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

Gene ID: 51428, updated on 27-Nov-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
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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: 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. Prevalence and clinical implications of germline predisposition gene mutations in patients with acute myeloid leukemia. Kim B, et al. Sci Rep, 2020 Aug 31. PMID 32868804, Free PMC Article
  2. Germline and Somatic Defects in DDX41 and its Impact on Myeloid Neoplasms. Badar T, et al. Curr Hematol Malig Rep, 2022 Oct. PMID 35781188, Free PMC Article
  3. The genetic landscape of germline DDX41 variants predisposing to myeloid neoplasms. Li P, et al. Blood, 2022 Aug 18. PMID 35671390, Free PMC Article
  4. DDX41 is required for cGAS-STING activation against DNA virus infection. Singh RS, et al. Cell Rep, 2022 May 24. PMID 35613581, Free PMC Article
  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 (171) 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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