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

Summary

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: mouse all
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Genomic context

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_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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 EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH119625 (e-PCR)
- UniSTS:133943

G62712 (e-PCR)
- UniSTS:139837

RH91801 (e-PCR)
- UniSTS:86616

RH70757 (e-PCR)
- UniSTS:48526

SHGC-1232 (e-PCR)
- UniSTS:15761

SHGC-33475 (e-PCR)
- UniSTS:4020

RH102641 (e-PCR)
- UniSTS:96975

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)

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 ...
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
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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

74871362..74985123 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047434642.1 → XP_047290598.1 GATOR2 complex protein WDR59 isoform X5
XM_047434640.1 → XP_047290596.1 GATOR2 complex protein WDR59 isoform X4
XM_047434639.1 → XP_047290595.1 GATOR2 complex protein WDR59 isoform X3
XM_047434638.1 → XP_047290594.1 GATOR2 complex protein WDR59 isoform X2
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
XM_047434641.1 → XP_047290597.1 GATOR2 complex protein WDR59 isoform X4
XM_047434643.1 → XP_047290599.1 GATOR2 complex protein WDR59 isoform X6
XM_047434646.1 → XP_047290602.1 GATOR2 complex protein WDR59 isoform X8
XM_047434644.1 → XP_047290600.1 GATOR2 complex protein WDR59 isoform X7
XM_047434645.1 → XP_047290601.1 GATOR2 complex protein WDR59 isoform X7