DDX21

DExD-box helicase 21, the group of DEAD-box helicases|B-WICH chromatin-remodelling complex subunits

Basic information

Region (hg38): 10:68956135-68985068

Links

ENSG00000165732 ∙ NCBI:9188 ∙ OMIM:606357 ∙ HGNC:2744 ∙ Uniprot:Q9NR30 ∙ 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 DDX21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX21 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				1	1	2
missense			26	3	1	30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	4	2

Variants in DDX21

This is a list of pathogenic ClinVar variants found in the DDX21 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-68959962-G-A		not specified	Uncertain significance (Aug 13, 2021)
10-68960005-G-C		not specified	Uncertain significance (Jun 13, 2024)
10-68960115-A-T		not specified	Uncertain significance (Dec 07, 2021)
10-68960148-A-G		not specified	Likely benign (Jan 06, 2023)
10-68960167-T-C		not specified	Uncertain significance (Dec 28, 2023)
10-68960194-C-T		not specified	Likely benign (Nov 09, 2021)
10-68960230-G-A		not specified	Uncertain significance (Jan 06, 2023)
10-68960246-G-T		not specified	Likely benign (Dec 13, 2023)
10-68962109-G-A		not specified	Uncertain significance (Aug 30, 2022)
10-68962110-C-A		not specified	Uncertain significance (Dec 02, 2022)
10-68962118-A-C			Uncertain significance (Dec 01, 2017)
10-68962125-C-A		not specified	Uncertain significance (May 10, 2024)
10-68963336-A-G		not specified	Uncertain significance (Jan 03, 2024)
10-68963354-A-G			Benign (Jul 04, 2018)
10-68963355-G-C		not specified	Uncertain significance (Jun 10, 2024)
10-68967023-C-T		not specified	Uncertain significance (Jun 26, 2023)
10-68967024-G-A		not specified	Uncertain significance (Dec 08, 2023)
10-68967025-C-T			Likely benign (Apr 01, 2022)
10-68967026-A-G		not specified	Uncertain significance (May 06, 2024)
10-68967135-T-C		not specified	Uncertain significance (Oct 29, 2021)
10-68967150-A-C		not specified	Uncertain significance (Jan 24, 2024)
10-68969051-A-T		not specified	Uncertain significance (May 02, 2024)
10-68969106-G-A			Likely benign (Oct 01, 2024)
10-68970279-G-A		not specified	Uncertain significance (Apr 25, 2023)
10-68970319-A-G		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX21	protein_coding	protein_coding	ENST00000354185	15	28946

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000350	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	283	425	0.665	0.0000225	5148
Missense in Polyphen		35	107.75	0.32482		1318
Synonymous	1.51	122	145	0.840	0.00000745	1486
Loss of Function	5.59	3	42.2	0.0711	0.00000237	499

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II: promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) (PubMed:25470060). Binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs (PubMed:25470060). In the nucleolus, localizes to rDNA locus, where it directly binds rRNAs and snoRNAs, and promotes rRNA transcription, processing and modification. Required for rRNA 2'- O-methylation, possibly by promoting the recruitment of late- acting snoRNAs SNORD56 and SNORD58 with pre-ribosomal complexes (PubMed:25470060, PubMed:25477391). In the nucleoplasm, binds 7SK RNA and is recruited to the promoters of Pol II-transcribed genes: acts by facilitating the release of P-TEFb from inhibitory 7SK snRNP in a manner that is dependent on its helicase activity, thereby promoting transcription of its target genes (PubMed:25470060). Functions as cofactor for JUN-activated transcription: required for phosphorylation of JUN at 'Ser-77' (PubMed:11823437, PubMed:25260534). Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase) (PubMed:9461305). Involved in rRNA processing (PubMed:14559904, PubMed:18180292). May bind to specific miRNA hairpins (PubMed:28431233). 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 (By similarity). {ECO:0000250|UniProtKB:Q9JIK5, ECO:0000269|PubMed:11823437, ECO:0000269|PubMed:14559904, ECO:0000269|PubMed:18180292, ECO:0000269|PubMed:25260534, ECO:0000269|PubMed:25470060, ECO:0000269|PubMed:25477391, ECO:0000269|PubMed:28431233, ECO:0000269|PubMed:9461305}.
• Pathway: B-WICH complex positively regulates rRNA expression;Positive epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription) (Consensus)

Recessive Scores

• pRec: 0.229

Intolerance Scores

• loftool: 0.358
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.85

Haploinsufficiency Scores

• pHI: 0.391
• hipred: Y
• hipred_score: 0.598
• ghis: 0.596

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.954

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx21
• 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: osteoblast differentiation;positive regulation of myeloid dendritic cell cytokine production;rRNA processing;transcription by RNA polymerase II;positive regulation of I-kappaB kinase/NF-kappaB signaling;response to exogenous dsRNA;innate immune response;positive regulation of gene expression, epigenetic;defense response to virus
• Cellular component: nucleus;nucleoplasm;nucleolus;mitochondrion;cytosol;membrane
• Molecular function: RNA binding;double-stranded RNA binding;ATP-dependent RNA helicase activity;protein binding;ATP binding;rRNA binding;snoRNA binding;miRNA binding;identical protein binding;7SK snRNA binding