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

Summary

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: Contributes to guanyl-nucleotide exchange factor activity. Involved in regulation of autophagy. Located in cytoplasm. Part of guanyl-nucleotide exchange factor complex. Colocalizes with Atg1/ULK1 kinase complex. [provided by Alliance of Genome Resources, Apr 2022]
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

Location:: 5q13.3-q14.1

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (77430933..77620577, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (77913542..78103190, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (76726758..76788141, complement)

Chromosome 5 - NC_000005.10 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

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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.

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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 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

RH80473 (e-PCR)
- UniSTS:88835

SHGC-64313 (e-PCR)
- UniSTS:66654

RH44392 (e-PCR)
- UniSTS:58479

SHGC-133093 (e-PCR)
- UniSTS:173984

WI-20907 (e-PCR)
- UniSTS:70595

D5S2319 (e-PCR)
- UniSTS:64207

RH44320 (e-PCR)
- UniSTS:61401

SHGC-57669 (e-PCR)
- UniSTS:745

SHGC-36700 (e-PCR)
- UniSTS:76526

SHGC-36223 (e-PCR)
- UniSTS:31735

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 positive regulation of GTPase activity	IMP Inferred from Mutant Phenotype 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
part_of Atg1/ULK1 kinase complex	IDA Inferred from Direct Assay more info	PubMed
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 more info	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)

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

77430933..77620577 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
XM_047417350.1 → XP_047273306.1 WD repeat-containing protein 41 isoform X3
XM_047417349.1 → XP_047273305.1 WD repeat-containing protein 41 isoform X3
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 ...
XM_017009606.2 → XP_016865095.1 WD repeat-containing protein 41 isoform X2

UniProtKB/TrEMBL

A0A0S2Z5D8
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 ...
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 ...
XM_047417351.1 → XP_047273307.1 WD repeat-containing protein 41 isoform X5