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WDR19 WD repeat domain 19 [ Homo sapiens (human) ]

Gene ID: 57728, updated on 12-Aug-2018

Summary

Official Symbol
WDR19provided by HGNC
Official Full Name
WD repeat domain 19provided by HGNC
Primary source
HGNC:HGNC:18340
See related
Ensembl:ENSG00000157796 MIM:608151; Vega:OTTHUMG00000160466
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
ATD5; CED4; DYF-2; ORF26; Oseg6; PWDMP; SRTD5; IFT144; NPHP13
Summary
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]
Expression
Broad expression in thyroid (RPKM 9.7), testis (RPKM 8.9) and 25 other tissues See more
Orthologs

Genomic context

See WDR19 in Genome Data Viewer
Location:
4p14
Exon count:
38
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (39182404..39285810)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (39184024..39287430)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene transmembrane protein 156 Neighboring gene uncharacterized LOC105374418 Neighboring gene kelch like family member 5 Neighboring gene RNA, U6 small nuclear 32, pseudogene Neighboring gene replication factor C subunit 1 Neighboring gene RNA, U6 small nuclear 887, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Asphyxiating thoracic dystrophy 5
MedGen: C3280598 OMIM: 614376 GeneReviews: Not available
Compare labs
Cranioectodermal dysplasia 4
MedGen: C3280616 OMIM: 614378 GeneReviews: Cranioectodermal Dysplasia
Compare labs
Nephronophthisis 13
MedGen: C3280612 OMIM: 614377 GeneReviews: Nephronophthisis
Compare labs
Senior-Loken syndrome 8
MedGen: C4225376 OMIM: 616307 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Heritability and genetic association analysis of cognition in the Diabetes Heart Study.
NHGRI GWA Catalog

Pathways from BioSystems

  • Cilium Assembly, organism-specific biosystem (from REACTOME)
    Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
  • Hedgehog 'off' state, organism-specific biosystem (from REACTOME)
    Hedgehog 'off' state, organism-specific biosystemHedgehog is a secreted morphogen that has evolutionarily conserved roles in body organization by regulating the activity of the Ci/Gli transcription factor family. In Drosophila in the absence of Hh ...
  • Intraflagellar transport, organism-specific biosystem (from REACTOME)
    Intraflagellar transport, organism-specific biosystemIntraflagellar transport (IFT) is a motor-based process that controls the anterograde and retrograde transport of large protein complexes, ciliary cargo and structural components along the ciliary ax...
  • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
    Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Hedgehog, organism-specific biosystem (from REACTOME)
    Signaling by Hedgehog, organism-specific biosystemHedgehog (Hh) is a secreted morphogen that regulates developmental processes in vertebrates including limb bud formation, neural tube patterning, cell growth and differentiation (reviewed in Hui and ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ23127, KIAA1638

Gene Ontology Provided by GOA

Process Evidence Code Pubs
cell morphogenesis IEA
Inferred from Electronic Annotation
more info
 
ciliary receptor clustering involved in smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
digestive system development IEA
Inferred from Electronic Annotation
more info
 
ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic camera-type eye development IEA
Inferred from Electronic Annotation
more info
 
embryonic cranial skeleton morphogenesis IEA
Inferred from Electronic Annotation
more info
 
embryonic limb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
gonad development IEA
Inferred from Electronic Annotation
more info
 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
intraciliary retrograde transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary retrograde transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
intraciliary transport involved in cilium assembly TAS
Traceable Author Statement
more info
 
myotome development IEA
Inferred from Electronic Annotation
more info
 
nervous system process IEA
Inferred from Electronic Annotation
more info
 
smoothened signaling pathway involved in dorsal/ventral neural tube patterning IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
ciliary tip TAS
Traceable Author Statement
more info
 
cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cilium TAS
Traceable Author Statement
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
intraciliary transport particle A IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intraciliary transport particle A IDA
Inferred from Direct Assay
more info
PubMed 
motile cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
non-motile cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
photoreceptor connecting cilium ISS
Inferred from Sequence or Structural Similarity
more info
 
photoreceptor outer segment IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
WD repeat-containing protein 19
Names
WD repeat membrane protein PWDMP
intraflagellar transport 144 homolog

NCBI Reference Sequences (RefSeq)

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_031813.1 RefSeqGene

    Range
    5001..108407
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001317924.1NP_001304853.1  WD repeat-containing protein 19 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in its 5' UTR compared to variant 1. This variant represents translation initiation at a downstream start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream start codon to encode an isoform (2) that has a shorter N-terminus, compared to isoform 1
    Source sequence(s)
    AK225588, AK294730, AY029257
    UniProtKB/Swiss-Prot
    Q8NEZ3
    UniProtKB/TrEMBL
    B4DGR6
    Conserved Domains (8) summary
    COG0457
    Location:702982
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    COG2319
    Location:2186
    WD40; WD40 repeat [General function prediction only]
    COG5290
    Location:672770
    COG5290; IkappaB kinase complex, IKAP component [Transcription]
    sd00006
    Location:619643
    TPR; TPR repeat [structural motif]
    pfam12773
    Location:10931135
    DZR; Double zinc ribbon
    pfam15911
    Location:348404
    WD40_3; WD domain, G-beta repeat
    sd00039
    Location:73112
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:114186
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. NM_025132.3NP_079408.3  WD repeat-containing protein 19 isoform 1

    See identical proteins and their annotated locations for NP_079408.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB046858, AK026780, AK122908, AY029257, BC032578
    Consensus CDS
    CCDS47042.1
    UniProtKB/Swiss-Prot
    Q8NEZ3
    Related
    ENSP00000382717.3, OTTHUMP00000218257, ENST00000399820.7, OTTHUMT00000360689
    Conserved Domains (8) summary
    COG0457
    Location:8621142
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    COG2319
    Location:19345
    WD40; WD40 repeat [General function prediction only]
    COG5290
    Location:832930
    COG5290; IkappaB kinase complex, IKAP component [Transcription]
    sd00006
    Location:779803
    TPR; TPR repeat [structural motif]
    pfam12773
    Location:12531295
    DZR; Double zinc ribbon
    pfam15911
    Location:508564
    WD40_3; WD domain, G-beta repeat
    sd00039
    Location:5798
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:26302
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    39182404..39285810
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513725.2XP_011512027.1  WD repeat-containing protein 19 isoform X2

    Conserved Domains (8) summary
    COG0457
    Location:8441124
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    COG2319
    Location:32323
    WD40; WD40 repeat [General function prediction only]
    COG5290
    Location:814912
    COG5290; IkappaB kinase complex, IKAP component [Transcription]
    sd00006
    Location:761785
    TPR; TPR repeat [structural motif]
    pfam12773
    Location:12351277
    DZR; Double zinc ribbon
    pfam15911
    Location:486542
    WD40_3; WD domain, G-beta repeat
    sd00039
    Location:3576
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:32324
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. XM_011513724.1XP_011512026.1  WD repeat-containing protein 19 isoform X1

    Conserved Domains (8) summary
    COG0457
    Location:8661146
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    COG2319
    Location:19345
    WD40; WD40 repeat [General function prediction only]
    COG5290
    Location:836934
    COG5290; IkappaB kinase complex, IKAP component [Transcription]
    sd00006
    Location:783807
    TPR; TPR repeat [structural motif]
    pfam12773
    Location:12571299
    DZR; Double zinc ribbon
    pfam15911
    Location:508564
    WD40_3; WD domain, G-beta repeat
    sd00039
    Location:5798
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:26302
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  3. XM_011513726.3XP_011512028.1  WD repeat-containing protein 19 isoform X3

    See identical proteins and their annotated locations for XP_011512028.1

    Conserved Domains (8) summary
    COG0457
    Location:706986
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    COG2319
    Location:2186
    WD40; WD40 repeat [General function prediction only]
    COG5290
    Location:676774
    COG5290; IkappaB kinase complex, IKAP component [Transcription]
    sd00006
    Location:623647
    TPR; TPR repeat [structural motif]
    pfam12773
    Location:10971139
    DZR; Double zinc ribbon
    pfam15911
    Location:348404
    WD40_3; WD domain, G-beta repeat
    sd00039
    Location:73112
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:114186
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  4. XM_011513727.1XP_011512029.1  WD repeat-containing protein 19 isoform X3

    See identical proteins and their annotated locations for XP_011512029.1

    Conserved Domains (8) summary
    COG0457
    Location:706986
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    COG2319
    Location:2186
    WD40; WD40 repeat [General function prediction only]
    COG5290
    Location:676774
    COG5290; IkappaB kinase complex, IKAP component [Transcription]
    sd00006
    Location:623647
    TPR; TPR repeat [structural motif]
    pfam12773
    Location:10971139
    DZR; Double zinc ribbon
    pfam15911
    Location:348404
    WD40_3; WD domain, G-beta repeat
    sd00039
    Location:73112
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:114186
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  5. XM_017008501.1XP_016863990.1  WD repeat-containing protein 19 isoform X4

    UniProtKB/TrEMBL
    B4DGR6
    Conserved Domains (8) summary
    COG0457
    Location:702982
    TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
    COG2319
    Location:2186
    WD40; WD40 repeat [General function prediction only]
    COG5290
    Location:672770
    COG5290; IkappaB kinase complex, IKAP component [Transcription]
    sd00006
    Location:619643
    TPR; TPR repeat [structural motif]
    pfam12773
    Location:10931135
    DZR; Double zinc ribbon
    pfam15911
    Location:348404
    WD40_3; WD domain, G-beta repeat
    sd00039
    Location:73112
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:114186
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

  1. XR_001741308.1 RNA Sequence

  2. XR_925155.1 RNA Sequence

  3. XR_001741306.1 RNA Sequence

  4. XR_001741310.1 RNA Sequence

  5. XR_001741309.1 RNA Sequence

  6. XR_001741307.1 RNA Sequence

    Related
    ENST00000506869.5, OTTHUMT00000360691
  7. XR_001741312.1 RNA Sequence

  8. XR_001741311.2 RNA Sequence

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