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Aliases for HPS4 Gene

Aliases for HPS4 Gene

  • HPS4, Biogenesis Of Lysosomal Organelles Complex 3 Subunit 2 2 3
  • Hermansky-Pudlak Syndrome 4 2 3 5
  • Light-Ear Protein Homolog 3 4
  • KIAA1667 4
  • BLOC3S2 3
  • LE 3

External Ids for HPS4 Gene

Previous GeneCards Identifiers for HPS4 Gene

  • GC22M023544
  • GC22M025172
  • GC22M025177
  • GC22M026840
  • GC22M009795

Summaries for HPS4 Gene

Entrez Gene Summary for HPS4 Gene

  • 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]

GeneCards Summary for HPS4 Gene

HPS4 (HPS4, Biogenesis Of Lysosomal Organelles Complex 3 Subunit 2) is a Protein Coding gene. Diseases associated with HPS4 include hermansky-pudlak syndrome 4 and hermansky-pudlak syndrome with pulmonary fibrosis. GO annotations related to this gene include protein homodimerization activity and protein dimerization activity.

UniProtKB/Swiss-Prot for HPS4 Gene

  • May function in the pathway of organelle biogenesis.

Gene Wiki entry for HPS4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HPS4 Gene

Genomics for HPS4 Gene

Regulatory Elements for HPS4 Gene

Promoters for HPS4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around HPS4 on UCSC Golden Path with GeneCards custom track

Genomic Location for HPS4 Gene

Chromosome:
22
Start:
26,443,423 bp from pter
End:
26,483,863 bp from pter
Size:
40,441 bases
Orientation:
Minus strand

Genomic View for HPS4 Gene

Genes around HPS4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HPS4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HPS4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HPS4 Gene

Proteins for HPS4 Gene

  • Protein details for HPS4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQG7-HPS4_HUMAN
    Recommended name:
    Hermansky-Pudlak syndrome 4 protein
    Protein Accession:
    Q9NQG7
    Secondary Accessions:
    • B1AHQ4
    • Q5H8V6
    • Q96LX6
    • Q9BY93
    • Q9UH37
    • Q9UH38

    Protein attributes for HPS4 Gene

    Size:
    708 amino acids
    Molecular mass:
    76919 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB33337.1; Type=Frameshift; Positions=237; Evidence={ECO:0000305}; Sequence=BAB33337.1; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305}; Sequence=BC035614; Type=Miscellaneous discrepancy; Note=Intron retention.; Evidence={ECO:0000305};

    Alternative splice isoforms for HPS4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HPS4 Gene

Proteomics data for HPS4 Gene at MOPED

Post-translational modifications for HPS4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for HPS4 Gene

Domains & Families for HPS4 Gene

Gene Families for HPS4 Gene

Protein Domains for HPS4 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with HPS4: view

No data available for UniProtKB/Swiss-Prot for HPS4 Gene

Function for HPS4 Gene

Molecular function for HPS4 Gene

UniProtKB/Swiss-Prot Function:
May function in the pathway of organelle biogenesis.

Gene Ontology (GO) - Molecular Function for HPS4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042803 protein homodimerization activity IPI 12663659
genes like me logo Genes that share ontologies with HPS4: view
genes like me logo Genes that share phenotypes with HPS4: view

Human Phenotype Ontology for HPS4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for HPS4 Gene

Localization for HPS4 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for HPS4 Gene COMPARTMENTS Subcellular localization image for HPS4 gene
Compartment Confidence
cytosol 5
lysosome 5
vacuole 5
nucleus 3
cytoskeleton 2
endosome 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for HPS4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IDA 12756248
GO:0042470 melanosome IDA 12663659
genes like me logo Genes that share ontologies with HPS4: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for HPS4 Gene

Pathways & Interactions for HPS4 Gene

SuperPathways for HPS4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HPS4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006996 organelle organization IEA --
GO:0007596 blood coagulation IEA --
GO:0030318 melanocyte differentiation IEA --
genes like me logo Genes that share ontologies with HPS4: view

No data available for Pathways by source and SIGNOR curated interactions for HPS4 Gene

Drugs & Compounds for HPS4 Gene

No Compound Related Data Available

Transcripts for HPS4 Gene

Unigene Clusters for HPS4 Gene

Hermansky-Pudlak syndrome 4:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for HPS4 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^
SP1: - -
SP2: - -
SP3:
SP4: - -
SP5: - -
SP6: -
SP7: - - - - - -
SP8:
SP9: - -
SP10: - - - - -
SP11: - - - -
SP12:

ExUns: 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b · 19c ^ 20
SP1: - -
SP2:
SP3: -
SP4: - - -
SP5: - - - -
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12: - -

Relevant External Links for HPS4 Gene

GeneLoc Exon Structure for
HPS4
ECgene alternative splicing isoforms for
HPS4

Expression for HPS4 Gene

mRNA expression in normal human tissues for HPS4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HPS4 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (50.3) and CD4 Tcells (14.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for HPS4 Gene



SOURCE GeneReport for Unigene cluster for HPS4 Gene Hs.474436

genes like me logo Genes that share expression patterns with HPS4: view

Protein tissue co-expression partners for HPS4 Gene

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for HPS4 Gene

Orthologs for HPS4 Gene

This gene was present in the common ancestor of animals.

Orthologs for HPS4 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia HPS4 35
  • 75.61 (n)
  • 68.58 (a)
HPS4 36
  • 68 (a)
OneToOne
dog
(Canis familiaris)
Mammalia HPS4 35
  • 78.24 (n)
  • 71.69 (a)
HPS4 36
  • 70 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Hps4 35
  • 72.26 (n)
  • 65.82 (a)
Hps4 16
Hps4 36
  • 64 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia HPS4 35
  • 99.01 (n)
  • 98.45 (a)
HPS4 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Hps4 35
  • 68.59 (n)
  • 63.14 (a)
oppossum
(Monodelphis domestica)
Mammalia HPS4 36
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves HPS4 35
  • 70.3 (n)
  • 68.68 (a)
HPS4 36
  • 46 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia hps4 35
  • 60.8 (n)
  • 58.3 (a)
zebrafish
(Danio rerio)
Actinopterygii -- 35
hps4 36
  • 37 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta HPS4 36
  • 16 (a)
OneToOne
Species with no ortholog for HPS4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HPS4 Gene

ENSEMBL:
Gene Tree for HPS4 (if available)
TreeFam:
Gene Tree for HPS4 (if available)

Paralogs for HPS4 Gene

(1) SIMAP similar genes for HPS4 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with HPS4: view

No data available for Paralogs for HPS4 Gene

Variants for HPS4 Gene

Sequence variations from dbSNP and Humsavar for HPS4 Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1894704 - 26,457,939(+) CGATC(A/C)TGCGG intron-variant, nc-transcript-variant, reference, missense
rs2014410 - 26,464,303(+) TTCGA(C/G)CTGCT nc-transcript-variant, reference, missense
rs1894706 - 26,458,475(+) GTAAT(A/G)TGTGA intron-variant, nc-transcript-variant, reference, missense
rs713998 - 26,466,246(+) CATCC(C/T)CTCCC nc-transcript-variant, reference, missense, utr-variant-5-prime
rs5752330 - 26,463,976(+) CAGCA(C/G/T)CAGCC nc-transcript-variant, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for HPS4 Gene

Variant ID Type Subtype PubMed ID
nsv7350 OTHER Inversion 18451855
nsv519472 CNV Loss 19592680

Variation tolerance for HPS4 Gene

Residual Variation Intolerance Score: 73.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.20; 69.77% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HPS4 Gene

HapMap Linkage Disequilibrium report
HPS4
Human Gene Mutation Database (HGMD)
HPS4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HPS4 Gene

Disorders for HPS4 Gene

MalaCards: The human disease database

(8) MalaCards diseases for HPS4 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hermansky-pudlak syndrome 4
  • platelet storage pool deficiency
hermansky-pudlak syndrome with pulmonary fibrosis
  • hps with pulmonary fibrosis
hermansky-pudlak syndrome
  • hps
oculocutaneous albinism
  • albinism, oculocutaneous
intestinal disease
  • intestinal diseases
- elite association - COSMIC cancer census association via MalaCards
Search HPS4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HPS4_HUMAN
  • Hermansky-Pudlak syndrome 4 (HPS4) [MIM:614073]: A form of Hermansky-Pudlak syndrome, a genetically heterogeneous autosomal recessive disorder characterized by oculocutaneous albinism, bleeding due to platelet storage pool deficiency, and lysosomal storage defects. This syndrome results from defects of diverse cytoplasmic organelles including melanosomes, platelet dense granules and lysosomes. Ceroid storage in the lungs is associated with pulmonary fibrosis, a common cause of premature death in individuals with HPS. {ECO:0000269 PubMed:11836498}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for HPS4

Genetic Association Database (GAD)
HPS4
Human Genome Epidemiology (HuGE) Navigator
HPS4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HPS4
genes like me logo Genes that share disorders with HPS4: view

No data available for Genatlas for HPS4 Gene

Publications for HPS4 Gene

  1. Hermansky-Pudlak syndrome is caused by mutations in HPS4, the human homolog of the mouse light-ear gene. (PMID: 11836498) Suzuki T. … Spritz R.A. (Nat. Genet. 2002) 2 3 4 23 67
  2. Comprehensive analysis of oculocutaneous albinism among non-Hispanic caucasians shows that OCA1 is the most prevalent OCA type. (PMID: 18463683) Hutton S.M. … Spritz R.A. (J. Invest. Dermatol. 2008) 3 23
  3. Hermansky-Pudlak syndrome type 4 in a patient from Sri Lanka with pulmonary fibrosis. (PMID: 15108212) Bachli E.B. … Gahl W.A. (Am. J. Med. Genet. A 2004) 3 23
  4. The Hermansky-Pudlak syndrome 1 (HPS1) and HPS4 proteins are components of two complexes, BLOC-3 and BLOC-4, involved in the biogenesis of lysosome-related organelles. (PMID: 12663659) Chiang P.W. … Spritz R.A. (J. Biol. Chem. 2003) 2 3
  5. Hermansky-Pudlak syndrome type 4 (HPS-4): clinical and molecular characteristics. (PMID: 12664304) Anderson P.D. … Gahl W.A. (Hum. Genet. 2003) 3 23

Products for HPS4 Gene

Sources for HPS4 Gene

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