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

Gene ID: 3257, updated on 8-Jul-2018
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]
Expression
Ubiquitous expression in spleen (RPKM 13.6), bone marrow (RPKM 13.3) and 25 other tissues See more
Orthologs
See HPS1 in Genome Data Viewer
Location:
10q24.2
Exon count:
22
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (98416193..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 
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
 
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
    ENSP00000355310.4, OTTHUMP00000020246, ENST00000361490.8, 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
    ENSP00000326649.6, OTTHUMP00000020244, ENST00000325103.10, 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
    ENSP00000343638.5, OTTHUMP00000020245, ENST00000338546.9, OTTHUMT00000049777

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_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    98416193..98446963 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024447971.1XP_024303739.1  Hermansky-Pudlak syndrome 1 protein isoform X1

  2. XM_017016170.1XP_016871659.1  Hermansky-Pudlak syndrome 1 protein isoform X3

  3. XM_017016171.2XP_016871660.1  Hermansky-Pudlak syndrome 1 protein isoform X4

  4. XM_024447972.1XP_024303740.1  Hermansky-Pudlak syndrome 1 protein isoform X5

  5. XM_017016172.2XP_016871661.1  Hermansky-Pudlak syndrome 1 protein isoform X5

    Conserved Domains (1) summary
    cl24019
    Location:325371
    CSN8_PSD8_EIF3K; CSN8/PSMD8/EIF3K family
  6. XM_005269757.4XP_005269814.1  Hermansky-Pudlak syndrome 1 protein isoform X2

    See identical proteins and their annotated locations for XP_005269814.1

    UniProtKB/Swiss-Prot
    Q92902
  7. XM_017016173.1XP_016871662.1  Hermansky-Pudlak syndrome 1 protein isoform X6

RNA

  1. XR_001747098.1 RNA Sequence

  2. XR_001747101.2 RNA Sequence

    Related
    ENST00000467246.5
  3. XR_001747099.2 RNA Sequence

  4. XR_001747100.2 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.
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