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HPS1 Gene(Protein Coding)

HPS1, Biogenesis Of Lysosomal Organelles Complex 3 Subunit 1

GCID:
GC10M098416
GIFtS:
55
Genes Participants
UDN Logo

Aliases for HPS1 Gene

Aliases for HPS1 Gene

  • HPS1, Biogenesis Of Lysosomal Organelles Complex 3 Subunit 1 2 3 5
  • HPS 3 4
  • Hermansky-Pudlak Syndrome 1 Protein Isoform 3
  • Hermansky-Pudlak Syndrome 1 Protein 3
  • Hermansky-Pudlak Syndrome 1 2
  • Hermansky-Pudlak Syndrome 2
  • BLOC3S1 3

External Ids for HPS1 Gene

Previous HGNC Symbols for HPS1 Gene

  • HPS

Previous GeneCards Identifiers for HPS1 Gene

  • GC10M099069
  • GC10M099409
  • GC10M100307
  • GC10M099840
  • GC10M100165
  • GC10M093800

Summaries for HPS1 Gene

Entrez Gene Summary for HPS1 Gene

  • This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. The encoded protein is a component of three different protein complexes termed biogenesis of lysosome-related organelles complex (BLOC)-3, BLOC4, and BLOC5. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 1. Alternative splicing results in multiple transcript variants. A pseudogene related to this gene is located on chromosome 22. [provided by RefSeq, Aug 2015]

GeneCards Summary for HPS1 Gene

HPS1 (HPS1, Biogenesis Of Lysosomal Organelles Complex 3 Subunit 1) is a Protein Coding gene. Diseases associated with HPS1 include Hermansky-Pudlak Syndrome 1 and Hermansky-Pudlak Syndrome With Pulmonary Fibrosis. Among its related pathways are Vesicle-mediated transport and RAB GEFs exchange GTP for GDP on RABs. GO annotations related to this gene include protein dimerization activity.

UniProtKB/Swiss-Prot for HPS1 Gene

  • Component of the BLOC-3 complex, a complex that acts as a guanine exchange factor (GEF) for RAB32 and RAB38, promotes the exchange of GDP to GTP, converting them from an inactive GDP-bound form into an active GTP-bound form. The BLOC-3 complex plays an important role in the control of melanin production and melanosome biogenesis and promotes the membrane localization of RAB32 and RAB38 (PubMed:23084991).

Gene Wiki entry for HPS1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPS1 Gene

Genomics for HPS1 Gene

Products:

  1. Regulatory Element

Regulatory Elements for HPS1 Gene

Enhancers for HPS1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10G098466 1.2 Ensembl ENCODE 17.7 -20.6 -20605 1.7 HDGF PKNOX1 ATF1 ARNT SIN3A ZNF2 ZNF48 GATA2 ZNF143 ZNF207 HPS1 PYROXD2 HPSE2 PIR35546 GC10M098426
GH10G098469 1 ENCODE 11.8 -22.8 -22756 0.1 ATF1 CREB3L1 ARID4B SIN3A DMAP1 YY1 GLIS2 ELK1 ZNF207 ZHX2 HPS1 PYROXD2 GC10M098426 PIR35546
GH10G098459 1.6 Ensembl ENCODE dbSUPER 6.1 -13.9 -13930 2.4 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 YY1 ZNF766 FOS DEK PYROXD2 LOXL4 HPS1 HPSE2 PIR35546 GC10M098426
GH10G098339 1.1 Ensembl ENCODE 8.8 +106.5 106522 1.5 TBP ELF3 FOXA2 TBL1XR1 RAD21 YY1 GATA2 SCRT2 FOS ETV6 HPS1 GC10M098326 LOC105378449
GH10G098445 1.1 ENCODE 7.4 +0.8 772 2.8 MLX SIN3A ZNF2 ZNF143 ZNF207 FOS SP3 MXD4 REST ZNF592 R3HCC1L ENSG00000230928 HPS1 PYROXD2 LOC101927278 MIR4685
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HPS1 on UCSC Golden Path with GeneCards custom track

Promoters for HPS1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000032323 363 1201 MLX SIN3A ZNF2 ZNF143 ZNF207 FOS SP3 MXD4 REST ZNF592

Transcription factor binding sites by QIAGEN in the HPS1 gene promoter:

Genomic Location for HPS1 Gene

Chromosome:
10
Start:
98,416,198 bp from pter
End:
98,446,963 bp from pter
Size:
30,766 bases
Orientation:
Minus strand

Genomic View for HPS1 Gene

Genes around HPS1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPS1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPS1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HPS1 Gene

Proteins for HPS1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HPS1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92902-HPS1_HUMAN
    Recommended name:
    Hermansky-Pudlak syndrome 1 protein
    Protein Accession:
    Q92902
    Secondary Accessions:
    • A8MRT2
    • O15402
    • O15502
    • Q5TAA3
    • Q8WXE5

    Protein attributes for HPS1 Gene

    Size:
    700 amino acids
    Molecular mass:
    79292 Da
    Quaternary structure:
    • Component of the biogenesis of lysosome-related organelles complex-3 (or BLOC-3), a heterodimer of HPS1 and HPS4 (PubMed:20048159, PubMed:23084991). HPS1 cannot but BLOC-3 complex (heterodimer of HPS1 and HPS4) can interact with the GTP-bound form of RAB9A and RAB9B. HPS1 and BLOC-3 complex do not interact with the GDP-bound form of RAB9A and RAB9B (PubMed:20048159).

    Alternative splice isoforms for HPS1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HPS1 Gene

Protein Expression for HPS1 Gene

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

Post-translational modifications for HPS1 Gene

  • Ubiquitination at isoforms=2, 4518
  • Modification sites at PhosphoSitePlus

Other Protein References for HPS1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HPS1 Gene

Domains & Families for HPS1 Gene

Gene Families for HPS1 Gene

HGNC:

Protein Domains for HPS1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HPS1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HPS1: view

No data available for UniProtKB/Swiss-Prot for HPS1 Gene

Function for HPS1 Gene

Products:

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

Molecular function for HPS1 Gene

UniProtKB/Swiss-Prot Function:
Component of the BLOC-3 complex, a complex that acts as a guanine exchange factor (GEF) for RAB32 and RAB38, promotes the exchange of GDP to GTP, converting them from an inactive GDP-bound form into an active GTP-bound form. The BLOC-3 complex plays an important role in the control of melanin production and melanosome biogenesis and promotes the membrane localization of RAB32 and RAB38 (PubMed:23084991).

Gene Ontology (GO) - Molecular Function for HPS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 contributes_to guanyl-nucleotide exchange factor activity IDA 23084991
GO:0005515 protein binding IPI 12756248
GO:0046983 protein dimerization activity IPI 12663659
genes like me logo Genes that share ontologies with HPS1: view
genes like me logo Genes that share phenotypes with HPS1: view

Human Phenotype Ontology for HPS1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

miRNA for HPS1 Gene

miRTarBase miRNAs that target HPS1

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for HPS1 Gene

Localization for HPS1 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 HPS1 gene
Compartment Confidence
cytosol 5
lysosome 5
plasma membrane 4
nucleus 2
peroxisome 1

Gene Ontology (GO) - Cellular Components for HPS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm TAS 10625677
GO:0005764 lysosome TAS 10625677
GO:0005829 cytosol TAS --
GO:0005887 integral component of plasma membrane TAS 8896559
GO:0031085 BLOC-3 complex IPI 12756248
genes like me logo Genes that share ontologies with HPS1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for HPS1 Gene

Pathways & Interactions for HPS1 Gene

genes like me logo Genes that share pathways with HPS1: view

Pathways by source for HPS1 Gene

Gene Ontology (GO) - Biological Process for HPS1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007040 lysosome organization TAS 10625677
GO:0007601 visual perception IEA --
GO:0043547 positive regulation of GTPase activity IEA --
GO:0050896 response to stimulus IEA --
GO:0061024 membrane organization TAS --
genes like me logo Genes that share ontologies with HPS1: view

No data available for SIGNOR curated interactions for HPS1 Gene

Drugs & Compounds for HPS1 Gene

Products:

  1. Drug

(1) Drugs for HPS1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for HPS1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with HPS1: view

Transcripts for HPS1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for HPS1 Gene

(25) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(218) Selected AceView cDNA sequences:
(15) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HPS1 Gene

Hermansky-Pudlak syndrome 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HPS1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c · 6d ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11a · 11b ^
SP1: - - - - - - - -
SP2: - -
SP3: - - - - - - - - - -
SP4: - - - - - - - - -
SP5: - - - - - -
SP6: - - - - - - -
SP7: - - - - - - - -
SP8: - - - - - - - - - -
SP9: - - -
SP10: -
SP11: - - -
SP12: - -
SP13:
SP14: -
SP15:
SP16:
SP17:

ExUns: 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21a · 21b
SP1: - -
SP2: -
SP3:
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:
SP16:
SP17:

Relevant External Links for HPS1 Gene

GeneLoc Exon Structure for
HPS1
ECgene alternative splicing isoforms for
HPS1

Expression for HPS1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HPS1 Gene

mRNA expression in normal human tissues for HPS1 Gene
mRNA expression by BioGPS for HPS1 GenemRNA expression by GTEx for HPS1 Gene

mRNA differential expression in normal tissues according to GTEx for HPS1 Gene

This gene is overexpressed in Whole Blood (x4.6).

Protein differential expression in normal tissues from HIPED for HPS1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (42.0), Urine (10.8), and Platelet (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HPS1 Gene



Protein tissue co-expression partners for HPS1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HPS1 Gene:

HPS1

SOURCE GeneReport for Unigene cluster for HPS1 Gene:

Hs.404568

mRNA Expression by UniProt/SwissProt for HPS1 Gene:

Q92902-HPS1_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for HPS1 Gene

  • Nervous system(2.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HPS1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • nervous
  • respiratory
  • urinary
Organs:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • face
  • head
  • mouth
  • nose
Thorax:
  • heart
  • heart valve
  • lung
Abdomen:
  • intestine
  • kidney
  • large intestine
  • small intestine
Pelvis:
  • anus
  • ureter
  • urinary bladder
General:
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with HPS1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for HPS1 Gene

Orthologs for HPS1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HPS1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HPS1 34 35
  • 99.62 (n)
dog
(Canis familiaris)
 Mammalia HPS1 34 35
  • 86.48 (n)
cow
(Bos Taurus)
 Mammalia HPS1 34 35
  • 86.17 (n)
rat
(Rattus norvegicus)
 Mammalia Hps1 34
  • 83.91 (n)
mouse
(Mus musculus)
 Mammalia Hps1 34 16 35
  • 83.57 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia HPS1 35
  • 72 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia HPS1 35
  • 69 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves HPS1 34 35
  • 70.74 (n)
lizard
(Anolis carolinensis)
 Reptilia HPS1 35
  • 60 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hps1 34
  • 63.8 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.32472 34
zebrafish
(Danio rerio)
 Actinopterygii hps1 34 35
  • 62.56 (n)
fruit fly
(Drosophila melanogaster)
 Insecta HPS1 35
  • 26 (a)
 OneToOne
Species where no ortholog for HPS1 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)
  • 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)
  • 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 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 HPS1 Gene

ENSEMBL:
Gene Tree for HPS1 (if available)
TreeFam:
Gene Tree for HPS1 (if available)

Paralogs for HPS1 Gene

(1) SIMAP similar genes for HPS1 Gene using alignment to 5 proteins:

Pseudogenes.org Pseudogenes for HPS1 Gene

genes like me logo Genes that share paralogs with HPS1: view

No data available for Paralogs for HPS1 Gene

Variants for HPS1 Gene

Sequence variations from dbSNP and Humsavar for HPS1 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs121908385 Pathogenic 98,417,671(-) GCTAC(A/G/T)AGCTG nc-transcript-variant, reference, missense, stop-gained
rs121908386 Pathogenic 98,435,273(-) GAAAG(A/G/T)AGTGA intron-variant, nc-transcript-variant, reference, missense, stop-gained, utr-variant-5-prime
rs281865073 Pathogenic 98,435,722(+) GAGGA(-/GAT)GATGA nc-transcript-variant, cds-indel
rs281865074 Pathogenic 98,435,382(+) TGGTC(-/A)CCATT intron-variant, nc-transcript-variant, reference, frameshift-variant, utr-variant-5-prime
rs281865075 Pathogenic 98,435,315(+) AAAGT(-/G)CACTT intron-variant, nc-transcript-variant, reference, frameshift-variant, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for HPS1 Gene

Variant ID Type Subtype PubMed ID
dgv276e212 CNV loss 25503493
nsv515723 CNV loss 19592680
nsv524427 CNV loss 19592680
nsv831955 CNV gain 17160897

Variation tolerance for HPS1 Gene

Residual Variation Intolerance Score: 86.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.74; 86.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HPS1 Gene

Human Gene Mutation Database (HGMD)
HPS1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HPS1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPS1 Gene

Disorders for HPS1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for HPS1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search HPS1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HPS1_HUMAN
  • Hermansky-Pudlak syndrome 1 (HPS1) [MIM:203300]: 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:9497254}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for HPS1

Genetic Association Database (GAD)
HPS1
Human Genome Epidemiology (HuGE) Navigator
HPS1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HPS1
genes like me logo Genes that share disorders with HPS1: view

No data available for Genatlas for HPS1 Gene

Publications for HPS1 Gene

  1. A comprehensive analysis reveals mutational spectra and common alleles in Chinese patients with oculocutaneous albinism. (PMID: 19865097) Wei A. … Li W. (J. Invest. Dermatol. 2010) 3 22 46 64
  2. Gene variants associated with ischemic stroke: the cardiovascular health study. (PMID: 19023099) Luke M.M. … Psaty B.M. (Stroke 2009) 3 22 46 64
  3. Comprehensive analysis of oculocutaneous albinism among non-Hispanic caucasians shows that OCA1 is the most prevalent OCA type. (PMID: 18463683) Hutton S.M. … Spritz R.A. (J. Invest. Dermatol. 2008) 3 22 46 64
  4. Genetic testing for oculocutaneous albinism type 1 and 2 and Hermansky-Pudlak syndrome type 1 and 3 mutations in Puerto Rico. (PMID: 16417222) Santiago Borrero P.J. … Cadilla C.L. (J. Invest. Dermatol. 2006) 3 22 46 64
  5. Characterization of a partial pseudogene homologous to the Hermansky- Pudlak syndrome gene HPS-1; relevance for mutation detection. (PMID: 10798370) Huizing M. … Gahl W.A. (Hum. Genet. 2000) 3 4 22 64

Products for HPS1 Gene

Sources for HPS1 Gene

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