Format

Send to:

Choose Destination

HPS4 HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 [ Homo sapiens (human) ]

Gene ID: 89781, updated on 8-Oct-2017
Official Symbol
HPS4provided by HGNC
Official Full Name
HPS4, biogenesis of lysosomal organelles complex 3 subunit 2provided by HGNC
Primary source
HGNC:HGNC:15844
See related
Ensembl:ENSG00000100099 MIM:606682; Vega:OTTHUMG00000030459
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
LE; BLOC3S2
Summary
This gene encodes a protein component of biogenesis of lysosome-related organelles complexes (BLOC). BLOC complexes are important for the formation of endosomal-lysosomal organelles such as melanosomes and platelet dense granules. Mutations in this gene result in subtype 4 of Hermansky-Pudlak syndrome, a form of albinism. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]
Orthologs
Location:
22q12.1
Exon count:
21
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 22 NC_000022.11 (26443613..26483863, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (26846848..26879829, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 495 Neighboring gene ribosomal protein S3A pseudogene Neighboring gene aspartate beta-hydroxylase domain containing 2 Neighboring gene SRR1 domain containing Neighboring gene tuftelin interacting protein 11 Neighboring gene uncharacterized LOC100507599

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • 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

  • KIAA1667

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
blood coagulation IEA
Inferred from Electronic Annotation
more info
 
hemostasis TAS
Traceable Author Statement
more info
PubMed 
lysosome organization IDA
Inferred from Direct Assay
more info
PubMed 
melanocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
melanosome assembly IDA
Inferred from Direct Assay
more info
PubMed 
membrane organization TAS
Traceable Author Statement
more info
 
positive regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
positive regulation of eye pigmentation TAS
Traceable Author Statement
more info
PubMed 
positive regulation of protein targeting to mitochondrion IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein stabilization IPI
Inferred from Physical Interaction
more info
PubMed 
protein targeting IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
BLOC-3 complex IPI
Inferred from Physical Interaction
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 
melanosome IDA
Inferred from Direct Assay
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
platelet dense granule IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
Hermansky-Pudlak syndrome 4 protein
Names
light-ear protein homolog

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_009763.2 RefSeqGene

    Range
    5001..37982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_590

mRNA and Protein(s)

  1. NM_001349896.1NP_001336825.1  Hermansky-Pudlak syndrome 4 protein isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes isoform a.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  2. NM_001349898.1NP_001336827.1  Hermansky-Pudlak syndrome 4 protein isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes isoform a.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  3. NM_001349899.1NP_001336828.1  Hermansky-Pudlak syndrome 4 protein isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) encodes isoform a.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  4. NM_001349900.1NP_001336829.1  Hermansky-Pudlak syndrome 4 protein isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) encodes isoform c.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:432549
    dnaA; chromosomal replication initiation protein; Provisional
  5. NM_001349901.1NP_001336830.1  Hermansky-Pudlak syndrome 4 protein isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) encodes isoform c.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:432549
    dnaA; chromosomal replication initiation protein; Provisional
  6. NM_001349902.1NP_001336831.1  Hermansky-Pudlak syndrome 4 protein isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) encodes isoform d.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  7. NM_001349903.1NP_001336832.1  Hermansky-Pudlak syndrome 4 protein isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) encodes isoform d.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  8. NM_001349904.1NP_001336833.1  Hermansky-Pudlak syndrome 4 protein isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12) encodes isoform e.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  9. NM_001349905.1NP_001336834.1  Hermansky-Pudlak syndrome 4 protein isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (13) encodes isoform e.
    Source sequence(s)
    Z99714
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  10. NM_022081.5NP_071364.4  Hermansky-Pudlak syndrome 4 protein isoform a

    See identical proteins and their annotated locations for NP_071364.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    AK290211, AY043416, BC065030, BQ185676, Z99714
    Consensus CDS
    CCDS13835.1
    UniProtKB/Swiss-Prot
    Q9NQG7
    UniProtKB/TrEMBL
    A8K2E6, Q6P1K3
    Related
    ENSP00000381213.2, OTTHUMP00000198859, ENST00000398145.6, OTTHUMT00000320778
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  11. NM_152841.2NP_690054.1  Hermansky-Pudlak syndrome 4 protein isoform b

    See identical proteins and their annotated locations for NP_690054.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (b) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AL365512, BQ185676, Z99714
    Consensus CDS
    CCDS46677.1
    UniProtKB/Swiss-Prot
    Q9NQG7
    Related
    ENSP00000384185.3, OTTHUMP00000199897, ENST00000402105.7, OTTHUMT00000320781
    Conserved Domains (1) summary
    PRK14086
    Location:409526
    dnaA; chromosomal replication initiation protein; Provisional

RNA

  1. NR_073135.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site at the 5' end and at an internal region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL365512, BC028625, BC050285, BQ185676, Z99714
  2. NR_073136.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs at the 5' end and contains multiple internal differences, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 2, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AY043416, BC028625, BC035614, BQ185676, Z99714
  3. NR_146311.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (14) is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    Z99714
  4. NR_146312.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (15) is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    Z99714
  5. NR_146313.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (16) is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    Z99714
  6. NR_146314.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (17) is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    Z99714
  7. NR_146315.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (18) is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    Z99714
  8. NR_146316.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (19) is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    Z99714

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p7 Primary Assembly

    Range
    26443613..26483863 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017029048.1XP_016884537.1  Hermansky-Pudlak syndrome 4 protein isoform X11

    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  2. XM_017029045.1XP_016884534.1  Hermansky-Pudlak syndrome 4 protein isoform X8

  3. XM_011530492.1XP_011528794.1  Hermansky-Pudlak syndrome 4 protein isoform X6

    Conserved Domains (1) summary
    PRK14086
    Location:458575
    dnaA; chromosomal replication initiation protein; Provisional
  4. XM_017029049.1XP_016884538.1  Hermansky-Pudlak syndrome 4 protein isoform X11

    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  5. XM_017029050.1XP_016884539.1  Hermansky-Pudlak syndrome 4 protein isoform X12

    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  6. XM_017029052.1XP_016884541.1  Hermansky-Pudlak syndrome 4 protein isoform X13

  7. XM_017029047.1XP_016884536.1  Hermansky-Pudlak syndrome 4 protein isoform X10

  8. XM_011530493.2XP_011528795.1  Hermansky-Pudlak syndrome 4 protein isoform X7

    Conserved Domains (1) summary
    PRK14086
    Location:458575
    dnaA; chromosomal replication initiation protein; Provisional
  9. XM_011530485.1XP_011528787.1  Hermansky-Pudlak syndrome 4 protein isoform X1

    See identical proteins and their annotated locations for XP_011528787.1

    Conserved Domains (1) summary
    PRK14086
    Location:458575
    dnaA; chromosomal replication initiation protein; Provisional
  10. XM_017029051.1XP_016884540.1  Hermansky-Pudlak syndrome 4 protein isoform X12

    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  11. XM_017029042.1XP_016884531.1  Hermansky-Pudlak syndrome 4 protein isoform X5

    UniProtKB/Swiss-Prot
    Q9NQG7
    Related
    ENSP00000338457.5, OTTHUMP00000198860, ENST00000336873.9, OTTHUMT00000320779
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  12. XM_017029043.1XP_016884532.1  Hermansky-Pudlak syndrome 4 protein isoform X5

    UniProtKB/Swiss-Prot
    Q9NQG7
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  13. XM_017029044.1XP_016884533.1  Hermansky-Pudlak syndrome 4 protein isoform X5

    UniProtKB/Swiss-Prot
    Q9NQG7
    Conserved Domains (1) summary
    cl28271
    Location:414531
    dnaA; chromosomal replication initiation protein; Provisional
  14. XM_017029059.1XP_016884548.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  15. XM_017029063.1XP_016884552.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  16. XM_017029062.1XP_016884551.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  17. XM_017029055.1XP_016884544.1  Hermansky-Pudlak syndrome 4 protein isoform X17

    Conserved Domains (1) summary
    PRK14086
    Location:194311
    dnaA; chromosomal replication initiation protein; Provisional
  18. XM_017029046.1XP_016884535.1  Hermansky-Pudlak syndrome 4 protein isoform X9

  19. XM_006724353.3XP_006724416.1  Hermansky-Pudlak syndrome 4 protein isoform X3

    Conserved Domains (1) summary
    cl28271
    Location:432549
    dnaA; chromosomal replication initiation protein; Provisional
  20. XM_017029057.1XP_016884546.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  21. XM_017029054.1XP_016884543.1  Hermansky-Pudlak syndrome 4 protein isoform X15

  22. XM_017029061.1XP_016884550.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  23. XM_011530490.2XP_011528792.1  Hermansky-Pudlak syndrome 4 protein isoform X2

    Conserved Domains (1) summary
    PRK14086
    Location:440557
    dnaA; chromosomal replication initiation protein; Provisional
  24. XM_017029056.1XP_016884545.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  25. XM_006724354.3XP_006724417.1  Hermansky-Pudlak syndrome 4 protein isoform X3

    Conserved Domains (1) summary
    cl28271
    Location:432549
    dnaA; chromosomal replication initiation protein; Provisional
  26. XM_011530486.2XP_011528788.1  Hermansky-Pudlak syndrome 4 protein isoform X1

    See identical proteins and their annotated locations for XP_011528788.1

    Conserved Domains (1) summary
    PRK14086
    Location:458575
    dnaA; chromosomal replication initiation protein; Provisional
  27. XM_011530487.2XP_011528789.1  Hermansky-Pudlak syndrome 4 protein isoform X1

    See identical proteins and their annotated locations for XP_011528789.1

    Conserved Domains (1) summary
    PRK14086
    Location:458575
    dnaA; chromosomal replication initiation protein; Provisional
  28. XM_017029060.1XP_016884549.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  29. XM_011530488.2XP_011528790.1  Hermansky-Pudlak syndrome 4 protein isoform X1

    See identical proteins and their annotated locations for XP_011528790.1

    Conserved Domains (1) summary
    PRK14086
    Location:458575
    dnaA; chromosomal replication initiation protein; Provisional
  30. XM_017029064.1XP_016884553.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  31. XM_017029058.1XP_016884547.1  Hermansky-Pudlak syndrome 4 protein isoform X18

  32. XM_011530489.2XP_011528791.1  Hermansky-Pudlak syndrome 4 protein isoform X1

    See identical proteins and their annotated locations for XP_011528791.1

    Conserved Domains (1) summary
    PRK14086
    Location:458575
    dnaA; chromosomal replication initiation protein; Provisional
  33. XM_011530494.2XP_011528796.1  Hermansky-Pudlak syndrome 4 protein isoform X17

    See identical proteins and their annotated locations for XP_011528796.1

    Conserved Domains (1) summary
    PRK14086
    Location:194311
    dnaA; chromosomal replication initiation protein; Provisional
  34. XM_006724360.3XP_006724423.1  Hermansky-Pudlak syndrome 4 protein isoform X16

    See identical proteins and their annotated locations for XP_006724423.1

    Conserved Domains (1) summary
    PRK14086
    Location:243360
    dnaA; chromosomal replication initiation protein; Provisional
  35. XM_011530495.2XP_011528797.1  Hermansky-Pudlak syndrome 4 protein isoform X16

    See identical proteins and their annotated locations for XP_011528797.1

    Conserved Domains (1) summary
    PRK14086
    Location:243360
    dnaA; chromosomal replication initiation protein; Provisional
  36. XM_011530496.2XP_011528798.1  Hermansky-Pudlak syndrome 4 protein isoform X17

    See identical proteins and their annotated locations for XP_011528798.1

    Conserved Domains (1) summary
    PRK14086
    Location:194311
    dnaA; chromosomal replication initiation protein; Provisional
  37. XM_017029053.1XP_016884542.1  Hermansky-Pudlak syndrome 4 protein isoform X14

  38. XM_011530491.2XP_011528793.1  Hermansky-Pudlak syndrome 4 protein isoform X4

    Conserved Domains (1) summary
    PRK14086
    Location:458575
    dnaA; chromosomal replication initiation protein; Provisional

RNA

  1. XR_001755366.1 RNA Sequence

  2. XR_001755362.1 RNA Sequence

  3. XR_001755361.1 RNA Sequence

  4. XR_937947.1 RNA Sequence

  5. XR_001755364.1 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018933.2 Alternate CHM1_1.1

    Range
    26806304..26839247 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_152840.1: Suppressed sequence

    Description
    NM_152840.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
  2. NM_152842.1: Suppressed sequence

    Description
    NM_152842.1: This RefSeq was permanently suppressed because it is a nonsense-mediated decay (NMD) candidate.
  3. NM_152843.1: Suppressed sequence

    Description
    NM_152843.1: This RefSeq was permanently suppressed because currently there is not sufficient data to support this transcript.
Support Center