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

Gene ID: 11234, updated on 12-Aug-2018

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; Vega:OTTHUMG00000166612
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

Genomic context

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See HPS5 in Genome Data Viewer
Location:
11p15.1
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (18278670..18322498, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (18300217..18343751, 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 serum amyloid A1 Neighboring gene general transcription factor IIH subunit 1 Neighboring gene uncharacterized LOC105376577 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
  • 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

Bibliography

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Related articles in PubMed

  1. 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
  2. Hermansky-Pudlak syndrome (HPS5) in a nonagenarian. Ringeisen AL, et al. J AAPOS, 2013 Jun. PMID 23607980
  3. Improper trafficking of melanocyte-specific proteins in Hermansky-Pudlak syndrome type-5. Helip-Wooley A, et al. J Invest Dermatol, 2007 Jun. PMID 17301833
  4. Cellular, molecular and clinical characterization of patients with Hermansky-Pudlak syndrome type 5. Huizing M, et al. Traffic, 2004 Sep. PMID 15296495
  5. NGS-based 100-gene panel of hypopigmentation identifies mutations in Chinese Hermansky-Pudlak syndrome patients. Wei A, et al. Pigment Cell Melanoma Res, 2016 Nov. PMID 27593200

See all (27) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into FunctionsWhat'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
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NHGRI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
NHGRI GWA Catalog
Genome-wide association study identifies two novel regions at 11p15.5-p13 and 1p31 with major impact on acute-phase serum amyloid A.
NHGRI GWA Catalog
Human metabolic individuality in biomedical and pharmaceutical research.
NHGRI GWA 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
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
blood coagulation IEA
Inferred from Electronic Annotation
more info
  
organelle organization IEA
Inferred from Electronic Annotation
more info
  
pigmentation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
BLOC-2 complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
Hermansky-Pudlak syndrome 5 protein
Names
alpha integrin binding protein 63
ruby-eye protein 2 homolog

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_008877.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_007216.3 → NP_009147.3  Hermansky-Pudlak syndrome 5 protein 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)
    AA886415, AF534402, BC033640
    Consensus CDS
    CCDS7837.1
    UniProtKB/Swiss-Prot
    Q9UPZ3
    Related
    ENSP00000379552.3, OTTHUMP00000233766, ENST00000396253.7, OTTHUMT00000390807

  2. NM_181507.1 → NP_852608.1  Hermansky-Pudlak syndrome 5 protein 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)
    AA886415, AF534401
    Consensus CDS
    CCDS7836.1
    UniProtKB/Swiss-Prot
    Q9UPZ3
    Related
    ENSP00000265967.5, OTTHUMP00000233767, ENST00000349215.7, OTTHUMT00000390808
    Conserved Domains (1) summary
    sd00039
    Location:37 → 75
    7WD40; WD40 repeat [structural motif]

  3. NM_181508.1 → NP_852609.1  Hermansky-Pudlak syndrome 5 protein 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, OTTHUMP00000236630, ENST00000438420.6, OTTHUMT00000395865

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    18278670..18322498 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519865.1 → XP_011518167.1  Hermansky-Pudlak syndrome 5 protein isoform X3

  2. XM_011519868.3 → XP_011518170.1  Hermansky-Pudlak syndrome 5 protein isoform X5

    See identical proteins and their annotated locations for XP_011518170.1

  3. XM_017017151.2 → XP_016872640.1  Hermansky-Pudlak syndrome 5 protein isoform X3

  4. XM_011519863.1 → XP_011518165.1  Hermansky-Pudlak syndrome 5 protein 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]

  5. XM_011519866.1 → XP_011518168.1  Hermansky-Pudlak syndrome 5 protein isoform X5

    See identical proteins and their annotated locations for XP_011518168.1

  6. XM_011519864.1 → XP_011518166.1  Hermansky-Pudlak syndrome 5 protein 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]

  7. XM_011519867.1 → XP_011518169.1  Hermansky-Pudlak syndrome 5 protein isoform X5

    See identical proteins and their annotated locations for XP_011518169.1

  8. XM_011519862.1 → XP_011518164.1  Hermansky-Pudlak syndrome 5 protein 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]

  9. XM_017017152.1 → XP_016872641.1  Hermansky-Pudlak syndrome 5 protein isoform X4

  10. XM_017017149.1 → XP_016872638.1  Hermansky-Pudlak syndrome 5 protein isoform X2

    UniProtKB/Swiss-Prot
    Q9UPZ3
    Conserved Domains (1) summary
    sd00039
    Location:37 → 75
    7WD40; WD40 repeat [structural motif]

  11. XM_017017150.1 → XP_016872639.1  Hermansky-Pudlak syndrome 5 protein isoform X2

    UniProtKB/Swiss-Prot
    Q9UPZ3
    Conserved Domains (1) summary
    sd00039
    Location:37 → 75
    7WD40; WD40 repeat [structural motif]

  12. XM_017017154.1 → XP_016872643.1  Hermansky-Pudlak syndrome 5 protein isoform X6

    UniProtKB/Swiss-Prot
    Q9UPZ3

  13. XM_017017153.2 → XP_016872642.1  Hermansky-Pudlak syndrome 5 protein isoform X4

RNA

  1. XR_001747752.1 RNA Sequence

  2. XR_001747753.1 RNA Sequence

  3. XR_001747750.1 RNA Sequence

  4. XR_001747751.1 RNA Sequence

  5. XR_001747756.2 RNA Sequence

  6. XR_001747755.2 RNA Sequence

  7. XR_001747754.2 RNA Sequence

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

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