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    WDR41 WD repeat domain 41 [ Homo sapiens (human) ]

    Gene ID: 55255, updated on 10-Dec-2024

    Summary

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    Official Symbol
    WDR41provided by HGNC
    Official Full Name
    WD repeat domain 41provided by HGNC
    Primary source
    HGNC:HGNC:25601
    See related
    Ensembl:ENSG00000164253 MIM:617502; AllianceGenome:HGNC:25601
    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
    MSTP048
    Summary
    Enables GTPase activator activity. Contributes to guanyl-nucleotide exchange factor activity. Involved in regulation of autophagy. Located in Atg1/ULK1 kinase complex. Part of guanyl-nucleotide exchange factor complex. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 15.6), brain (RPKM 8.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See WDR41 in Genome Data Viewer
    Location:
    5q13.3-q14.1
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (77430933..77620577, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (77913542..78103190, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (76726758..76788141, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ZBED3 antisense RNA 1 Neighboring gene phosphodiesterase 8B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:76468397-76468898 Neighboring gene high mobility group box 1 pseudogene 35 Neighboring gene aldehyde dehydrogenase 7 family member A1 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76618089-76618784 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:76672412-76673040 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:76752518-76752693 Neighboring gene uncharacterized LOC124901009 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:76787603-76788526 Neighboring gene ribosomal protein S2 pseudogene 24 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76924162-76924727 Neighboring gene ribosomal protein L7 pseudogene 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22700 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:76928018-76928518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22701 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76934524-76935080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:76935081-76935635 Neighboring gene VISTA enhancer hs262 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16113 Neighboring gene orthopedia homeobox Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:77047116-77047753 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:77068972-77069857 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:77069858-77070742 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16115 Neighboring gene tubulin folding cofactor A

    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. Aberrant methylation of WD-repeat protein 41 contributes to tumour progression in triple-negative breast cancer. Wang H, et al. J Cell Mol Med, 2020 Jun. PMID 32394588, Free PMC Article
    2. WDR41 supports lysosomal response to changes in amino acid availability. Amick J, et al. Mol Biol Cell, 2018 Sep 1. PMID 29995611, Free PMC Article
    3. Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids. Talaia G, et al. Proc Natl Acad Sci U S A, 2021 Feb 23. PMID 33597295, Free PMC Article
    4. Discovery and replication of dopamine-related gene effects on caudate volume in young and elderly populations (N=1198) using genome-wide search. Stein JL, et al. Mol Psychiatry, 2011 Sep. PMID 21502949, Free PMC Article
    5. Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a. Tang D, et al. Proc Natl Acad Sci U S A, 2020 May 5. PMID 32303654, Free PMC Article

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids.
      Title: Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids.
    2. Aberrant methylation of WD-repeat protein 41 contributes to tumour progression in triple-negative breast cancer.
      Title: Aberrant methylation of WD-repeat protein 41 contributes to tumour progression in triple-negative breast cancer.
    3. Structure of the C9orf72 ARF GAP complex that is haploinsufficient in ALS and FTD.
      Title: Structure of the C9orf72 ARF GAP complex that is haploinsufficient in ALS and FTD.
    4. Our study not only illustrates the basis of C9ORF72-SMCR8-WDR41 complex assembly but also reveals the GAP activity of the C9ORF72-SMCR8 complex
      Title: Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a.
    5. Study reveals an essential role for WDR41 in supporting the regulated binding of C9orf72 to lysosomes and solidifies the requirement for a larger C9orf72 containing protein complex in coordinating lysosomal responses to changes in amino acid availability.
      Title: WDR41 supports lysosomal response to changes in amino acid availability.
    6. Study describes the identification of two binding partners for C9orf72: SMCR8 and WDR41 and demonstrated that C9orf72/SMCR8/WDR41 interacts with the FIP200/Ulk1/ATG13/ATG101 complex.
      Title: The ALS/FTLD associated protein C9orf72 associates with SMCR8 and WDR41 to regulate the autophagy-lysosome pathway.
    7. The peak of association was found in and around two genes, WDR41 and PDE8B, involved in dopamine signaling and development.
      Title: Discovery and replication of dopamine-related gene effects on caudate volume in young and elderly populations (N=1198) using genome-wide search.
    8. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    10. 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.
    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
    Discovery and replication of dopamine-related gene effects on caudate volume in young and elderly populations (N=1198) using genome-wide search.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10904

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTPase activator activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    contributes_to guanyl-nucleotide exchange factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of exocytosis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of immune response NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of autophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of autophagy NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of guanyl-nucleotide exchange factor complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of guanyl-nucleotide exchange factor complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in lysosomal membrane HDA PubMed 

    General protein information

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    Preferred Names
    WD repeat-containing protein 41

    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_018268.4 → NP_060738.2  WD repeat-containing protein 41

      See identical proteins and their annotated locations for NP_060738.2

      Status: VALIDATED

      Source sequence(s)
      BC040241, BG113002, BM818066, BP276774, BQ000743, CD656920
      Consensus CDS
      CCDS4038.1
      UniProtKB/Swiss-Prot
      B4DT55, Q7Z792, Q8IWG3, Q8IXA9, Q8NDA7, Q9HAD4, Q9NV62
      UniProtKB/TrEMBL
      A0A0S2Z5D8, A0A0S2Z5E0
      Related
      ENSP00000296679.4, ENST00000296679.9
      Conserved Domains (2) summary
      sd00039
      Location:88 → 131
      7WD40; WD40 repeat [structural motif]
      cl29593
      Location:38 → 350
      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: 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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      77430933..77620577 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543505.3 → XP_011541807.1  WD repeat-containing protein 41 isoform X1

      UniProtKB/TrEMBL
      A0A0S2Z5D8
      Conserved Domains (3) summary
      COG2319
      Location:7 → 429
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:85 → 128
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:35 → 347
      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_047417350.1 → XP_047273306.1  WD repeat-containing protein 41 isoform X3

      UniProtKB/TrEMBL
      A0A0S2Z5D8

    3. XM_047417349.1 → XP_047273305.1  WD repeat-containing protein 41 isoform X3

      UniProtKB/TrEMBL
      A0A0S2Z5D8

    4. XM_005248551.5 → XP_005248608.1  WD repeat-containing protein 41 isoform X4

      UniProtKB/TrEMBL
      H0YAA3
      Related
      ENSP00000426499.1, ENST00000515253.5
      Conserved Domains (3) summary
      COG2319
      Location:34 → 294
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:87 → 133
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:38 → 374
      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_017009606.2 → XP_016865095.1  WD repeat-containing protein 41 isoform X2

      UniProtKB/TrEMBL
      A0A0S2Z5D8

    6. XM_011543507.3 → XP_011541809.1  WD repeat-containing protein 41 isoform X7

      Conserved Domains (3) summary
      COG2319
      Location:29 → 254
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:87 → 133
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:38 → 330
      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 ...

    7. XM_005248552.4 → XP_005248609.1  WD repeat-containing protein 41 isoform X6

      Conserved Domains (3) summary
      COG2319
      Location:10 → 357
      WD40; WD40 repeat [General function prediction only]
      sd00039
      Location:88 → 131
      7WD40; WD40 repeat [structural motif]
      cl02567
      Location:38 → 350
      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 ...

    8. XM_047417351.1 → XP_047273307.1  WD repeat-containing protein 41 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      77913542..78103190 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352879.1 → XP_054208854.1  WD repeat-containing protein 41 isoform X1

      UniProtKB/TrEMBL
      A0A0S2Z5D8

    2. XM_054352881.1 → XP_054208856.1  WD repeat-containing protein 41 isoform X3

      UniProtKB/TrEMBL
      A0A0S2Z5D8

    3. XM_054352882.1 → XP_054208857.1  WD repeat-containing protein 41 isoform X4

      UniProtKB/TrEMBL
      H0YAA3

    4. XM_054352880.1 → XP_054208855.1  WD repeat-containing protein 41 isoform X2

      UniProtKB/TrEMBL
      A0A0S2Z5D8

    5. XM_054352885.1 → XP_054208860.1  WD repeat-containing protein 41 isoform X7

    6. XM_054352884.1 → XP_054208859.1  WD repeat-containing protein 41 isoform X6

    7. XM_054352883.1 → XP_054208858.1  WD repeat-containing protein 41 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HAD4.3 GenPept UniProtKB/Swiss-Prot:Q9HAD4

    Gene LinkOut

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

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