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    DDX41 DEAD-box helicase 41 [ Homo sapiens (human) ]

    Gene ID: 51428, updated on 27-Dec-2024

    Summary

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    Official Symbol
    DDX41provided by HGNC
    Official Full Name
    DEAD-box helicase 41provided by HGNC
    Primary source
    HGNC:HGNC:18674
    See related
    Ensembl:ENSG00000183258 MIM:608170; AllianceGenome:HGNC:18674
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ABS; MPLPF
    Summary
    DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene is a member of the DEAD box protein family and interacts with several spliceosomal proteins. In addition, the encoded protein may recognize the bacterial second messengers cyclic di-GMP and cyclic di-AMP, resulting in the induction of genes involved in the innate immune response. [provided by RefSeq, Jan 2017]
    Expression
    Ubiquitous expression in bone marrow (RPKM 17.2), testis (RPKM 14.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DDX41 in Genome Data Viewer
    Location:
    5q35.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (177511577..177516961, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (178054559..178059943, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (176938578..176943962, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176911017-176911732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176911733-176912448 Neighboring gene Sharpr-MPRA regulatory region 15492 Neighboring gene PDZ and LIM domain 7 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176918835-176919378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176919379-176919920 Neighboring gene Sharpr-MPRA regulatory region 583 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:176923257-176923998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176925479-176926218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23721 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23723 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176929555-176930508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:176930509-176931460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23726 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23727 Neighboring gene docking protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176943204-176944028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23728 Neighboring gene family with sequence similarity 193 member B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16702 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:176981263-176981766 Neighboring gene CRISPRi-validated cis-regulatory element chr5.4836 Neighboring gene FAM193B divergent transcript Neighboring gene CRISPRi-validated cis-regulatory element chr5.4837

    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. Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide. Omura H, et al. Sci Rep, 2016 Oct 10. PMID 27721487, Free PMC Article
    2. Ribosome profiling analysis reveals the roles of DDX41 in translational regulation. Tungalag S, et al. Int J Hematol, 2023 Jun. PMID 36780110
    3. Structural and functional analyses of human DDX41 DEAD domain. Jiang Y, et al. Protein Cell, 2017 Jan. PMID 27928732, Free PMC Article
    4. Clinical and Pathologic Spectrum of DDX41-Mutated Hematolymphoid Neoplasms. Goyal T, et al. Am J Clin Pathol, 2021 Oct 13. PMID 33929502
    5. R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Mosler T, et al. Nat Commun, 2021 Dec 16. PMID 34916496, Free PMC Article

    See all (172) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Evaluation of the pathogenic potential of germline DDX41 variants in hematopoietic neoplasms using the ACMG/AMP guidelines.
      Title: Evaluation of the pathogenic potential of germline DDX41 variants in hematopoietic neoplasms using the ACMG/AMP guidelines.
    2. Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage.
      Title: Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage.
    3. The clinical and genomic landscape of patients with DDX41 variants identified during diagnostic sequencing.
      Title: The clinical and genomic landscape of patients with DDX41 variants identified during diagnostic sequencing.
    4. Clinical and molecular correlates of somatic and germline DDX41 variants in patients and families with myeloid neoplasms.
      Title: Clinical and molecular correlates of somatic and germline DDX41 variants in patients and families with myeloid neoplasms.
    5. Germline DDX41 mutant predisposition syndromes: Slow driver states to hematological malignancies.
      Title: Germline DDX41 mutant predisposition syndromes: Slow driver states to hematological malignancies.
    6. Somatic mutational landscape of hereditary hematopoietic malignancies caused by germline variants in RUNX1, GATA2, and DDX41.
      Title: Somatic mutational landscape of hereditary hematopoietic malignancies caused by germline variants in RUNX1, GATA2, and DDX41.
    7. Prevalence and significance of DDX41 gene variants in the general population.
      Title: Prevalence and significance of DDX41 gene variants in the general population.
    8. Ribosome profiling analysis reveals the roles of DDX41 in translational regulation.
      Title: Ribosome profiling analysis reveals the roles of DDX41 in translational regulation.
    9. DDX41-associated susceptibility to myeloid neoplasms.
      Title: DDX41-associated susceptibility to myeloid neoplasms.
    10. Germ line DDX41 mutations define a unique subtype of myeloid neoplasms.
      Title: Germ line DDX41 mutations define a unique subtype of myeloid neoplasms.
    Submit: New GeneRIF Correction See all GeneRIFs (40)

    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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2022-02-09)

    ClinGen Genome Curation PagePubMed
    Triplosensitivity

    No evidence available (Last evaluated 2022-02-09)

    ClinGen Genome Curation Page

    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

    • MGC8828

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cGAS/STING signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IC
    Inferred by Curator
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    probable ATP-dependent RNA helicase DDX41
    Names
    Abstrakt
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 41
    DEAD box protein 41
    DEAD box protein abstrakt homolog
    DEAD-box protein abstrakt
    putative RNA helicase
    NP_001308661.1
    NP_001308759.1
    NP_057306.2

    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.

    Genomic

    1. NG_046846.2 RefSeqGene

      Range
      5001..10385
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1386

    mRNA and Protein(s)

    1. NM_001321732.2 → NP_001308661.1  probable ATP-dependent RNA helicase DDX41 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC145098
      UniProtKB/TrEMBL
      B3KRK2
      Related
      ENST00000503078.5
      Conserved Domains (2) summary
      COG0513
      Location:27 → 440
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd17951
      Location:66 → 271
      DEADc_DDX41; DEAD-box helicase domain of DEAD box protein 41

    2. NM_001321830.2 → NP_001308759.1  probable ATP-dependent RNA helicase DDX41 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC145098
      UniProtKB/TrEMBL
      B3KRK2
      Conserved Domains (2) summary
      COG0513
      Location:27 → 440
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd17951
      Location:66 → 271
      DEADc_DDX41; DEAD-box helicase domain of DEAD box protein 41

    3. NM_016222.4 → NP_057306.2  probable ATP-dependent RNA helicase DDX41 isoform 1

      See identical proteins and their annotated locations for NP_057306.2

      Status: REVIEWED

      Source sequence(s)
      AC145098
      Consensus CDS
      CCDS4427.1
      UniProtKB/Swiss-Prot
      B2RDC8, Q96BK6, Q96K05, Q9NT96, Q9NW04, Q9UJV9
      UniProtKB/TrEMBL
      Q53HI2
      Related
      ENSP00000330349.8, ENST00000330503.12
      Conserved Domains (2) summary
      COG0513
      Location:153 → 566
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd17951
      Location:192 → 397
      DEADc_DDX41; DEAD-box helicase domain of DEAD box protein 41

    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
      177511577..177516961 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      178054559..178059943 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UJV9.2 GenPept UniProtKB/Swiss-Prot:Q9UJV9

    Gene LinkOut

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

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