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    HPS1 HPS1, biogenesis of lysosomal organelles complex 3 subunit 1 [ Homo sapiens (human) ]

    Gene ID: 3257, updated on 18-Mar-2017
    Official Symbol
    HPS1provided by HGNC
    Official Full Name
    HPS1, biogenesis of lysosomal organelles complex 3 subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:5163
    See related
    Ensembl:ENSG00000107521 MIM:604982; Vega:OTTHUMG00000018876
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    HPS; BLOC3S1
    Summary
    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]
    Orthologs
    Location:
    10q24.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 10 NC_000010.11 (98415068..98446963, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (100175955..100206720, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378449 Neighboring gene pyridine nucleotide-disulphide oxidoreductase domain 2 Neighboring gene uncharacterized LOC101927278 Neighboring gene microRNA 1287 Neighboring gene microRNA 4685 Neighboring gene heparanase 2 (inactive) Neighboring gene microRNA 6507 Neighboring gene ADP ribosylation factor like GTPase 5A pseudogene 2

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    Related articles in PubMed

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Hermansky-Pudlak syndrome 1
    MedGen: C2931875 OMIM: 203300 GeneReviews: Hermansky-Pudlak Syndrome
    Compare labs

    NHGRI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    NHGRI GWA Catalog
    • Membrane Trafficking, organism-specific biosystem (from REACTOME)
      Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
    • RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystem (from REACTOME)
      RAB GEFs exchange GTP for GDP on RABs, organism-specific biosystemHuman cells have more than 60 RAB proteins that are key regulators of intracellular membrane trafficking. These small GTPases contribute to trafficking specificity by localizing to the membranes of d...
    • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
      Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC5277

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein dimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    lysosome organization TAS
    Traceable Author Statement
    more info
    PubMed 
    melanosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    membrane organization TAS
    Traceable Author Statement
    more info
     
    positive regulation of GTPase activity IEA
    Inferred from Electronic Annotation
    more info
     
    response to stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    BLOC-3 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    cytoplasm TAS
    Traceable Author Statement
    more info
    PubMed 
    cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    lysosome TAS
    Traceable Author Statement
    more info
    PubMed 
    Preferred Names
    Hermansky-Pudlak syndrome 1 protein
    Names
    Hermansky-Pudlak syndrome 1 protein isoform

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009646.1 RefSeqGene

      Range
      4985..35750
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000195.4NP_000186.2  Hermansky-Pudlak syndrome 1 protein isoform a

      See identical proteins and their annotated locations for NP_000186.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1, 6, and 7 all encode the same isoform (a).
      Source sequence(s)
      AL139243, AL833734, BF447504, DA385131, DA479757, U65676
      Consensus CDS
      CCDS7475.1
      UniProtKB/Swiss-Prot
      Q92902
      UniProtKB/TrEMBL
      Q658M9
      Related
      ENSP00000355310, OTTHUMP00000020246, ENST00000361490, OTTHUMT00000049778
    2. NM_001311345.1NP_001298274.1  Hermansky-Pudlak syndrome 1 protein isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and initaites translation at a downstream start codon, compared to variant 1. It encodes isoform e, which is shorter at the N-terminus, compared to isoform a. Variants 5, 16, and 17 all encode the same isoform (e).
      Source sequence(s)
      AL139243, BC002514, BF447504, DA385131, DA479757
      Conserved Domains (1) summary
      cl24019
      Location:325371
      CSN8_PSD8_EIF3K; CSN8/PSMD8/EIF3K family
    3. NM_001322476.1NP_001309405.1  Hermansky-Pudlak syndrome 1 protein isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), along with variants 1 and 7, encodes isoform a.
      Source sequence(s)
      AL139243
      Consensus CDS
      CCDS7475.1
      UniProtKB/Swiss-Prot
      Q92902
    4. NM_001322477.1NP_001309406.1  Hermansky-Pudlak syndrome 1 protein isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7), along with variants 1 and 6, encodes isoform a.
      Source sequence(s)
      AL139243
      Consensus CDS
      CCDS7475.1
      UniProtKB/Swiss-Prot
      Q92902
      Related
      ENSP00000326649, OTTHUMP00000020244, ENST00000325103, OTTHUMT00000049776
    5. NM_001322478.1NP_001309407.1  Hermansky-Pudlak syndrome 1 protein isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) and variant 9 both encode isoform f.
      Source sequence(s)
      AL139243
      UniProtKB/Swiss-Prot
      Q92902
    6. NM_001322479.1NP_001309408.1  Hermansky-Pudlak syndrome 1 protein isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) and variant 8 both encode isoform f.
      Source sequence(s)
      AL139243
      UniProtKB/Swiss-Prot
      Q92902
    7. NM_001322480.1NP_001309409.1  Hermansky-Pudlak syndrome 1 protein isoform g

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) and variant 11 both encode isoform g.
      Source sequence(s)
      AL139243
      Conserved Domains (1) summary
      PRK12323
      Location:86263
      PRK12323; DNA polymerase III subunits gamma and tau; Provisional
    8. NM_001322481.1NP_001309410.1  Hermansky-Pudlak syndrome 1 protein isoform g

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) and variant 10 both encode isoform g.
      Source sequence(s)
      AL139243
      Conserved Domains (1) summary
      PRK12323
      Location:86263
      PRK12323; DNA polymerase III subunits gamma and tau; Provisional
    9. NM_001322482.1NP_001309411.1  Hermansky-Pudlak syndrome 1 protein isoform h

      Status: REVIEWED

      Source sequence(s)
      AL139243
    10. NM_001322483.1NP_001309412.1  Hermansky-Pudlak syndrome 1 protein isoform i

      Status: REVIEWED

      Description
      Transcript Variant: This variant (13) and variant 14 both encode isoform i.
      Source sequence(s)
      AL139243
    11. NM_001322484.1NP_001309413.1  Hermansky-Pudlak syndrome 1 protein isoform i

      Status: REVIEWED

      Description
      Transcript Variant: This variant (14) and variant 13 both encode isoform i.
      Source sequence(s)
      AL139243
    12. NM_001322485.1NP_001309414.1  Hermansky-Pudlak syndrome 1 protein isoform j

      Status: REVIEWED

      Source sequence(s)
      AL139243
    13. NM_001322487.1NP_001309416.1  Hermansky-Pudlak syndrome 1 protein isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (17), along with variants 5 and 16, encodes isoform e.
      Source sequence(s)
      AL139243
      Conserved Domains (1) summary
      cl24019
      Location:325371
      CSN8_PSD8_EIF3K; CSN8/PSMD8/EIF3K family
    14. NM_001322489.1NP_001309418.1  Hermansky-Pudlak syndrome 1 protein isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (17), along with variants 5 and 16, encodes isoform e.
      Source sequence(s)
      AL139243
      Conserved Domains (1) summary
      cl24019
      Location:325371
      CSN8_PSD8_EIF3K; CSN8/PSMD8/EIF3K family
    15. NM_001322490.1NP_001309419.1  Hermansky-Pudlak syndrome 1 protein isoform k

      Status: REVIEWED

      Source sequence(s)
      AL139243
      Conserved Domains (1) summary
      pfam05956
      Location:179283
      APC_basic; APC basic domain
    16. NM_001322491.1NP_001309420.1  Hermansky-Pudlak syndrome 1 protein isoform l

      Status: REVIEWED

      Source sequence(s)
      AL139243
      UniProtKB/TrEMBL
      A0A0S2Z3U1
    17. NM_001322492.1NP_001309421.1  Hermansky-Pudlak syndrome 1 protein isoform m

      Status: REVIEWED

      Source sequence(s)
      AL139243
    18. NM_182639.3NP_872577.1  Hermansky-Pudlak syndrome 1 protein isoform c

      See identical proteins and their annotated locations for NP_872577.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and contains an alternate 3' exon structure compared to variant 1. It encodes isoform c, which has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      BC000175, BI966698, DA385131, DA479757, U96721
      Consensus CDS
      CCDS7476.1
      UniProtKB/Swiss-Prot
      Q92902
      UniProtKB/TrEMBL
      A0A0S2Z3U9
      Related
      ENSP00000343638, OTTHUMP00000020245, ENST00000338546, OTTHUMT00000049777

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p7 Primary Assembly

      Range
      98415068..98446963 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017016171.1XP_016871660.1  Hermansky-Pudlak syndrome 1 protein isoform X3

    2. XM_017016170.1XP_016871659.1  Hermansky-Pudlak syndrome 1 protein isoform X2

    3. XM_017016172.1XP_016871661.1  Hermansky-Pudlak syndrome 1 protein isoform X4

      Conserved Domains (1) summary
      cl24019
      Location:325371
      CSN8_PSD8_EIF3K; CSN8/PSMD8/EIF3K family
    4. XM_005269757.4XP_005269814.1  Hermansky-Pudlak syndrome 1 protein isoform X1

      See identical proteins and their annotated locations for XP_005269814.1

      UniProtKB/Swiss-Prot
      Q92902
    5. XM_017016173.1XP_016871662.1  Hermansky-Pudlak syndrome 1 protein isoform X5

    RNA

    1. XR_001747097.1 RNA Sequence

      Related
      ENST00000467246
    2. XR_001747098.1 RNA Sequence

    3. XR_001747101.1 RNA Sequence

    4. XR_001747099.1 RNA Sequence

    5. XR_001747100.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018921.2 Alternate CHM1_1.1

      Range
      100457816..100488581 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_182637.1: Suppressed sequence

      Description
      NM_182637.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    2. NM_182638.1: Suppressed sequence

      Description
      NM_182638.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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