Human Gene HPS3 (ENST00000296051.7_6) from GENCODE V47lift37
  Description: HPS3 biogenesis of lysosomal organelles complex 2 subunit 1, transcript variant 1 (from RefSeq NM_032383.5)
Gencode Transcript: ENST00000296051.7_6
Gencode Gene: ENSG00000163755.9_10
Transcript (Including UTRs)
   Position: hg19 chr3:148,847,425-148,891,519 Size: 44,095 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr3:148,847,511-148,890,009 Size: 42,499 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:148,847,425-148,891,519)mRNA (may differ from genome)Protein (1004 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HPS3_HUMAN
DESCRIPTION: RecName: Full=Hermansky-Pudlak syndrome 3 protein;
FUNCTION: Involved in early stages of melanosome biogenesis and maturation (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
TISSUE SPECIFICITY: Widely expressed. Higher levels of expression are observed in kidney, liver and placenta.
DISEASE: Defects in HPS3 are the cause of Hermansky-Pudlak syndrome type 3 (HPS3) [MIM:614072]. Hermansky-Pudlak syndrome (HPS) is a genetically heterogeneous, rare, 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.
SEQUENCE CAUTION: Sequence=AAH16901.1; Type=Erroneous initiation; Sequence=AAH22062.2; Type=Erroneous initiation; Sequence=BAB71221.1; Type=Erroneous initiation;
WEB RESOURCE: Name=Mutations of the HPS3 gene; Note=Retina International's Scientific Newsletter; URL="http://www.retina-international.org/files/sci-news/hps3mut.htm";
WEB RESOURCE: Name=Albinism database (ADB); Note=HPS3 mutations; URL="http://albinismdb.med.umn.edu/hps3mut.html";
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/HPS3";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: HPS3
Diseases sorted by gene-association score: hermansky-pudlak syndrome 3* (1381), hermansky-pudlak syndrome without pulmonary fibrosis* (202), hermansky-pudlak syndrome (48), oculocutaneous albinism (14), pulmonary fibrosis (9), storage pool platelet disease (9)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.59 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 214.86 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.1086-0.420 Picture PostScript Text
3' UTR -298.181510-0.197 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR017216 - BLOC-2_complex_Hps3_subunit

Pfam Domains:
PF14761 - Hermansky-Pudlak syndrome 3
PF14762 - Hermansky-Pudlak syndrome 3, middle region
PF14763 - Hermansky-Pudlak syndrome 3, C-terminal

ModBase Predicted Comparative 3D Structure on Q969F9
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006996 organelle organization
GO:0043473 pigmentation

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0031084 BLOC-2 complex


-  Descriptions from all associated GenBank mRNAs
  AY033141 - Homo sapiens Hermansky-Pudlak syndrome type-3 protein (HPS3) mRNA, complete cds.
AK291631 - Homo sapiens cDNA FLJ78661 complete cds, highly similar to Homo sapiens Hermansky-Pudlak syndrome 3 (HPS3), mRNA.
AK055245 - Homo sapiens cDNA FLJ30683 fis, clone FCBBF2000232.
BC040359 - Homo sapiens Hermansky-Pudlak syndrome 3, mRNA (cDNA clone MGC:21683 IMAGE:4385940), complete cds.
AK298478 - Homo sapiens cDNA FLJ58519 complete cds, highly similar to Hermansky-Pudlak syndrome 3 protein.
JD461901 - Sequence 442925 from Patent EP1572962.
JD467267 - Sequence 448291 from Patent EP1572962.
KJ899790 - Synthetic construct Homo sapiens clone ccsbBroadEn_09184 HPS3 gene, encodes complete protein.
CU691866 - Synthetic construct Homo sapiens gateway clone IMAGE:100017878 5' read HPS3 mRNA.
DQ894360 - Synthetic construct Homo sapiens clone IMAGE:100008820; FLH169882.01L; RZPDo839H0395D Hermansky-Pudlak syndrome 3 (HPS3) gene, encodes complete protein.
DQ891178 - Synthetic construct clone IMAGE:100003808; FLH169886.01X; RZPDo839H0396D Hermansky-Pudlak syndrome 3 (HPS3) gene, encodes complete protein.
BC022062 - Homo sapiens Hermansky-Pudlak syndrome 3, mRNA (cDNA clone IMAGE:2989325), partial cds.
AK056575 - Homo sapiens cDNA FLJ32013 fis, clone NTONG1000033.
AL832735 - Homo sapiens mRNA; cDNA DKFZp686F0413 (from clone DKFZp686F0413).
AL833878 - Homo sapiens mRNA; cDNA DKFZp762O156 (from clone DKFZp762O156).
BC016901 - Homo sapiens Hermansky-Pudlak syndrome 3, mRNA (cDNA clone IMAGE:4415076), complete cds.
AK026357 - Homo sapiens cDNA: FLJ22704 fis, clone HSI12602.
JD026158 - Sequence 7182 from Patent EP1572962.
JD020202 - Sequence 1226 from Patent EP1572962.
JD032046 - Sequence 13070 from Patent EP1572962.
JD564011 - Sequence 545035 from Patent EP1572962.
JD083016 - Sequence 64040 from Patent EP1572962.
JD099016 - Sequence 80040 from Patent EP1572962.
JD244625 - Sequence 225649 from Patent EP1572962.
JD111154 - Sequence 92178 from Patent EP1572962.
JD428593 - Sequence 409617 from Patent EP1572962.
JD046467 - Sequence 27491 from Patent EP1572962.
JD337103 - Sequence 318127 from Patent EP1572962.
JD261914 - Sequence 242938 from Patent EP1572962.
JD113959 - Sequence 94983 from Patent EP1572962.
JD113754 - Sequence 94778 from Patent EP1572962.
JD410970 - Sequence 391994 from Patent EP1572962.
JD473366 - Sequence 454390 from Patent EP1572962.
JD348855 - Sequence 329879 from Patent EP1572962.
JD296126 - Sequence 277150 from Patent EP1572962.
JD256295 - Sequence 237319 from Patent EP1572962.
JD110259 - Sequence 91283 from Patent EP1572962.
JD357048 - Sequence 338072 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6G6, ENST00000296051.1, ENST00000296051.2, ENST00000296051.3, ENST00000296051.4, ENST00000296051.5, ENST00000296051.6, HPS3_HUMAN, NM_032383, Q8WTV6, Q969F9, Q96AP1, Q96MR3, Q9H608, uc317lqu.1, uc317lqu.2
UCSC ID: ENST00000296051.7_6
RefSeq Accession: NM_032383.5
Protein: Q969F9 (aka HPS3_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene HPS3:
hps (Hermansky-Pudlak Syndrome)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.