis carolinensis)
Reptilia HPS6 34
  • 39 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hps6 33
  • 48.32 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC101882947 33
  • 46.53 (n)
HPS6 34
  • 33 (a)
OneToOne
Species where no ortholog for HPS6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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 HPS6 Gene

ENSEMBL:
Gene Tree for HPS6 (if available)
TreeFam:
Gene Tree for HPS6 (if available)

Paralogs for HPS6 Gene

No data available for Paralogs for HPS6 Gene

Variants for HPS6 Gene

Sequence variations from dbSNP and Humsavar for HPS6 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs139517839 uncertain-significance, Hermansky-Pudlak syndrome 102,066,513(+) G/A/T coding_sequence_variant, missense_variant
rs139591041 benign, likely-benign, not specified, Hermansky-Pudlak syndrome 102,065,573(+) A/G/T coding_sequence_variant, synonymous_variant
rs145597717 benign, likely-benign, not specified, Hermansky-Pudlak syndrome 102,067,238(+) G/A coding_sequence_variant, synonymous_variant
rs146521433 uncertain-significance, Hermansky-Pudlak syndrome 102,066,655(+) T/C coding_sequence_variant, missense_variant
rs199518658 uncertain-significance, Hermansky-Pudlak syndrome 102,067,655(+) A/G coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for HPS6 Gene

Variant ID Type Subtype PubMed ID
nsv482149 CNV gain 20164927

Variation tolerance for HPS6 Gene

Residual Variation Intolerance Score: 22.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.90; 35.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HPS6 Gene

Human Gene Mutation Database (HGMD)
HPS6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HPS6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPS6 Gene

Disorders for HPS6 Gene

MalaCards: The human disease database

(8) MalaCards diseases for HPS6 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hermansky-pudlak syndrome 6
  • albinism with hemorrhagic diathesis and pigmented reticuloendothelial cells
hermansky-pudlak syndrome without pulmonary fibrosis
  • hps without pulmonary fibrosis
hermansky-pudlak syndrome
  • albinism with hemorrhagic diathesis and pigmented reticuloendothelial cells
hermansky-pudlak syndrome 5
  • hps5
oculocutaneous albinism
  • albinism, oculocutaneous
- elite association - COSMIC cancer census association via MalaCards
Search HPS6 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HPS6_HUMAN
  • Hermansky-Pudlak syndrome 6 (HPS6) [MIM:614075]: A form of Hermansky-Pudlak syndrome, a genetically heterogeneous autosomal recessive disorder characterized by oculocutaneous albinism, bleeding due to platelet storage pool deficiency, and lysosomal storage defects. This syndrome results from defects of diverse cytoplasmic organelles including melanosomes, platelet dense granules and lysosomes. Ceroid storage in the lungs is associated with pulmonary fibrosis, a common cause of premature death in individuals with HPS. {ECO:0000269 PubMed:12548288, ECO:0000269 PubMed:17041891}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HPS6

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 HPS6: view

No data available for Genatlas for HPS6 Gene

Publications for HPS6 Gene

  1. Characterization of BLOC-2, a complex containing the Hermansky-Pudlak syndrome proteins HPS3, HPS5 and HPS6. (PMID: 15030569) Di Pietro SM … Dell'Angelica EC (Traffic (Copenhagen, Denmark) 2004) 3 4 22 58
  2. Ru2 and Ru encode mouse orthologs of the genes mutated in human Hermansky-Pudlak syndrome types 5 and 6. (PMID: 12548288) Zhang Q … Swank RT (Nature genetics 2003) 2 3 4 58
  3. HPS6 interacts with dynactin p150Glued to mediate retrograde trafficking and maturation of lysosomes. (PMID: 25189619) Li K … Liu JJ (Journal of cell science 2014) 3 4 58
  4. Clinical and cellular characterisation of Hermansky-Pudlak syndrome type 6. (PMID: 19843503) Huizing M … Gahl WA (Journal of medical genetics 2009) 3 22 58
  5. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 44 58

Products for HPS6 Gene

Sources for HPS6 Gene

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