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

Gene ID: 79726, updated on 10-Dec-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
Predicted to enable signaling adaptor activity. Involved in cellular response to amino acid starvation and positive regulation of TORC1 signaling. Located in cytosol and lysosomal membrane. Part of GATOR2 complex. [provided by Alliance of Genome Resources, Dec 2024]
Expression
Ubiquitous expression in skin (RPKM 11.4), thyroid (RPKM 10.4) and 25 other tissues See more
Orthologs
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (74871362..74985123, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (80918078..81031872, complement)
RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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. Structure of the nutrient-sensing hub GATOR2. Valenstein ML, et al. Nature, 2022 Jul. PMID 35831510, Free PMC Article
  4. 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
  5. Ring domains are essential for GATOR2-dependent mTORC1 activation. Jiang C, et al. Mol Cell, 2023 Jan 5. PMID 36528027, Free PMC Article

See all (51) 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)

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
Names
CDw12 antigen
GATOR complex protein WDR59
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_2024_08

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  GATOR2 complex protein WDR59 isoform X5

  2. XM_047434640.1 → XP_047290596.1  GATOR2 complex protein WDR59 isoform X4

  3. XM_047434639.1 → XP_047290595.1  GATOR2 complex protein WDR59 isoform X3

  4. XM_047434638.1 → XP_047290594.1  GATOR2 complex protein WDR59 isoform X2

  5. XM_005256146.4 → XP_005256203.1  GATOR2 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  GATOR2 complex protein WDR59 isoform X4

  7. XM_047434643.1 → XP_047290599.1  GATOR2 complex protein WDR59 isoform X6

  8. XM_047434646.1 → XP_047290602.1  GATOR2 complex protein WDR59 isoform X8

  9. XM_047434644.1 → XP_047290600.1  GATOR2 complex protein WDR59 isoform X7

  10. XM_047434645.1 → XP_047290601.1  GATOR2 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  GATOR2 complex protein WDR59 isoform X5

  2. XM_054313936.1 → XP_054169911.1  GATOR2 complex protein WDR59 isoform X4

  3. XM_054313935.1 → XP_054169910.1  GATOR2 complex protein WDR59 isoform X3

  4. XM_054313934.1 → XP_054169909.1  GATOR2 complex protein WDR59 isoform X2

  5. XM_054313933.1 → XP_054169908.1  GATOR2 complex protein WDR59 isoform X1

  6. XM_054313937.1 → XP_054169912.1  GATOR2 complex protein WDR59 isoform X4

  7. XM_054313939.1 → XP_054169914.1  GATOR2 complex protein WDR59 isoform X6

  8. XM_054313942.1 → XP_054169917.1  GATOR2 complex protein WDR59 isoform X8

  9. XM_054313940.1 → XP_054169915.1  GATOR2 complex protein WDR59 isoform X7

  10. XM_054313941.1 → XP_054169916.1  GATOR2 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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