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

Gene ID: 3257, updated on 3-Apr-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
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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 response to stimulus IEA
Inferred from Electronic Annotation
more info
 
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.