U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 3257, updated on 2-May-2024

    Summary

    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; AllianceGenome:HGNC:5163
    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]
    Expression
    Ubiquitous expression in spleen (RPKM 13.6), bone marrow (RPKM 13.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See HPS1 in Genome Data Viewer
    Location:
    10q24.2
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (98413948..98446935, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (99296171..99326913, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (100175955..100206692, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378449 Neighboring gene Sharpr-MPRA regulatory region 15191 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:100127757-100128375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:100134557-100135058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:100135059-100135558 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3866 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3867 Neighboring gene MPRA-validated peak1064 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100182997-100183558 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100183559-100184120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2688 Neighboring gene pyridine nucleotide-disulphide oxidoreductase domain 2 Neighboring gene NANOG hESC enhancer GRCh37_chr10:100213105-100213606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100215497-100216036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:100216595-100217198 Neighboring gene microRNA 1287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2689 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2690 Neighboring gene microRNA 4685 Neighboring gene HPS1 antisense RNA 1 Neighboring gene heparanase 2 (inactive) Neighboring gene MPRA-validated peak1065 silencer Neighboring gene microRNA 6507 Neighboring gene ARL5A pseudogene 2

    Genomic regions, transcripts, and products

    Expression

    • 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

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

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC5277

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to guanyl-nucleotide exchange factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    contributes_to guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein dimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in intracellular transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in lysosome organization TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in melanosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in melanosome assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in melanosome assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in platelet dense granule organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of BLOC-3 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of BLOC-3 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in lysosome TAS
    Traceable Author Statement
    more info
    PubMed 

    General protein information

    Preferred Names
    BLOC-3 complex member HPS1
    Names
    Hermansky-Pudlak syndrome 1 protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      5013..35750
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_562

    mRNA and Protein(s)

    1. NM_000195.5NP_000186.2  BLOC-3 complex member HPS1 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, U65676
      Consensus CDS
      CCDS7475.1
      UniProtKB/Swiss-Prot
      A8MRT2, O15402, O15502, Q5TAA3, Q8WXE5, Q92902
      UniProtKB/TrEMBL
      A0A8V8TN99
      Related
      ENSP00000355310.4, ENST00000361490.9
    2. NM_001311345.2NP_001298274.1  BLOC-3 complex member HPS1 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
      UniProtKB/TrEMBL
      Q658M9
    3. NM_001322476.2NP_001309405.1  BLOC-3 complex member HPS1 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
      A8MRT2, O15402, O15502, Q5TAA3, Q8WXE5, Q92902
      UniProtKB/TrEMBL
      A0A8V8TN99
      Related
      ENSP00000514159.1, ENST00000699142.1
    4. NM_001322477.2NP_001309406.1  BLOC-3 complex member HPS1 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
      A8MRT2, O15402, O15502, Q5TAA3, Q8WXE5, Q92902
      UniProtKB/TrEMBL
      A0A8V8TN99
      Related
      ENSP00000326649.6, ENST00000325103.10
    5. NM_001322478.2NP_001309407.1  BLOC-3 complex member HPS1 isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) and variant 9 both encode isoform f.
      Source sequence(s)
      AL139243
      Consensus CDS
      CCDS91316.1
      UniProtKB/TrEMBL
      A0A8V8TN90
      Related
      ENSP00000514153.1, ENST00000699136.1
      Conserved Domains (3) summary
      pfam19036
      Location:2159
      Fuz_longin_1; First Longin domain of FUZ, MON1 and HPS1
      pfam19037
      Location:204372
      Fuz_longin_2; Second Longin domain of FUZ, MON1 and HPS1
      pfam19038
      Location:507662
      Fuz_longin_3; Third Longin domain of FUZ, MON1 and HPS1
    6. NM_001322479.2NP_001309408.1  BLOC-3 complex member HPS1 isoform f

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) and variant 8 both encode isoform f.
      Source sequence(s)
      AL139243
      Consensus CDS
      CCDS91316.1
      UniProtKB/TrEMBL
      A0A8V8TN90
      Related
      ENSP00000514157.1, ENST00000699140.1
      Conserved Domains (3) summary
      pfam19036
      Location:2159
      Fuz_longin_1; First Longin domain of FUZ, MON1 and HPS1
      pfam19037
      Location:204372
      Fuz_longin_2; Second Longin domain of FUZ, MON1 and HPS1
      pfam19038
      Location:507662
      Fuz_longin_3; Third Longin domain of FUZ, MON1 and HPS1
    7. NM_001322480.2NP_001309409.1  BLOC-3 complex member HPS1 isoform g

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10) and variant 11 both encode isoform g.
      Source sequence(s)
      AL139243
      Consensus CDS
      CCDS91314.1
      UniProtKB/TrEMBL
      A0A8V8TN94, A0A8V8TP59
      Related
      ENSP00000514146.1, ENST00000699125.1
      Conserved Domains (1) summary
      PRK12323
      Location:86263
      PRK12323; DNA polymerase III subunits gamma and tau; Provisional
    8. NM_001322481.2NP_001309410.1  BLOC-3 complex member HPS1 isoform g

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11) and variant 10 both encode isoform g.
      Source sequence(s)
      AL139243
      Consensus CDS
      CCDS91314.1
      UniProtKB/TrEMBL
      A0A8V8TN94, A0A8V8TP59
      Related
      ENSP00000514156.1, ENST00000699139.1
    9. NM_001322482.2NP_001309411.1  BLOC-3 complex member HPS1 isoform h

      Status: REVIEWED

      Source sequence(s)
      AL139243
      Consensus CDS
      CCDS91313.1
      UniProtKB/TrEMBL
      A0A8V8TMQ9, A0A8V8TP59
      Related
      ENSP00000514137.1, ENST00000699112.1
    10. NM_001322483.2NP_001309412.1  BLOC-3 complex member HPS1 isoform i

      Status: REVIEWED

      Description
      Transcript Variant: This variant (13) and variant 14 both encode isoform i.
      Source sequence(s)
      AL139243
    11. NM_001322484.2NP_001309413.1  BLOC-3 complex member HPS1 isoform i

      Status: REVIEWED

      Description
      Transcript Variant: This variant (14) and variant 13 both encode isoform i.
      Source sequence(s)
      AL139243
    12. NM_001322485.2NP_001309414.1  BLOC-3 complex member HPS1 isoform j

      Status: REVIEWED

      Source sequence(s)
      AL139243
    13. NM_001322487.2NP_001309416.1  BLOC-3 complex member HPS1 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (17), along with variants 5 and 16, encodes isoform e.
      Source sequence(s)
      AL139243
      UniProtKB/TrEMBL
      Q658M9
      Conserved Domains (1) summary
      cl24019
      Location:325371
      CSN8_PSD8_EIF3K; CSN8/PSMD8/EIF3K family
    14. NM_001322489.2NP_001309418.1  BLOC-3 complex member HPS1 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (17), along with variants 5 and 16, encodes isoform e.
      Source sequence(s)
      AL139243
      UniProtKB/TrEMBL
      Q658M9
      Conserved Domains (1) summary
      cl24019
      Location:325371
      CSN8_PSD8_EIF3K; CSN8/PSMD8/EIF3K family
    15. NM_001322490.2NP_001309419.1  BLOC-3 complex member HPS1 isoform k

      Status: REVIEWED

      Source sequence(s)
      AL139243
      UniProtKB/TrEMBL
      A0A0S2Z3Z8
    16. NM_001322491.2NP_001309420.1  BLOC-3 complex member HPS1 isoform l

      Status: REVIEWED

      Source sequence(s)
      AL139243
      Consensus CDS
      CCDS91315.1
      UniProtKB/TrEMBL
      A0A0S2Z3U1, B4DIX6, H0Y4K4
    17. NM_001322492.2NP_001309421.1  BLOC-3 complex member HPS1 isoform m

      Status: REVIEWED

      Source sequence(s)
      AL139243
      UniProtKB/TrEMBL
      A0A0S2Z3X2
    18. NM_182639.4NP_872577.1  BLOC-3 complex member HPS1 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, U96721
      Consensus CDS
      CCDS7476.1
      UniProtKB/TrEMBL
      A0A0S2Z3U9, B4DIX6
      Related
      ENSP00000343638.5, ENST00000338546.9

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      98413948..98446935 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425149.1XP_047281105.1  BLOC-3 complex member HPS1 isoform X2

      UniProtKB/TrEMBL
      A0A8V8TN94
    2. XM_047425147.1XP_047281103.1  BLOC-3 complex member HPS1 isoform X1

      UniProtKB/Swiss-Prot
      A8MRT2, O15402, O15502, Q5TAA3, Q8WXE5, Q92902
    3. XM_047425148.1XP_047281104.1  BLOC-3 complex member HPS1 isoform X2

      UniProtKB/TrEMBL
      A0A8V8TN94
    4. XM_047425146.1XP_047281102.1  BLOC-3 complex member HPS1 isoform X1

      UniProtKB/Swiss-Prot
      A8MRT2, O15402, O15502, Q5TAA3, Q8WXE5, Q92902
    5. XM_005269757.5XP_005269814.1  BLOC-3 complex member HPS1 isoform X1

      See identical proteins and their annotated locations for XP_005269814.1

      UniProtKB/Swiss-Prot
      A8MRT2, O15402, O15502, Q5TAA3, Q8WXE5, Q92902
      UniProtKB/TrEMBL
      A0A8V8TN99
    6. XM_047425150.1XP_047281106.1  BLOC-3 complex member HPS1 isoform X3

    7. XM_047425151.1XP_047281107.1  BLOC-3 complex member HPS1 isoform X4

      UniProtKB/TrEMBL
      A0A0S2Z3U1, H0Y4K4
      Related
      ENSP00000392462.2, ENST00000414009.2
    8. XM_017016173.2XP_016871662.1  BLOC-3 complex member HPS1 isoform X5

      UniProtKB/TrEMBL
      A0A0S2Z3X2
    9. XM_047425152.1XP_047281108.1  BLOC-3 complex member HPS1 isoform X4

      UniProtKB/TrEMBL
      A0A0S2Z3U1, H0Y4K4

    RNA

    1. XR_007061961.1 RNA Sequence

    2. XR_001747098.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      99296171..99326913 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365707.1XP_054221682.1  BLOC-3 complex member HPS1 isoform X2

      UniProtKB/TrEMBL
      A0A8V8TN94
    2. XM_054365705.1XP_054221680.1  BLOC-3 complex member HPS1 isoform X1

      UniProtKB/Swiss-Prot
      A8MRT2, O15402, O15502, Q5TAA3, Q8WXE5, Q92902
    3. XM_054365706.1XP_054221681.1  BLOC-3 complex member HPS1 isoform X2

      UniProtKB/TrEMBL
      A0A8V8TN94
    4. XM_054365704.1XP_054221679.1  BLOC-3 complex member HPS1 isoform X1

      UniProtKB/Swiss-Prot
      A8MRT2, O15402, O15502, Q5TAA3, Q8WXE5, Q92902
    5. XM_054365708.1XP_054221683.1  BLOC-3 complex member HPS1 isoform X3

    6. XM_054365709.1XP_054221684.1  BLOC-3 complex member HPS1 isoform X4

      UniProtKB/TrEMBL
      A0A0S2Z3U1, H0Y4K4
    7. XM_054365711.1XP_054221686.1  BLOC-3 complex member HPS1 isoform X5

    8. XM_054365710.1XP_054221685.1  BLOC-3 complex member HPS1 isoform X4

      UniProtKB/TrEMBL
      A0A0S2Z3U1, H0Y4K4

    RNA

    1. XR_008488201.1 RNA Sequence

    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.