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    HPS5 HPS5 biogenesis of lysosomal organelles complex 2 subunit 2 [ Homo sapiens (human) ]

    Gene ID: 11234, updated on 3-Nov-2024

    Summary

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    Official Symbol
    HPS5provided by HGNC
    Official Full Name
    HPS5 biogenesis of lysosomal organelles complex 2 subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:17022
    See related
    Ensembl:ENSG00000110756 MIM:607521; AllianceGenome:HGNC:17022
    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
    AIBP63; BLOC2S2
    Summary
    This gene encodes a protein that may play a role in organelle biogenesis associated with melanosomes, platelet dense granules, and lysosomes. This protein interacts with Hermansky-Pudlak syndrome 6 protein and may interact with the cytoplasmic domain of integrin, alpha-3. Mutations in this gene are associated with Hermansky-Pudlak syndrome type 5. Multiple transcript variants encoding two distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 12.4), liver (RPKM 9.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HPS5 in Genome Data Viewer
    Location:
    11p15.1
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (18278670..18322174, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (18374199..18417811, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (18300217..18343721, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 334 Neighboring gene ST13, Hsp70 interacting protein pseudogene 5 Neighboring gene MPRA-validated peak1223 silencer Neighboring gene serum amyloid A1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4494 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4495 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:18343272-18344471 Neighboring gene general transcription factor IIH subunit 1 Neighboring gene uncharacterized LOC105376577 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4498 Neighboring gene microRNA 3159

    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 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. Improper trafficking of melanocyte-specific proteins in Hermansky-Pudlak syndrome type-5. Helip-Wooley A, et al. J Invest Dermatol, 2007 Jun. PMID 17301833, Free PMC Article
    2. Hermansky-Pudlak syndrome (HPS5) in a nonagenarian. Ringeisen AL, et al. J AAPOS, 2013 Jun. PMID 23607980
    3. Hermansky-Pudlak syndrome subtype 5 (HPS-5) novel mutation in a 65 year-old with oculocutaneous hypopigmentation and mild bleeding diathesis: The importance of recognizing a subtle phenotype. Botero JP, et al. Platelets, 2018 Jan. PMID 29090612
    4. Cellular, molecular and clinical characterization of patients with Hermansky-Pudlak syndrome type 5. Huizing M, et al. Traffic, 2004 Sep. PMID 15296495
    5. BioID screen of Salmonella type 3 secreted effectors reveals host factors involved in vacuole positioning and stability during infection. D'Costa VM, et al. Nat Microbiol, 2019 Dec. PMID 31611645

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. This case underscores the importance of recognizing the mild clinical phenotype of HPS-5 and utilization of both laboratory and molecular testing for diagnosis, prognostication, and surveillance for end organ damage in patients affected with HPS.
      Title: Hermansky-Pudlak syndrome subtype 5 (HPS-5) novel mutation in a 65 year-old with oculocutaneous hypopigmentation and mild bleeding diathesis: The importance of recognizing a subtle phenotype.
    2. HPS5 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.
    3. We report a 92-year-old man with HPS 5 who, to our knowledge, is the oldest patient with HPS documented in the literature.
      Title: Hermansky-Pudlak syndrome (HPS5) in a nonagenarian.
    4. Seven mutations (six previously unreported) were described in the HPS1, HPS4, and HPS5 genes among Hermansky-Pudlak Syndrome patients of Mexican, Uruguayan, Honduran, Cuban, Venezuelan, and Salvadoran ancestries.
      Title: Clinical, molecular, and cellular features of non-Puerto Rican Hermansky-Pudlak syndrome patients of Hispanic descent.
    5. 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.
    6. Tyrosinase and TYRP1 are mistrafficked, however, and fail to be efficiently delivered to melanosomes of HPS-5 melanocytes
      Title: Improper trafficking of melanocyte-specific proteins in Hermansky-Pudlak syndrome type-5.
    7. LAMP-3 distribution was restricted to the perinuclear region in HPS-5 fibroblasts, instead of extending to the periphery
      Title: Cellular, molecular and clinical characterization of patients with Hermansky-Pudlak syndrome type 5.
    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 5
    MedGen: C3888004 OMIM: 614074 GeneReviews: Hermansky-Pudlak Syndrome
    		Compare labs

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Genome-wide association study identifies two novel regions at 11p15.5-p13 and 1p31 with major impact on acute-phase serum amyloid A.
    EBI GWAS Catalog
    Human metabolic individuality in biomedical and pharmaceutical research.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1017

    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 blood coagulation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in developmental pigmentation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 platelet dense granule organization NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    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 IDA
    Inferred from Direct Assay
    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 HPS5
    Names
    Hermansky-Pudlak syndrome 5 protein
    alpha integrin binding protein 63
    ruby-eye protein 2 homolog

    NCBI Reference Sequences (RefSeq)

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    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_008877.1 RefSeqGene

      Range
      5001..48505
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_586

    mRNA and Protein(s)

    1. NM_007216.4 → NP_009147.3  BLOC-2 complex member HPS5 isoform b

      See identical proteins and their annotated locations for NP_009147.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame segment of the coding region, compared to variant 1. These differences cause translation initiation at a downstream ATG and an isoform (b) with a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AC084117, AC107948
      Consensus CDS
      CCDS7837.1
      UniProtKB/Swiss-Prot
      Q9UPZ3
      Related
      ENSP00000379552.3, ENST00000396253.7

    2. NM_181507.2 → NP_852608.1  BLOC-2 complex member HPS5 isoform a

      See identical proteins and their annotated locations for NP_852608.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript, and encodes the longer isoform (a).
      Source sequence(s)
      AC084117, AC107948
      Consensus CDS
      CCDS7836.1
      UniProtKB/Swiss-Prot
      A8K6J8, A8K8S1, D3DQX9, D3DQY0, O95942, Q8N4U0, Q9UPZ3
      Related
      ENSP00000265967.5, ENST00000349215.8
      Conserved Domains (1) summary
      sd00039
      Location:37 → 75
      7WD40; WD40 repeat [structural motif]

    3. NM_181508.1 → NP_852609.1  BLOC-2 complex member HPS5 isoform b

      See identical proteins and their annotated locations for NP_852609.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame segment of the coding region, compared to variant 1. These differences cause translation initiation at a downstream ATG and an isoform (b) with a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AA886415, AF534400
      Consensus CDS
      CCDS7837.1
      UniProtKB/Swiss-Prot
      Q9UPZ3
      Related
      ENSP00000399590.2, ENST00000438420.6

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      18278670..18322174 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011519868.4 → XP_011518170.1  BLOC-2 complex member HPS5 isoform X5

      See identical proteins and their annotated locations for XP_011518170.1

    2. XM_047426325.1 → XP_047282281.1  BLOC-2 complex member HPS5 isoform X4

    3. XM_047426324.1 → XP_047282280.1  BLOC-2 complex member HPS5 isoform X3

    4. XM_017017150.2 → XP_016872639.1  BLOC-2 complex member HPS5 isoform X2

      UniProtKB/Swiss-Prot
      A8K6J8, A8K8S1, D3DQX9, D3DQY0, O95942, Q8N4U0, Q9UPZ3
      Conserved Domains (1) summary
      sd00039
      Location:37 → 75
      7WD40; WD40 repeat [structural motif]

    5. XM_011519864.2 → XP_011518166.1  BLOC-2 complex member HPS5 isoform X1

      See identical proteins and their annotated locations for XP_011518166.1

      Conserved Domains (1) summary
      sd00039
      Location:37 → 75
      7WD40; WD40 repeat [structural motif]

    6. XM_017017154.2 → XP_016872643.1  BLOC-2 complex member HPS5 isoform X7

      UniProtKB/Swiss-Prot
      Q9UPZ3

    7. XM_011519867.2 → XP_011518169.1  BLOC-2 complex member HPS5 isoform X5

      See identical proteins and their annotated locations for XP_011518169.1

    8. XM_017017153.3 → XP_016872642.1  BLOC-2 complex member HPS5 isoform X4

    9. XM_017017151.3 → XP_016872640.1  BLOC-2 complex member HPS5 isoform X3

    10. XM_017017149.2 → XP_016872638.1  BLOC-2 complex member HPS5 isoform X2

      UniProtKB/Swiss-Prot
      A8K6J8, A8K8S1, D3DQX9, D3DQY0, O95942, Q8N4U0, Q9UPZ3
      Conserved Domains (1) summary
      sd00039
      Location:37 → 75
      7WD40; WD40 repeat [structural motif]

    11. XM_011519863.2 → XP_011518165.1  BLOC-2 complex member HPS5 isoform X1

      See identical proteins and their annotated locations for XP_011518165.1

      Conserved Domains (1) summary
      sd00039
      Location:37 → 75
      7WD40; WD40 repeat [structural motif]

    12. XM_017017152.2 → XP_016872641.1  BLOC-2 complex member HPS5 isoform X4

    13. XM_011519865.2 → XP_011518167.1  BLOC-2 complex member HPS5 isoform X3

    14. XM_011519862.2 → XP_011518164.1  BLOC-2 complex member HPS5 isoform X1

      See identical proteins and their annotated locations for XP_011518164.1

      Conserved Domains (1) summary
      sd00039
      Location:37 → 75
      7WD40; WD40 repeat [structural motif]

    15. XM_047426326.1 → XP_047282282.1  BLOC-2 complex member HPS5 isoform X6

    16. XM_047426327.1 → XP_047282283.1  BLOC-2 complex member HPS5 isoform X8

    17. XM_047426329.1 → XP_047282285.1  BLOC-2 complex member HPS5 isoform X10

    18. XM_047426328.1 → XP_047282284.1  BLOC-2 complex member HPS5 isoform X9

    19. XM_047426330.1 → XP_047282286.1  BLOC-2 complex member HPS5 isoform X11

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_021160006.1 Reference GRCh38.p14 PATCHES

      Range
      27496..71101 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332520.1 → XP_054188495.1  BLOC-2 complex member HPS5 isoform X7

    2. XM_054332517.1 → XP_054188492.1  BLOC-2 complex member HPS5 isoform X5

    3. XM_054332515.1 → XP_054188490.1  BLOC-2 complex member HPS5 isoform X4

    4. XM_054332512.1 → XP_054188487.1  BLOC-2 complex member HPS5 isoform X3

    5. XM_054332509.1 → XP_054188484.1  BLOC-2 complex member HPS5 isoform X2

      UniProtKB/Swiss-Prot
      A8K6J8, A8K8S1, D3DQX9, D3DQY0, O95942, Q8N4U0, Q9UPZ3

    6. XM_054332507.1 → XP_054188482.1  BLOC-2 complex member HPS5 isoform X1

    7. XM_054332518.1 → XP_054188493.1  BLOC-2 complex member HPS5 isoform X5

    8. XM_054332516.1 → XP_054188491.1  BLOC-2 complex member HPS5 isoform X4

    9. XM_054332513.1 → XP_054188488.1  BLOC-2 complex member HPS5 isoform X3

    10. XM_054332510.1 → XP_054188485.1  BLOC-2 complex member HPS5 isoform X2

      UniProtKB/Swiss-Prot
      A8K6J8, A8K8S1, D3DQX9, D3DQY0, O95942, Q8N4U0, Q9UPZ3

    11. XM_054332508.1 → XP_054188483.1  BLOC-2 complex member HPS5 isoform X1

    12. XM_054332514.1 → XP_054188489.1  BLOC-2 complex member HPS5 isoform X4

    13. XM_054332511.1 → XP_054188486.1  BLOC-2 complex member HPS5 isoform X3

    14. XM_054332506.1 → XP_054188481.1  BLOC-2 complex member HPS5 isoform X1

    15. XM_054332519.1 → XP_054188494.1  BLOC-2 complex member HPS5 isoform X6

    16. XM_054332521.1 → XP_054188496.1  BLOC-2 complex member HPS5 isoform X8

    17. XM_054332523.1 → XP_054188498.1  BLOC-2 complex member HPS5 isoform X10

    18. XM_054332522.1 → XP_054188497.1  BLOC-2 complex member HPS5 isoform X9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      18374199..18417811 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367562.1 → XP_054223537.1  BLOC-2 complex member HPS5 isoform X7

    2. XM_054367559.1 → XP_054223534.1  BLOC-2 complex member HPS5 isoform X5

    3. XM_054367557.1 → XP_054223532.1  BLOC-2 complex member HPS5 isoform X4

    4. XM_054367554.1 → XP_054223529.1  BLOC-2 complex member HPS5 isoform X3

    5. XM_054367551.1 → XP_054223526.1  BLOC-2 complex member HPS5 isoform X2

      UniProtKB/Swiss-Prot
      A8K6J8, A8K8S1, D3DQX9, D3DQY0, O95942, Q8N4U0, Q9UPZ3

    6. XM_054367549.1 → XP_054223524.1  BLOC-2 complex member HPS5 isoform X1

    7. XM_054367560.1 → XP_054223535.1  BLOC-2 complex member HPS5 isoform X5

    8. XM_054367558.1 → XP_054223533.1  BLOC-2 complex member HPS5 isoform X4

    9. XM_054367555.1 → XP_054223530.1  BLOC-2 complex member HPS5 isoform X3

    10. XM_054367552.1 → XP_054223527.1  BLOC-2 complex member HPS5 isoform X2

      UniProtKB/Swiss-Prot
      A8K6J8, A8K8S1, D3DQX9, D3DQY0, O95942, Q8N4U0, Q9UPZ3

    11. XM_054367550.1 → XP_054223525.1  BLOC-2 complex member HPS5 isoform X1

    12. XM_054367556.1 → XP_054223531.1  BLOC-2 complex member HPS5 isoform X4

    13. XM_054367553.1 → XP_054223528.1  BLOC-2 complex member HPS5 isoform X3

    14. XM_054367548.1 → XP_054223523.1  BLOC-2 complex member HPS5 isoform X1

    15. XM_054367561.1 → XP_054223536.1  BLOC-2 complex member HPS5 isoform X6

    16. XM_054367563.1 → XP_054223538.1  BLOC-2 complex member HPS5 isoform X8

    17. XM_054367565.1 → XP_054223540.1  BLOC-2 complex member HPS5 isoform X10

    18. XM_054367564.1 → XP_054223539.1  BLOC-2 complex member HPS5 isoform X9

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPZ3.2 GenPept UniProtKB/Swiss-Prot:Q9UPZ3

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