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    WDR59 WD repeat domain 59 [ Homo sapiens (human) ]

    Gene ID: 79726, updated on 2-May-2024

    Summary

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    Official Symbol
    WDR59provided by HGNC
    Official Full Name
    WD repeat domain 59provided by HGNC
    Primary source
    HGNC:HGNC:25706
    See related
    Ensembl:ENSG00000103091 MIM:617418; AllianceGenome:HGNC:25706
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDW12; FP977; p90-120
    Summary
    Involved in cellular response to amino acid starvation and positive regulation of TOR signaling. Located in lysosomal membrane. Part of GATOR2 complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in skin (RPKM 11.4), thyroid (RPKM 10.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See WDR59 in Genome Data Viewer
    Location:
    16q23.1
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (74871362..74985123, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (80918078..81031872, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (74905260..75019021, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44395 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74763414-74763939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74763940-74764464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74767393-74767952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74771195-74771902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74781673-74782338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74782339-74783002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74786737-74787236 Neighboring gene fatty acid 2-hydroxylase Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:74793901-74795100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11109 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11110 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7701 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7702 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7703 Neighboring gene uncharacterized LOC105371343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11111 Neighboring gene Sharpr-MPRA regulatory region 8667 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74905369-74905917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:74908123-74908848 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:74909577-74910302 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:74997467-74997687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7704 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11112 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75020112-75020312 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11116 Neighboring gene zinc and ring finger 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:75095860-75097059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75108734-75109234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75109235-75109735 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75113000-75113201 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75113937-75114482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75121619-75122275 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75127186-75127378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75129219-75129949 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75129950-75130679 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75136275-75136776 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_44438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11121 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11122 Neighboring gene Sharpr-MPRA regulatory region 12749 Neighboring gene lactate dehydrogenase D

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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 Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Expression of CDw12 and CD17 cell surface antigens on leukemic cells from patients with blood malignancies. Marinov J, et al. Folia Biol (Praha), 1993. PMID 8157132
    2. The CASTOR Proteins Are Arginine Sensors for the mTORC1 Pathway. Chantranupong L, et al. Cell, 2016 Mar 24. PMID 26972053, Free PMC Article
    3. The Sestrins interact with GATOR2 to negatively regulate the amino-acid-sensing pathway upstream of mTORC1. Chantranupong L, et al. Cell Rep, 2014 Oct 9. PMID 25263562, Free PMC Article
    4. SZT2 dictates GATOR control of mTORC1 signalling. Peng M, et al. Nature, 2017 Mar 16. PMID 28199315, Free PMC Article
    5. A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1. Bar-Peled L, et al. Science, 2013 May 31. PMID 23723238, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12270, MGC11230

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling adaptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cellular response to amino acid starvation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to amino acid starvation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cellular response to nutrient levels IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of TORC1 signaling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of TORC1 signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of TORC1 signaling IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of TORC1 signaling NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of GATOR2 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of GATOR2 complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of Seh1-associated complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in vacuolar membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    GATOR2 complex protein WDR59; GATOR complex protein WDR59
    Names
    CDw12 antigen
    WD repeat-containing protein 59

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001324171.2 → NP_001311100.1  GATOR2 complex protein WDR59 isoform 2

      Status: VALIDATED

      Source sequence(s)
      BC004519, CA777098
      Consensus CDS
      CCDS82011.1
      UniProtKB/Swiss-Prot
      Q6PJI9
      Related
      ENSP00000482446.1, ENST00000616369.4
      Conserved Domains (3) summary
      smart00591
      Location:394 → 494
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cl25539
      Location:100 → 343
      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_001324172.2 → NP_001311101.1  GATOR2 complex protein WDR59 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL562571, BU850134, CA777098, R43806
      UniProtKB/TrEMBL
      B7Z7V6
      Related
      ENSP00000481730.1, ENST00000536050.5

    3. NM_030581.4 → NP_085058.3  GATOR2 complex protein WDR59 isoform 1

      See identical proteins and their annotated locations for NP_085058.3

      Status: VALIDATED

      Source sequence(s)
      AC009132, AC092383, AF370390, BC004519, CA777098
      Consensus CDS
      CCDS32488.1
      UniProtKB/Swiss-Prot
      B3KRC3, Q6PJI9, Q71RE7, Q96PW5, Q9BSW6, Q9HA43
      Related
      ENSP00000262144.6, ENST00000262144.11
      Conserved Domains (5) summary
      smart00591
      Location:394 → 494
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 328
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:100 → 343
      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 ...
      cl24077
      Location:924 → 972
      Zn_ribbon_17; Zinc-ribbon, C4HC2 type

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      74871362..74985123 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434642.1 → XP_047290598.1  GATOR complex protein WDR59 isoform X5

    2. XM_047434640.1 → XP_047290596.1  GATOR complex protein WDR59 isoform X4

    3. XM_047434639.1 → XP_047290595.1  GATOR complex protein WDR59 isoform X3

    4. XM_047434638.1 → XP_047290594.1  GATOR complex protein WDR59 isoform X2

    5. XM_005256146.4 → XP_005256203.1  GATOR complex protein WDR59 isoform X1

      Conserved Domains (5) summary
      smart00591
      Location:394 → 494
      RWD; domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain
      COG2319
      Location:34 → 328
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:62 → 103
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:100 → 343
      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 ...
      cl24077
      Location:943 → 991
      Zn_ribbon_17; Zinc-ribbon, C4HC2 type

    6. XM_047434641.1 → XP_047290597.1  GATOR complex protein WDR59 isoform X4

    7. XM_047434643.1 → XP_047290599.1  GATOR complex protein WDR59 isoform X6

    8. XM_047434646.1 → XP_047290602.1  GATOR complex protein WDR59 isoform X8

    9. XM_047434644.1 → XP_047290600.1  GATOR complex protein WDR59 isoform X7

    10. XM_047434645.1 → XP_047290601.1  GATOR complex protein WDR59 isoform X7

    RNA

    1. XR_007064915.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      80918078..81031872 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054313938.1 → XP_054169913.1  GATOR complex protein WDR59 isoform X5

    2. XM_054313936.1 → XP_054169911.1  GATOR complex protein WDR59 isoform X4

    3. XM_054313935.1 → XP_054169910.1  GATOR complex protein WDR59 isoform X3

    4. XM_054313934.1 → XP_054169909.1  GATOR complex protein WDR59 isoform X2

    5. XM_054313933.1 → XP_054169908.1  GATOR complex protein WDR59 isoform X1

    6. XM_054313937.1 → XP_054169912.1  GATOR complex protein WDR59 isoform X4

    7. XM_054313939.1 → XP_054169914.1  GATOR complex protein WDR59 isoform X6

    8. XM_054313942.1 → XP_054169917.1  GATOR complex protein WDR59 isoform X8

    9. XM_054313940.1 → XP_054169915.1  GATOR complex protein WDR59 isoform X7

    10. XM_054313941.1 → XP_054169916.1  GATOR complex protein WDR59 isoform X7

    RNA

    1. XR_008484737.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PJI9.2 GenPept UniProtKB/Swiss-Prot:Q6PJI9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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