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    HPS3 HPS3 biogenesis of lysosomal organelles complex 2 subunit 1 [ Homo sapiens (human) ]

    Gene ID: 84343, updated on 27-Nov-2024

    Summary

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    Official Symbol
    HPS3provided by HGNC
    Official Full Name
    HPS3 biogenesis of lysosomal organelles complex 2 subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:15597
    See related
    Ensembl:ENSG00000163755 MIM:606118; AllianceGenome:HGNC:15597
    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
    SUTAL; BLOC2S1
    Summary
    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]
    Expression
    Broad expression in liver (RPKM 82.9), lymph node (RPKM 10.8) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HPS3 in Genome Data Viewer
    Location:
    3q24
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (149129638..149173732)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (151880375..151924479)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (148847425..148891519)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene glycogenin 1 Neighboring gene helicase like transcription factor Neighboring gene OCT4-NANOG-H3K27ac hESC enhancers GRCh37_chr3:148803647-148804164 and GRCh37_chr3:148804165-148804682 Neighboring gene HLTF antisense RNA 1 Neighboring gene mediator complex subunit 28 pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:148847467-148847966 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:148914047-148914842 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:148914843-148915640 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:148915641-148916436 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:148916437-148917233 Neighboring gene ceruloplasmin Neighboring gene uncharacterized LOC101927942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20680 Neighboring gene ceruloplasmin and hephaestin like 1, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:148987331-148988530

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Report of Hermansky-Pudlak Syndrome in Two Families with Novel Variants in HPS3 and HPS4 Genes. Zaman Q, et al. Genes (Basel), 2023 Jan 5. PMID 36672886, Free PMC Article
    2. Subclinical hypopigmentation of the skin and hair in a Japanese patient with Hermansky-Pudlak syndrome type 3. Saito S, et al. J Dermatol, 2020 Jan. PMID 31621111
    3. Melanocyte-specific proteins are aberrantly trafficked in melanocytes of Hermansky-Pudlak syndrome-type 3. Boissy RE, et al. Am J Pathol, 2005 Jan. PMID 15632015, Free PMC Article
    4. Association of the Hermansky-Pudlak syndrome type-3 protein with clathrin. Helip-Wooley A, et al. BMC Cell Biol, 2005 Sep 13. PMID 16159387, Free PMC Article
    5. Newborn screening for hermansky-pudlak syndrome type 3 in Puerto Rico. Torres-Serrant M, et al. J Pediatr Hematol Oncol, 2010 Aug. PMID 20562649, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Report of Hermansky-Pudlak Syndrome in Two Families with Novel Variants in HPS3 and HPS4 Genes.
      Title: Report of Hermansky-Pudlak Syndrome in Two Families with Novel Variants in HPS3 and HPS4 Genes.
    2. Subclinical hypopigmentation of the skin and hair in a Japanese patient with Hermansky-Pudlak syndrome type 3.
      Title: Subclinical hypopigmentation of the skin and hair in a Japanese patient with Hermansky-Pudlak syndrome type 3.
    3. HPS3 mutation is associated with high hypopigmentation in Hermansky-Pudlak syndrome.
      Title: NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients.
    4. Observational study of genotype prevalence. (HuGE Navigator)
      Title: Newborn screening for hermansky-pudlak syndrome type 3 in Puerto Rico.
    5. HPS4 but not HPS3 associates with HPS1 in a complex, which we term biogenesis of lysosome-related organelles complex 3 (BLOC-3)
      Title: Biogenesis of lysosome-related organelles complex 3 (BLOC-3): a complex containing the Hermansky-Pudlak syndrome (HPS) proteins HPS1 and HPS4.
    6. Component of BLOC-2. Results suggest a common biological basis underlying the pathogenesis of HPS-3, -5 and -6 disease.
      Title: Characterization of BLOC-2, a complex containing the Hermansky-Pudlak syndrome proteins HPS3, HPS5 and HPS6.
    7. Description of mutations in HPS genes that cause Hermansky-Pudlak syndrome (review)
      Title: Disorders of vesicles of lysosomal lineage: the Hermansky-Pudlak syndromes.
    8. A specific subset of melanocyte proteins are aberrantly trafficked throughout the HPS-3 melanocyte and may be responsible for the reduction in melanin synthesis.
      Title: Melanocyte-specific proteins are aberrantly trafficked in melanocytes of Hermansky-Pudlak syndrome-type 3.
    9. HPS3 associates with clathrin, predominantly on small clathrin-containing vesicles in the perinuclear region. This association most likely occurs directly via a functional clathrin-binding domain in HPS3.
      Title: Association of the Hermansky-Pudlak syndrome type-3 protein with clathrin.
    10. mutational analysis in Ashkenazi Jews with Hermansky-Pudlak syndrome 3
      Title: Hermansky-Pudlak syndrome type 3 in Ashkenazi Jews and other non-Puerto Rican patients with hypopigmentation and platelet storage-pool deficiency.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Hermansky-Pudlak syndrome 3
    MedGen: C3888001 OMIM: 614072 GeneReviews: Hermansky-Pudlak Syndrome
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22704, DKFZp686F0413

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding 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 melanosome assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in organelle organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in platelet dense granule organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of BLOC-2 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of BLOC-2 complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    BLOC-2 complex member HPS3
    Names
    Hermansky-Pudlak syndrome 3 protein

    NCBI Reference Sequences (RefSeq)

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    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_009847.1 RefSeqGene

      Range
      5055..49149
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_563

    mRNA and Protein(s)

    1. NM_001308258.2 → NP_001295187.1  BLOC-2 complex member HPS3 isoform 2

      See identical proteins and their annotated locations for NP_001295187.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1.
      Source sequence(s)
      AC131209, AY033141, BC022062, CB241738
      Consensus CDS
      CCDS77836.1
      UniProtKB/TrEMBL
      B4DPS7, G5E9V4
      Related
      ENSP00000418230.1, ENST00000460120.5
      Conserved Domains (3) summary
      pfam14761
      Location:3 → 74
      HPS3_N; Hermansky-Pudlak syndrome 3
      pfam14762
      Location:91 → 474
      HPS3_Mid; Hermansky-Pudlak syndrome 3, middle region
      pfam14763
      Location:488 → 836
      HPS3_C; Hermansky-Pudlak syndrome 3, C-terminal

    2. NM_032383.5 → NP_115759.2  BLOC-2 complex member HPS3 isoform 1

      See identical proteins and their annotated locations for NP_115759.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC131209, AY033141, BC022062, CB241738
      Consensus CDS
      CCDS3140.1
      UniProtKB/Swiss-Prot
      A8K6G6, Q8WTV6, Q969F9, Q96AP1, Q96MR3, Q9H608
      UniProtKB/TrEMBL
      B4DPS7
      Related
      ENSP00000296051.2, ENST00000296051.7
      Conserved Domains (3) summary
      pfam14761
      Location:3 → 212
      HPS3_N; Hermansky-Pudlak syndrome 3
      pfam14762
      Location:256 → 639
      HPS3_Mid; Hermansky-Pudlak syndrome 3, middle region
      pfam14763
      Location:653 → 1001
      HPS3_C; Hermansky-Pudlak syndrome 3, C-terminal

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      149129638..149173732
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449064.1 → XP_047305020.1  BLOC-2 complex member HPS3 isoform X1

    2. XM_005247834.5 → XP_005247891.1  BLOC-2 complex member HPS3 isoform X2

      Conserved Domains (3) summary
      pfam14761
      Location:3 → 212
      HPS3_N; Hermansky-Pudlak syndrome 3
      pfam14762
      Location:256 → 639
      HPS3_Mid; Hermansky-Pudlak syndrome 3, middle region
      pfam14763
      Location:653 → 763
      HPS3_C; Hermansky-Pudlak syndrome 3, C-terminal

    RNA

    1. XR_001740328.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      151880375..151924479
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348091.1 → XP_054204066.1  BLOC-2 complex member HPS3 isoform X1

    2. XM_054348092.1 → XP_054204067.1  BLOC-2 complex member HPS3 isoform X2

    RNA

    1. XR_008486843.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969F9.1 GenPept UniProtKB/Swiss-Prot:Q969F9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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