Human Gene WDR19 (uc003gtw.1)
  Description: Homo sapiens WD repeat domain 19 (WDR19), mRNA.
RefSeq Summary (NM_025132): The protein encoded by this gene is a member of the WD (tryptophan-aspartic acid) repeat family, which is a large family of structurally-related proteins known to participate in a wide range of cellular processes. Each WD repeat typically contains about 40 amino acids that are usually bracketed by glycine-histidine and tryptophan-aspartic acid (WD) dipeptides. This protein contains six WD repeats, three transmembrane domains, and a clathrin heavy-chain repeat. Mutations in this gene have been described in individuals with a wide range of disorders affecting function of the cilium. These disorders are known as ciliopathies, and include Jeune syndrome, Sensenbrenner syndromes, Senior-Loken syndrome, combined or isolated nephronophthisis (NPHP), and retinitis pigmentosa (RP). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015].
Transcript (Including UTRs)
   Position: hg19 chr4:39,217,461-39,276,959 Size: 59,499 Total Exon Count: 23 Strand: +
Coding Region
   Position: hg19 chr4:39,217,791-39,276,582 Size: 58,792 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviews
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:39,217,461-39,276,959)mRNA (may differ from genome)Protein (836 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: WDR19_HUMAN
DESCRIPTION: RecName: Full=WD repeat-containing protein 19;
FUNCTION: May be involved in cilia function and/or assembly.
SUBCELLULAR LOCATION: Cell projection, cilium (By similarity). Cytoplasm, cytoskeleton, cilium basal body (By similarity). Note=Localizes to photoreceptor connecting cilia, to the base of motile cilia in brain ependymal cells and to the base of and along primary cilia in kidney cells (By similarity).
TISSUE SPECIFICITY: Some isoforms are tissue-specific. Highly expressed in the prostate. Lower expression in the cerebellum, pituitary gland, fetal lung, and pancreas. In normal prostate, expressed in both basal and luminal epithelial cells. No expression detected in fibromuscular stromal cells, endothelial cells, or infiltrating lymphocytes. Uniformed expression in prostate adenocarcinoma cells.
DEVELOPMENTAL STAGE: Expressed in fetal lung.
INDUCTION: By androgenic hormones. Expression increased 3-fold in an androgen-stimulated androgen-sensitive prostate adenocarcinoma cell line compared with androgen-deprived cells.
DISEASE: Defects in WDR19 are the cause of cranioectodermal dysplasia type 4 (CED4) [MIM:614378]. CED4 is a disorder primarily characterized by craniofacial, skeletal and ectodermal abnormalities. Clinical features include craniosynostosis, narrow rib cage, short limbs, brachydactyly, hypoplastic and widely spaced teeth, sparse hair, skin laxity and abnormal nails. Nephronophthisis leading to progressive renal failure, hepatic fibrosis, heart defects, and retinitis pigmentosa have also been described.
DISEASE: Defects in WDR19 are the cause of asphyxiating thoracic dystrophy type 5 (ATD5) [MIM:614376]. ATD5 is an autosomal recessive chondrodysplasia characterized by a severely constricted thoracic cage, short-limbed short stature, and polydactyly. It often leads to death in infancy because of respiratory insufficiency. Retinal degeneration, cystic renal disease and hepatic disease can be present in affected individuals who survive early childhood.
DISEASE: Defects in WDR19 are the cause of nephronophthisis type 13 (NPHP13) [MIM:614377]. NPHP13 is an autosomal recessive disorder resulting in end-stage renal disease. It is a progressive tubulo-interstitial kidney disorder histologically characterized by modifications of the tubules with thickening of the basement membrane, interstitial fibrosis and, in the advanced stages, medullary cysts.
SIMILARITY: Contains 6 TPR repeats.
SIMILARITY: Contains 6 WD repeats.
SEQUENCE CAUTION: Sequence=AAH32578.1; Type=Frameshift; Positions=421;

-  Primer design for this transcript
 

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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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): WDR19
CDC HuGE Published Literature: WDR19
Positive Disease Associations: Blood Pressure Determination
Related Studies:
  1. Blood Pressure Determination
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: WDR19
Diseases sorted by gene-association score: short-rib thoracic dysplasia 5 with or without polydactyly* (1380), cranioectodermal dysplasia 4* (1379), nephronophthisis 13* (1338), senior-loken syndrome 8* (1330), asphyxiating thoracic dystrophy* (238), cranioectodermal dysplasia 1* (213), nephronophthisis 16* (175), senior-loken syndrome-1* (164), prostate adenocarcinoma (19), caroli disease (18), nephronophthisis (16), choledochal cyst (8), ellis-van creveld syndrome (7), short-rib thoracic dysplasia 3 with or without polydactyly (5), cleft lip/palate (4), retinitis pigmentosa (3), ciliopathy (3), eye disease (1)
* = 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: 18.78 RPKM in Pituitary
Total median expression: 378.01 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -67.87248-0.274 Picture PostScript Text
3' UTR -131.55377-0.349 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
IPR011990 - TPR-like_helical
IPR015943 - WD40/YVTN_repeat-like_dom
IPR001680 - WD40_repeat
IPR017986 - WD40_repeat_dom

Pfam Domains:
PF15911 - WD domain, G-beta repeat

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q8NEZ3
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-  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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0000902 cell morphogenesis
GO:0001701 in utero embryonic development
GO:0007224 smoothened signaling pathway
GO:0008406 gonad development
GO:0030030 cell projection organization
GO:0030326 embryonic limb morphogenesis
GO:0031076 embryonic camera-type eye development
GO:0035721 intraciliary retrograde transport
GO:0035735 intraciliary transport involved in cilium assembly
GO:0042471 ear morphogenesis
GO:0048701 embryonic cranial skeleton morphogenesis
GO:0050877 neurological system process
GO:0055123 digestive system development
GO:0060271 cilium assembly
GO:0060830 ciliary receptor clustering involved in smoothened signaling pathway
GO:0060831 smoothened signaling pathway involved in dorsal/ventral neural tube patterning
GO:0061055 myotome development

Cellular Component:
GO:0001750 photoreceptor outer segment
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005929 cilium
GO:0016604 nuclear body
GO:0030991 intraciliary transport particle A
GO:0031514 motile cilium
GO:0032391 photoreceptor connecting cilium
GO:0042995 cell projection
GO:0097542 ciliary tip
GO:0097730 non-motile cilium


-  Descriptions from all associated GenBank mRNAs
  AY029257 - Homo sapiens WD repeat membrane protein mRNA, complete cds.
AK308803 - Homo sapiens cDNA, FLJ98844.
AK294730 - Homo sapiens cDNA FLJ57049 complete cds, highly similar to WD repeat protein 19.
AK026780 - Homo sapiens cDNA: FLJ23127 fis, clone LNG08350.
AK225588 - Homo sapiens mRNA for WD repeat domain 19 variant, clone: LNG08350.
AK304161 - Homo sapiens cDNA FLJ56808 complete cds, highly similar to WD repeat protein 19.
BC032578 - Homo sapiens WD repeat domain 19, mRNA (cDNA clone IMAGE:5493226), complete cds.
KJ904842 - Synthetic construct Homo sapiens clone ccsbBroadEn_14236 WDR19-like gene, encodes complete protein.
BC172278 - Synthetic construct Homo sapiens clone IMAGE:100068972, MGC:198983 WD repeat domain 19 (WDR19) mRNA, encodes complete protein.
AB046858 - Homo sapiens mRNA for KIAA1638 protein, partial cds.
AK296112 - Homo sapiens cDNA FLJ56611 complete cds, highly similar to WD repeat protein 19.
AK122908 - Homo sapiens cDNA FLJ16583 fis, clone TESTI2053723.
JD141758 - Sequence 122782 from Patent EP1572962.
JD446465 - Sequence 427489 from Patent EP1572962.
JD473172 - Sequence 454196 from Patent EP1572962.
JD145022 - Sequence 126046 from Patent EP1572962.
JD526626 - Sequence 507650 from Patent EP1572962.
JD472697 - Sequence 453721 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8NEZ3 (Reactome details) participates in the following event(s):

R-HSA-5617829 Assembly of IFT A complex
R-HSA-5624949 Assembly of the anterograde IFT train
R-HSA-5625424 The retrograde IFT train dissociates
R-HSA-5624952 Assembly of the retrograde IFT train
R-HSA-5625421 The anterograde IFT train dissociates
R-HSA-5610726 The IFT-A complex recruits TULP3
R-HSA-5610725 TULP3 is required for GPR161 localization in the cilium
R-HSA-5620924 Intraflagellar transport
R-HSA-5617833 Cilium Assembly
R-HSA-5610787 Hedgehog 'off' state
R-HSA-1852241 Organelle biogenesis and maintenance
R-HSA-5358351 Signaling by Hedgehog
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: AB046858, B5MEF2, KIAA1638, NM_025132, NP_079408, Q8N5B4, Q8NEZ3, Q9H5S0, Q9HCD4, WDR19_HUMAN
UCSC ID: uc003gtw.1
RefSeq Accession: NM_025132
Protein: Q8NEZ3 (aka WDR19_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene WDR19:
ce-dysp (Cranioectodermal Dysplasia)
nephron-ov (Nephronophthisis-Related Ciliopathies)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AB046858.1
exon count: 23CDS single in 3' UTR: no RNA size: 3095
ORF size: 2511CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5132.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 381# strange splices: 0
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.