DDX41 (DEAD-box helicase 41)

Gene

• Entrez ID: 51428
• Gene name: DEAD-box helicase 41
• Gene symbol: DDX41
• Synonyms (NCBI Gene): ABS, MPLPF
• Chromosome: 5
• Chromosome location: 5q35.3
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs141601766	C>T	Pathogenic, likely-pathogenic	5 prime UTR variant, initiator codon variant, missense variant
rs142143752	G>A	Risk-factor	Coding sequence variant, missense variant
rs200567842	C>A	Pathogenic	Coding sequence variant, 5 prime UTR variant, stop gained
rs376093707	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs746278774	G>A	Likely-pathogenic	Stop gained, coding sequence variant, 5 prime UTR variant
rs747072227	A>G	Risk-factor	Coding sequence variant, missense variant
rs762890562	->CATC	Pathogenic	Coding sequence variant, stop gained, inframe indel
rs774698335	C>A,T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs780209663	C>A	Pathogenic	Coding sequence variant, missense variant
rs869320762	CT>TG	Risk-factor	Splice acceptor variant
rs1554111073	->T	Pathogenic	Coding sequence variant, frameshift variant
rs1554111533	C>T	Pathogenic	Splice acceptor variant
rs1554111653	T>-	Pathogenic	Coding sequence variant, 5 prime UTR variant, frameshift variant
rs1554111683	->TT	Pathogenic	Coding sequence variant, 5 prime UTR variant, frameshift variant
rs1581805747	->A	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT031540	hsa-miR-16-5p	Proteomics	18668040
MIRT032281	hsa-let-7b-5p	Proteomics	18668040
MIRT041875	hsa-miR-484	CLASH	23622248
MIRT930697	hsa-miR-1270	CLIP-seq
MIRT930698	hsa-miR-151-3p	CLIP-seq
MIRT930699	hsa-miR-185	CLIP-seq
MIRT930700	hsa-miR-2110	CLIP-seq
MIRT930701	hsa-miR-3144-5p	CLIP-seq
MIRT930702	hsa-miR-3150a-3p	CLIP-seq
MIRT930703	hsa-miR-3154	CLIP-seq
MIRT930704	hsa-miR-3191	CLIP-seq
MIRT930705	hsa-miR-3199	CLIP-seq
MIRT930706	hsa-miR-34a	CLIP-seq
MIRT930707	hsa-miR-34c-5p	CLIP-seq
MIRT930708	hsa-miR-4306	CLIP-seq
MIRT930709	hsa-miR-432	CLIP-seq
MIRT930710	hsa-miR-4456	CLIP-seq
MIRT930711	hsa-miR-4463	CLIP-seq
MIRT930712	hsa-miR-4499	CLIP-seq
MIRT930713	hsa-miR-449a	CLIP-seq
MIRT930714	hsa-miR-449b	CLIP-seq
MIRT930715	hsa-miR-4531	CLIP-seq
MIRT930716	hsa-miR-4644	CLIP-seq
MIRT930717	hsa-miR-4652-5p	CLIP-seq
MIRT930718	hsa-miR-4709-3p	CLIP-seq
MIRT930719	hsa-miR-4740-5p	CLIP-seq
MIRT930720	hsa-miR-4757-5p	CLIP-seq
MIRT930721	hsa-miR-620	CLIP-seq
MIRT930722	hsa-miR-635	CLIP-seq
MIRT930723	hsa-miR-7	CLIP-seq
MIRT1975460	hsa-miR-1915	CLIP-seq
MIRT1975461	hsa-miR-1972	CLIP-seq
MIRT1975462	hsa-miR-3136-3p	CLIP-seq
MIRT1975463	hsa-miR-4663	CLIP-seq
MIRT1975464	hsa-miR-4726-3p	CLIP-seq
MIRT1975465	hsa-miR-4778-5p	CLIP-seq
MIRT2514815	hsa-miR-4514	CLIP-seq
MIRT2514816	hsa-miR-4692	CLIP-seq
MIRT2514815	hsa-miR-4514	CLIP-seq
MIRT2514816	hsa-miR-4692	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IC	11991638
GO:0000398	Process	MRNA splicing, via spliceosome	IEA
GO:0000398	Process	MRNA splicing, via spliceosome	IMP	25920683
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0003724	Function	RNA helicase activity	IBA
GO:0003724	Function	RNA helicase activity	IDA	35613581
GO:0003724	Function	RNA helicase activity	IEA
GO:0003729	Function	MRNA binding	IBA
GO:0004386	Function	Helicase activity	IEA
GO:0005515	Function	Protein binding	IPI	22365833, 25416956, 26030138, 28514442, 32296183, 32703943, 32814053, 33961781
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IDA	26712909
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IBA
GO:0005681	Component	Spliceosomal complex	IDA	25920683
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005829	Component	Cytosol	IDA	35613581
GO:0005829	Component	Cytosol	TAS
GO:0006397	Process	MRNA processing	IEA
GO:0006915	Process	Apoptotic process	TAS	10607561
GO:0008270	Function	Zinc ion binding	IEA
GO:0008283	Process	Cell population proliferation	IMP	25920683
GO:0008380	Process	RNA splicing	IEA
GO:0016020	Component	Membrane	HDA	19946888
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0030154	Process	Cell differentiation	IMP	25920683
GO:0032481	Process	Positive regulation of type I interferon production	IDA	25636800
GO:0035458	Process	Cellular response to interferon-beta	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051607	Process	Defense response to virus	IEA
GO:0071013	Component	Catalytic step 2 spliceosome	IDA	11991638
GO:0140896	Process	CGAS/STING signaling pathway	IDA	25636800
GO:0140896	Process	CGAS/STING signaling pathway	IDA	35613581

Other IDs

• MIM: 608170
• HGNC: 18674
• e!Ensembl: ENSG00000183258

Protein

• UniProt ID: Q9UJV9
• Protein name: Probable ATP-dependent RNA helicase DDX41 (EC 3.6.4.13) (DEAD box protein 41) (DEAD box protein abstrakt homolog)
• Protein function: Multifunctional protein that participates in many aspects of cellular RNA metabolism. Plays pivotal roles in innate immune sensing and hematopoietic homeostasis (PubMed:34473945). Recognizes foreign or self-nucleic acids generated during microbi
• PDB: 2P6N, 5GVR, 5GVS, 5H1Y, 8C6J
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00270	DEAD	205 → 385	DEAD/DEAH box helicase	Domain
  PF00271	Helicase_C	419 → 527	Helicase conserved C-terminal domain	Family

• Sequence:

  MEESEPERKRARTDEVPAGGSRSEAEDEDDEDYVPYVPLRQRRQLLLQKLLQRRRKGAAE
  EEQQDSGSEPRGDEDDIPLGPQSNVSLLDQHQHLKEKAEARKESAKEKQLKEEEKILESV
  AEGRALMSVKEMAKGITYDDPIKTSWTPPRYVLSMSEERHERVRKKYHILVEGDGIPPPI
  KSFKEMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDMIGIAFTGSGKTLVFTLPVI
  MFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPLLRCALCIGG
  MSVKEQMETIRHGVHMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRT
  IFSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQEVEYVKEEAK
  MVYLLECLQKTPPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRE
  GKKDVLVATDVASKGLDFPAIQHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKAC
  DESVLMDLKALLLEAKQKVPPVLQVLHCGDESMLDIGGERGCAFCGGLGHRITDCPKLEA
  MQTKQVSNIGRKDYLAHSSMDF

• Sequence length: 622

Pathways

KEGG:

Cytosolic DNA-sensing pathway

Reactome:

STING mediated induction of host immune responses
Regulation of innate immune responses to cytosolic DNA
IRF3-mediated induction of type I IFN

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Likely pathogenic; Pathogenic	rs762890562, rs866179648, rs1761157695, rs377745714	RCV000193600 RCV001256170 RCV001256168 RCV001256176
Bone marrow hypocellularity	Likely pathogenic; Pathogenic	rs141601766	RCV001256169
DDX41-related disorder	Pathogenic; Likely pathogenic	rs1411544367, rs144057590, rs754907965, rs762890562, rs141601766, rs2532088466, rs2532075547, rs2532085882, rs2532090465, rs746278774, rs866179648	RCV004752016 RCV003394152 RCV004752052 RCV004751355 RCV003907781 RCV003410309 RCV003408555 RCV003908981 RCV003941362 RCV003424157 RCV003393927
DDX41-related hematologic malignancy predisposition syndrome	Likely pathogenic; Pathogenic	rs760059747, rs1411544367, rs144057590, rs753425379, rs899399494, rs754907965, rs1170971274, rs1291520734, rs2127436444, rs199675507, rs1761145210, rs762890562, rs869320762, rs141601766, rs2532076691, rs2532074787, rs372190702, rs2532088466, rs2532091583, rs780643002, rs2532085882, rs2532083492, rs779029308, rs1554111073, rs774698335, rs1554111653, rs1554111683, rs746278774, rs866179648, rs766117035, rs377745714	RCV002504637 RCV003224812 RCV003224813 RCV001761407 RCV003470918 RCV003464144 RCV003224817 RCV003224818 RCV005412281 RCV003471290 RCV003224822 RCV005601929 RCV000210272 RCV000210273 RCV000210251 RCV004572860 RCV003224835 RCV003224836 RCV003224847 RCV003466155 RCV003466157 RCV003466158 RCV003466159 RCV003466160 RCV003466161 RCV000500690 RCV000504169 RCV000502578 RCV000503753 RCV001764696 RCV003224810 RCV005601729 RCV004570648
Focal segmental glomerulosclerosis 9	Pathogenic	rs899399494	RCV005863482
Inherited acute myeloid leukemia	Pathogenic	rs899399494	RCV003313232
Myelodysplasia	Likely pathogenic; Pathogenic	rs141601766, rs1297703150, rs766117035	RCV001256171 RCV001256172 RCV001256167

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
-	no classification for the single variant	rs376093707, rs780209663	-
Aplastic anemia	Uncertain significance	rs773991873	RCV001256174
Hereditary cancer-predisposing syndrome	Likely benign	rs757152503	RCV003988814
Myelodysplastic syndrome	Conflicting classifications of pathogenicity	rs2127435833	RCV002272707
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs374359854, rs200374307	RCV005922671 RCV005922710
Uterine carcinosarcoma	Benign; Likely benign	rs374359854	RCV005922672
Uveal melanoma	Likely benign	rs200374307	RCV005922709

Associations from Text Mining
Disease Name	Relationship Type	References
Alzheimer Disease	Associate	11815632, 29037261
Ataxia Telangiectasia	Associate	37874914
Atypical Squamous Cells of the Cervix	Associate	33626862
Bone Marrow Diseases	Associate	33626862
Breast Neoplasms	Associate	32965163
Carcinogenesis	Associate	33650667
Carcinoma Hepatocellular	Associate	33006365
Cerebral Amyloid Angiopathy	Associate	29037261
Cognitive Dysfunction	Associate	40596075
Colitis Ulcerative	Associate	36165492
Colorectal Neoplasms	Associate	31240215
Common Variable Immunodeficiency	Associate	32047491
GATA2 Deficiency	Associate	26693794
Hematologic Diseases	Associate	31484648
Hematologic Neoplasms	Associate	26712909, 29365323, 33626862, 35671390, 37406166, 37874914
Hemorrhage	Inhibit	31240215
Inflammation	Associate	34916496
Leukemia	Associate	37591941
Leukemia B Cell	Associate	35246110
Leukemia Myelogenous Chronic BCR ABL Positive	Associate	34784413
Leukemia Myeloid Acute	Associate	26693794, 26712909, 30926971, 30963592, 31484648, 32868804, 33626862, 34482403, 34644397, 34916496, 35246110, 35443031, 35671390, 36322930, 37450374, 37506341, 37591941, 37665752, 37874914
Leukemia Myelomonocytic Chronic	Associate	30963592, 37665752
Leukemia T Cell	Associate	34793200
Li Fraumeni Syndrome	Stimulate	29365323
Lymphoma	Associate	26712909
Lymphoma B Cell	Associate	35671390, 37874914
Lymphoma Follicular	Associate	26712909
Lymphoproliferative Disorders	Associate	34390506
Mesothelioma	Associate	37556141
Myelodysplastic Syndromes	Associate	26693794, 26712909, 30963592, 31484648, 33626862, 34644397, 35246110, 35443031, 35671390, 36322930, 36436542, 36989067, 37506341, 37665752, 37874914, 38597818, 40596075
Neoplasm Metastasis	Associate	29930723, 32965163
Neoplasms	Inhibit	26712909, 34916496
Neoplasms	Associate	30963592, 31240215, 31484648, 32047491, 32307695, 32965163, 33533142, 33626862, 33650667, 34390506, 34482403, 34644397, 35246110, 35671390, 36322930, 37665752, 37874914, 40596075
Neoplasms	Stimulate	37450374
Neoplasms Squamous Cell	Associate	33650667
Neoplastic Syndromes Hereditary	Associate	33626862
Nerve Degeneration	Associate	31097588
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	37874914
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	22237025
Syndrome	Associate	37406166