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. Alte... See more...

Aliases for HPS1 Gene

Aliases for HPS1 Gene

  • HPS1 Biogenesis Of Lysosomal Organelles Complex 3 Subunit 1 2 3 5
  • Hermansky-Pudlak Syndrome 1 Protein 3 4
  • HPS 3 4
  • Hermansky-Pudlak Syndrome 1 Protein Isoform 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. Among its related pathways are RAB GEFs exchange GTP for GDP on RABs and Vesicle-mediated transport. Gene Ontology (GO) annotations related to this gene include protein dimerization activity.

UniProtKB/Swiss-Prot Summary 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

Additional gene information for HPS1 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HPS1 Gene

Genomics for HPS1 Gene

GeneHancer (GH) Regulatory Elements for HPS1 Gene

Promoters and enhancers for HPS1 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
GH10J098444 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 507.3 +0.7 666 3 ZBTB40 SIN3A MYC POLR2G USF1 PHF8 FOS ZFX POLR2A ZBTB26 HPS1 ENSG00000287261 LOC101927278 NONHSAG006652.2 lnc-HPSE2-1 PYROXD2 piR-52294-018
GH10J097569 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 13.7 +873.7 873742 6.5 ZNF217 CTCF TCF12 JUND FOS TEAD4 ZNF10 ZIC2 REST RAD21 ANKRD2 MMS19 R3HCC1L HPS1 EXOSC1 LOXL4 LCOR RPL13AP5 MARVELD1 ENSG00000230928
GH10J098132 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas 13.7 +312.3 312326 3.5 EP300 ZBTB40 ZNF217 SIN3A NRF1 TCF12 USF1 POLR2G SP1 RBAK R3HCC1L LOXL4 HPS1 EXOSC1 MMS19 MARVELD1 HSALNG0079995
GH10J098466 Promoter/Enhancer 1.3 ENCODE CraniofacialAtlas 17.8 -20.5 -20528 0.9 ZNF217 CTCF NRF1 TEAD4 ZFX ZBTB11 ZNF423 AFF1 REST DNMT1 HPS1 PYROXD2 HPSE2 piR-42547 piR-30876-019
GH10J098459 Enhancer 1.2 ENCODE dbSUPER 15.1 -13.9 -13929 2.4 ZNF217 ZSCAN5C TCF12 JUND PHB2 FOS ZNF639 ZBTB5 REST ZBTB11 piR-42547 HPS1 PYROXD2 LOXL4 HPSE2 piR-30876-019
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HPS1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HPS1

Top Transcription factor binding sites by QIAGEN in the HPS1 gene promoter:
  • AhR
  • AML1a
  • C/EBPalpha
  • E47
  • GATA-1
  • GATA-2
  • GATA-3
  • Hand1
  • HFH-1
  • LCR-F1

Genomic Locations for HPS1 Gene

Genomic Locations for HPS1 Gene
chr10:98,416,198-98,446,963
(GRCh38/hg38)
Size:
30,766 bases
Orientation:
Minus strand
chr10:100,175,955-100,206,704
(GRCh37/hg19)
Size:
30,750 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 StructureGene Density

RefSeq DNA sequence for HPS1 Gene

Proteins for HPS1 Gene

  • 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

Post-translational modifications for HPS1 Gene

  • Ubiquitination at Lys518
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for HPS1 Gene

Domains & Families for HPS1 Gene

Gene Families for HPS1 Gene

Protein Domains for HPS1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for HPS1 Gene

GenScript: Design optimal peptide antigens:
  • Hermansky-Pudlak syndrome 1, isoform CRA_c (D3DR62_HUMAN)
  • Hermansky-Pudlak syndrome 1, isoform CRA_b (D3DR63_HUMAN)
  • Hermansky-Pudlak syndrome 1 protein (HPS1_HUMAN)
  • Hermansky-Pudlak syndrome 1 (Q5TAA5_HUMAN)
  • Hermansky-Pudlak syndrome 1 (Q5TAA8_HUMAN)
genes like me logo Genes that share domains with HPS1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for HPS1 Gene

Function for HPS1 Gene

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).

Phenotypes From GWAS Catalog for HPS1 Gene

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

CRISPR Products

miRNA for HPS1 Gene

miRTarBase miRNAs that target HPS1

Clone Products

  • Addgene plasmids for HPS1

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 4
lysosome 4
nucleus 2
peroxisome 1
endosome 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:0031085 BLOC-3 complex IPI 12756248
GO:0031410 cytoplasmic vesicle IDA 11836498
genes like me logo Genes that share ontologies with HPS1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) 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:0050896 response to stimulus IEA --
GO:1903232 melanosome assembly IDA 23084991
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

(2) Drugs for HPS1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with HPS1: view

Transcripts for HPS1 Gene

mRNA/cDNA for HPS1 Gene

20 REFSEQ mRNAs :
25 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for HPS1

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

Expression for HPS1 Gene

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



Protein tissue co-expression partners for HPS1 Gene

- Elite partner

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

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 31 30
  • 99.62 (n)
OneToOne
dog
(Canis familiaris)
Mammalia HPS1 31 30
  • 86.48 (n)
OneToOne
cow
(Bos Taurus)
Mammalia HPS1 31 30
  • 86.17 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hps1 30
  • 83.91 (n)
mouse
(Mus musculus)
Mammalia Hps1 17 31 30
  • 83.57 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia HPS1 31
  • 72 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia HPS1 31
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves HPS1 31 30
  • 70.74 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia HPS1 31
  • 60 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hps1 30
  • 63.8 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.32472 30
zebrafish
(Danio rerio)
Actinopterygii hps1 31 30
  • 62.56 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta HPS1 31
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for HPS1: view image

Paralogs for HPS1 Gene

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

  • HPS1_HUMAN
  • D3DR62_HUMAN
  • D3DR63_HUMAN
  • H0Y4K4_HUMAN
  • Q5TAA8_HUMAN

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HPS1 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
626969 Likely Pathogenic: Hermansky-Pudlak syndrome 98,425,877(-) G/T MISSENSE_VARIANT
627174 Likely Pathogenic: Hermansky-Pudlak syndrome 98,420,043(-) A/G SPLICE_DONOR_VARIANT
627179 Likely Pathogenic: Hermansky-Pudlak syndrome 98,431,284(-) T/C MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON_VARIANT
627612 Pathogenic: Hermansky-Pudlak syndrome 1 98,435,703(-) C/A NONSENSE,FIVE_PRIME_UTR_VARIANT
627613 Pathogenic: Hermansky-Pudlak syndrome 1 98,420,095(-) G/A NONSENSE

Additional dbSNP identifiers (rs#s) for HPS1 Gene

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)

Additional Variant Information for HPS1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for HPS1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
hermansky-pudlak syndrome 1
  • hps1
hermansky-pudlak syndrome
  • albinism with hemorrhagic diathesis and pigmented reticuloendothelial cells
hermansky-pudlak syndrome with pulmonary fibrosis
  • hps with pulmonary fibrosis
pulmonary fibrosis
  • fibrosis of lung
albinism
- 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.

Additional Disease Information for HPS1

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 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 (The Journal of investigative dermatology 2010) 3 23 41 54
  2. Gene variants associated with ischemic stroke: the cardiovascular health study. (PMID: 19023099) Luke MM … Psaty BM (Stroke 2009) 3 23 41 54
  3. Comprehensive analysis of oculocutaneous albinism among non-Hispanic caucasians shows that OCA1 is the most prevalent OCA type. (PMID: 18463683) Hutton SM … Spritz RA (The Journal of investigative dermatology 2008) 3 23 41 54
  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 PJ … Cadilla CL (The Journal of investigative dermatology 2006) 3 23 41 54
  5. Characterization of a partial pseudogene homologous to the Hermansky-Pudlak syndrome gene HPS-1; relevance for mutation detection. (PMID: 10798370) Huizing M … Gahl WA (Human genetics 2000) 3 4 23 54

Products for HPS1 Gene

Sources for HPS1 Gene