DDX1

DEAD-box helicase 1, the group of DEAD-box helicases|tRNA splicing ligase complex

Basic information

Region (hg38): 2:15591178-15634346

Links

ENSG00000079785 ∙ NCBI:1653 ∙ OMIM:601257 ∙ HGNC:2734 ∙ Uniprot:Q92499 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DDX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			32			32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	0	2

Variants in DDX1

This is a list of pathogenic ClinVar variants found in the DDX1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-15591940-G-A		not specified	Uncertain significance (Nov 03, 2022)
2-15591946-T-A		not specified	Uncertain significance (Dec 07, 2021)
2-15595510-C-A		not specified	Uncertain significance (Dec 14, 2023)
2-15597390-G-C		not specified	Uncertain significance (Jan 22, 2024)
2-15597412-C-T		not specified	Uncertain significance (May 18, 2022)
2-15599677-A-G		not specified	Uncertain significance (Jan 19, 2022)
2-15603224-C-G		not specified	Uncertain significance (Jul 14, 2023)
2-15603883-A-G		not specified	Uncertain significance (Feb 06, 2023)
2-15604448-G-A		not specified	Uncertain significance (Dec 14, 2022)
2-15605956-A-T		not specified	Uncertain significance (Jan 29, 2024)
2-15605988-A-G		not specified	Uncertain significance (Jun 13, 2024)
2-15606183-G-C		not specified	Uncertain significance (Oct 03, 2023)
2-15606228-G-T		not specified	Uncertain significance (Dec 19, 2023)
2-15606232-C-T		not specified	Uncertain significance (Aug 10, 2021)
2-15607295-T-C		not specified	Uncertain significance (Apr 07, 2022)
2-15613244-G-T		not specified	Uncertain significance (Dec 11, 2023)
2-15613283-G-A		not specified	Uncertain significance (Feb 05, 2024)
2-15617304-A-T		not specified	Uncertain significance (May 03, 2023)
2-15617310-T-C		not specified	Uncertain significance (Oct 17, 2023)
2-15618225-G-A		not specified	Likely benign (Apr 17, 2024)
2-15620220-T-C		not specified	Uncertain significance (Aug 10, 2021)
2-15620342-A-T			Benign (Apr 24, 2018)
2-15620353-A-C		not specified	Uncertain significance (Feb 23, 2023)
2-15621092-A-C		not specified	Uncertain significance (Aug 15, 2023)
2-15621096-G-T		not specified	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX1	protein_coding	protein_coding	ENST00000381341	26	39934

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00551	125731	0	16	125747	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.82	283	383	0.739	0.0000181	4877
Missense in Polyphen		77	145.3	0.52994		1833
Synonymous	0.146	129	131	0.984	0.00000674	1324
Loss of Function	5.35	7	46.3	0.151	0.00000203	603

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000944	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000213	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the NF- kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. Component of the tRNA-splicing ligase complex required to facilitate the enzymatic turnover of catalytic subunit RTCB: together with archease (ZBTB8OS), acts by facilitating the guanylylation of RTCB, a key intermediate step in tRNA ligation (PubMed:24870230). Component of a multi-helicase- TICAM1 complex that acts as a cytoplasmic sensor of viral double- stranded RNA (dsRNA) and plays a role in the activation of a cascade of antiviral responses including the induction of proinflammatory cytokines via the adapter molecule TICAM1. Specifically binds (via helicase ATP-binding domain) on both short and long poly(I:C) dsRNA (By similarity). {ECO:0000250|UniProtKB:Q91VR5, ECO:0000269|PubMed:12183465, ECO:0000269|PubMed:15567440, ECO:0000269|PubMed:18335541, ECO:0000269|PubMed:18710941, ECO:0000269|PubMed:20573827, ECO:0000269|PubMed:24870230}.; FUNCTION: (Microbial infection) Required for Coronavirus IBV replication. {ECO:0000269|PubMed:20573827}.
• Pathway: DDX1 as a regulatory component of the Drosha microprocessor;mRNA Processing;tRNA processing;Metabolism of RNA;tRNA processing in the nucleus (Consensus)

Recessive Scores

• pRec: 0.500

Intolerance Scores

• loftool: 0.253
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.331
• hipred: Y
• hipred_score: 0.783
• ghis: 0.648

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ddx1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: spliceosomal complex assembly;positive regulation of myeloid dendritic cell cytokine production;double-strand break repair;tRNA splicing, via endonucleolytic cleavage and ligation;regulation of translational initiation;multicellular organism development;DNA duplex unwinding;positive regulation of I-kappaB kinase/NF-kappaB signaling;response to exogenous dsRNA;innate immune response;defense response to virus;nucleic acid phosphodiester bond hydrolysis;regulation of nucleic acid-templated transcription;protein localization to cytoplasmic stress granule
• Cellular component: nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol;cytoplasmic stress granule;membrane;cleavage body;tRNA-splicing ligase complex;ribonucleoprotein complex
• Molecular function: DNA binding;chromatin binding;transcription coregulator activity;RNA binding;RNA helicase activity;double-stranded RNA binding;nuclease activity;exonuclease activity;protein binding;ATP binding;ATP-dependent helicase activity;poly(A) binding;DNA/RNA helicase activity