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

Gene ID: 84343, updated on 3-Apr-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
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Genomic context

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Location:
3q24
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (149129638..149173732)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (151880375..151924479)
105.20220307 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. 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
  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. 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

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.
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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
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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

  • 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_2023_10

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

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