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Aliases for HPS3 Gene

Aliases for HPS3 Gene

  • HPS3, Biogenesis Of Lysosomal Organelles Complex 2 Subunit 1 2 3 5
  • Hermansky-Pudlak Syndrome 3 Protein 3
  • Hermansky-Pudlak Syndrome 3 2
  • BLOC2S1 3
  • SUTAL 3

External Ids for HPS3 Gene

Previous GeneCards Identifiers for HPS3 Gene

  • GC03P145796
  • GC03P149732
  • GC03P150128
  • GC03P150168
  • GC03P150330
  • GC03P148847
  • GC03P146218

Summaries for HPS3 Gene

Entrez Gene Summary for HPS3 Gene

  • This gene encodes a protein containing a potential clathrin-binding motif, consensus dileucine signals, and tyrosine-based sorting signals for targeting to vesicles of lysosomal lineage. The encoded protein may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 3. [provided by RefSeq, Apr 2015]

GeneCards Summary for HPS3 Gene

HPS3 (HPS3, Biogenesis Of Lysosomal Organelles Complex 2 Subunit 1) is a Protein Coding gene. Diseases associated with HPS3 include Hermansky-Pudlak Syndrome 3 and Hermansky-Pudlak Syndrome Without Pulmonary Fibrosis.

UniProtKB/Swiss-Prot for HPS3 Gene

  • Involved in early stages of melanosome biogenesis and maturation.

Gene Wiki entry for HPS3 Gene

Additional gene information for HPS3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPS3 Gene

Genomics for HPS3 Gene

GeneHancer (GH) Regulatory Elements for HPS3 Gene

Promoters and enhancers for HPS3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J149128 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.7 +1.4 1429 4.4 PKNOX1 MLX ARID4B SIN3A DMAP1 YY1 ZNF207 ZNF143 SP3 SP5 HPS3 COMMD2 HLTF TM4SF18 CPHL1P GC03M149173
GH03J149365 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 24.1 +242.9 242939 14.3 PKNOX1 FOXA2 ARID4B NEUROD1 SIN3A ZBTB7B YY1 SLC30A9 ZNF207 FOS TM4SF1 HPS3 TM4SF18 TM4SF1-AS1 RPS25P5
GH03J149213 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 17.4 +90.3 90285 13 PKNOX1 FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 IRF4 YY1 SLC30A9 CP HPS3 HLTF LOC101927942 GC03M149178
GH03J149085 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.5 -43.5 -43485 2.2 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 POLR2B ZNF766 HLTF HLTF-AS1 HPS3 GYG1
GH03J149242 Enhancer 1.1 Ensembl ENCODE 16.5 +116.5 116479 6.2 PKNOX1 FOXA2 FEZF1 IRF4 TCF12 FOS RUNX3 RXRA JUNB REST CP HPS3 LOC101927942 ENSG00000244468 CPHL1P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HPS3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HPS3 gene promoter:
  • AP-2gamma
  • AP-2beta
  • AP-2alphaA
  • AP-2alpha
  • Nkx5-1
  • GATA-2
  • AREB6
  • GR-beta
  • GR-alpha
  • GR

Genomic Locations for HPS3 Gene

Genomic Locations for HPS3 Gene
44,149 bases
Plus strand
44,149 bases
Plus strand

Genomic View for HPS3 Gene

Genes around HPS3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPS3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPS3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HPS3 Gene

Proteins for HPS3 Gene

  • Protein details for HPS3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Hermansky-Pudlak syndrome 3 protein
    Protein Accession:
    Secondary Accessions:
    • A8K6G6
    • Q8WTV6
    • Q96AP1
    • Q96MR3
    • Q9H608

    Protein attributes for HPS3 Gene

    1004 amino acids
    Molecular mass:
    113736 Da
    Quaternary structure:
    • Component of the biogenesis of lysosome-related organelles complex-2 (or BLOC2) composed of HPS3, HPS5 and HPS6. Interacts with HPS5 (PubMed:15030569). Interacts with HPS6 (PubMed:15030569, PubMed:25189619).
    • Sequence=AAH16901.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH22062.2; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB71221.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for HPS3 Gene


neXtProt entry for HPS3 Gene

Post-translational modifications for HPS3 Gene

  • Ubiquitination at Lys938
  • Modification sites at PhosphoSitePlus

Other Protein References for HPS3 Gene

No data available for DME Specific Peptides for HPS3 Gene

Domains & Families for HPS3 Gene

Gene Families for HPS3 Gene

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

Protein Domains for HPS3 Gene


Suggested Antigen Peptide Sequences for HPS3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HPS3: view

No data available for UniProtKB/Swiss-Prot for HPS3 Gene

Function for HPS3 Gene

Molecular function for HPS3 Gene

UniProtKB/Swiss-Prot Function:
Involved in early stages of melanosome biogenesis and maturation.

Gene Ontology (GO) - Molecular Function for HPS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25189619
genes like me logo Genes that share ontologies with HPS3: view
genes like me logo Genes that share phenotypes with HPS3: view

Human Phenotype Ontology for HPS3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HPS3

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for HPS3 Gene

Localization for HPS3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HPS3 Gene

Cytoplasm. Cytoplasm, cytosol.

Subcellular locations from

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 HPS3 gene
Compartment Confidence
cytosol 5
plasma membrane 3
nucleus 2
lysosome 2
golgi apparatus 2
cytoskeleton 1
mitochondrion 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for HPS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA --
GO:0031084 BLOC-2 complex IPI 15030569
genes like me logo Genes that share ontologies with HPS3: view

Pathways & Interactions for HPS3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HPS3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006996 organelle organization IEA --
GO:0043473 pigmentation IEA --
genes like me logo Genes that share ontologies with HPS3: view

No data available for Pathways by source and SIGNOR curated interactions for HPS3 Gene

Drugs & Compounds for HPS3 Gene

No Compound Related Data Available

Transcripts for HPS3 Gene

Unigene Clusters for HPS3 Gene

Hermansky-Pudlak syndrome 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HPS3

Alternative Splicing Database (ASD) splice patterns (SP) for HPS3 Gene

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

Relevant External Links for HPS3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HPS3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HPS3 Gene

Protein differential expression in normal tissues from HIPED for HPS3 Gene

This gene is overexpressed in Platelet (17.1), Heart (16.7), and Blymphocyte (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for HPS3 Gene

Protein tissue co-expression partners for HPS3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of HPS3 Gene:


SOURCE GeneReport for Unigene cluster for HPS3 Gene:


mRNA Expression by UniProt/SwissProt for HPS3 Gene:

Tissue specificity: Widely expressed. Higher levels of expression are observed in kidney, liver and placenta.

Evidence on tissue expression from TISSUES for HPS3 Gene

  • Intestine(4.2)
  • Kidney(4.2)
  • Nervous system(2.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HPS3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • cardiovascular
  • integumentary
  • nervous
Head and neck:
  • brain
  • cranial nerve
  • eye
  • face
  • head
  • nose
  • blood
  • blood vessel
  • coagulation system
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with HPS3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for HPS3 Gene

Orthologs for HPS3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HPS3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HPS3 34 33
  • 99.63 (n)
(Canis familiaris)
Mammalia HPS3 34 33
  • 90.66 (n)
(Bos Taurus)
Mammalia HPS3 34 33
  • 89.4 (n)
(Mus musculus)
Mammalia Hps3 16 34 33
  • 83.8 (n)
(Rattus norvegicus)
Mammalia Hps3 33
  • 83.5 (n)
(Monodelphis domestica)
Mammalia HPS3 34
  • 75 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 70 (a)
-- 34
  • 68 (a)
-- 34
  • 66 (a)
(Gallus gallus)
Aves HPS3 34 33
  • 67.9 (n)
(Anolis carolinensis)
Reptilia HPS3 34
  • 61 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia hps3 33
  • 62.58 (n)
(Danio rerio)
Actinopterygii hps3 34 33
  • 56.1 (n)
Species where no ortholog for HPS3 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)
  • 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 HPS3 Gene

Gene Tree for HPS3 (if available)
Gene Tree for HPS3 (if available)
Evolutionary constrained regions (ECRs) for HPS3: view image

Paralogs for HPS3 Gene

(1) SIMAP similar genes for HPS3 Gene using alignment to 5 proteins:

  • G5E9V4_HUMAN
  • H7C5G2_HUMAN
genes like me logo Genes that share paralogs with HPS3: view

No data available for Paralogs for HPS3 Gene

Variants for HPS3 Gene

Sequence variations from dbSNP and Humsavar for HPS3 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1050450815 uncertain-significance, Hermansky-Pudlak syndrome 149,141,020(+) T/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1053669 benign, Hermansky-Pudlak syndrome, Deficiency of ferroxidase 149,172,945(+) C/T 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs10693502 likely-benign, uncertain-significance, Hermansky-Pudlak syndrome 149,141,201(+) TTTTTTTTTTTTT/TTTTTTTTTTTT/TTTTTTTTTTTTTT/TTTTTTTTTTTTTTT/TTTTTTTTTTTTTTTT/TTTTTTTTTTTTTTTTT/TTTTTTTTTTTTTTTTTT intron_variant
rs113381494 uncertain-significance, Hermansky-Pudlak syndrome 149,145,535(+) C/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for HPS3 Gene

Variant ID Type Subtype PubMed ID
esv2672056 CNV deletion 23128226
esv3598139 CNV loss 21293372
esv3598140 CNV loss 21293372
nsv998572 CNV loss 25217958

Variation tolerance for HPS3 Gene

Residual Variation Intolerance Score: 49.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.26; 52.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HPS3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPS3 Gene

Disorders for HPS3 Gene

MalaCards: The human disease database

(6) MalaCards diseases for HPS3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
hermansky-pudlak syndrome 3
  • albinism with hemorrhagic diathesis and pigmented reticuloendothelial cells
hermansky-pudlak syndrome without pulmonary fibrosis
  • hps without pulmonary fibrosis
hermansky-pudlak syndrome
  • hps
oculocutaneous albinism
  • albinism, oculocutaneous
storage pool platelet disease
  • platelet storage pool deficiency
- elite association - COSMIC cancer census association via MalaCards
Search HPS3 in MalaCards View complete list of genes associated with diseases


  • Hermansky-Pudlak syndrome 3 (HPS3) [MIM:614072]: 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:11455388, ECO:0000269 PubMed:11590544}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HPS3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HPS3: view

No data available for Genatlas for HPS3 Gene

Publications for HPS3 Gene

  1. Mutation of a new gene causes a unique form of Hermansky-Pudlak syndrome in a genetic isolate of central Puerto Rico. (PMID: 11455388) Anikster Y … Toro JR (Nature genetics 2001) 2 3 4 22 58
  2. 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 22 44 58
  3. 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
  4. Hermansky-Pudlak syndrome type 3 in Ashkenazi Jews and other non-Puerto Rican patients with hypopigmentation and platelet storage-pool deficiency. (PMID: 11590544) Huizing M … Gahl WA (American journal of human genetics 2001) 3 4 22 58
  5. 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

Products for HPS3 Gene

Sources for HPS3 Gene

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