DDX20

DEAD-box helicase 20, the group of DEAD-box helicases|Gemins

Basic information

Region (hg38): 1:111754832-111775602

Links

ENSG00000064703 ∙ NCBI:11218 ∙ OMIM:606168 ∙ HGNC:2743 ∙ Uniprot:Q9UHI6 ∙ 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 DDX20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX20 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						0
missense			38	3	1	42
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	4	1

Variants in DDX20

This is a list of pathogenic ClinVar variants found in the DDX20 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-111755929-C-G		not specified	Uncertain significance (Mar 23, 2022)
1-111755943-G-T		not specified	Uncertain significance (Dec 01, 2022)
1-111755959-C-T		not specified	Uncertain significance (Nov 19, 2022)
1-111755961-G-A		not specified	Likely benign (Nov 18, 2022)
1-111755976-A-C		not specified	Uncertain significance (Feb 28, 2024)
1-111756105-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-111756106-C-T		not specified	Uncertain significance (Mar 21, 2022)
1-111756176-G-C		not specified	Uncertain significance (Jun 16, 2023)
1-111756196-A-T		not specified	Uncertain significance (Dec 17, 2023)
1-111756685-G-C		not specified	Uncertain significance (Aug 11, 2022)
1-111756720-C-G		not specified	Uncertain significance (Aug 17, 2022)
1-111756723-G-A		not specified	Uncertain significance (Mar 22, 2023)
1-111759413-C-G			Likely benign (Jan 19, 2018)
1-111760512-C-G		not specified	Uncertain significance (Nov 01, 2022)
1-111760541-T-A		not specified	Uncertain significance (Nov 13, 2024)
1-111760815-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-111760843-T-A		not specified	Uncertain significance (Nov 09, 2021)
1-111761007-G-A		not specified	Likely benign (Aug 08, 2023)
1-111761058-C-A		not specified	Uncertain significance (Sep 24, 2024)
1-111761076-A-G		not specified	Uncertain significance (May 16, 2024)
1-111761249-T-C		not specified	Uncertain significance (Mar 04, 2024)
1-111761270-C-A		not specified	Uncertain significance (Nov 09, 2021)
1-111762276-G-A		not specified	Uncertain significance (Aug 10, 2021)
1-111762756-A-G		not specified	Uncertain significance (Feb 14, 2023)
1-111762779-T-G		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX20	protein_coding	protein_coding	ENST00000369702	11	12772

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.76e-14	0.397	125589	0	159	125748	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0794	428	433	0.989	0.0000210	5387
Missense in Polyphen		150	155.52	0.9645		1895
Synonymous	0.479	148	156	0.951	0.00000738	1564
Loss of Function	1.37	25	33.5	0.745	0.00000142	459

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000595	0.000572
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00185	0.00185
European (Non-Finnish)	0.000691	0.000686
Middle Eastern	0.000164	0.000163
South Asian	0.000759	0.000752
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The SMN complex plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also play a role in the metabolism of small nucleolar ribonucleoprotein (snoRNPs). {ECO:0000269|PubMed:18984161}.
• Pathway: RNA transport - Homo sapiens (human);mRNA Processing;mets affect on macrophage differentiation;snRNP Assembly;Metabolism of RNA;Metabolism of non-coding RNA (Consensus)

Recessive Scores

• pRec: 0.274

Intolerance Scores

• loftool: 0.899
• rvis_EVS: 1.73
• rvis_percentile_EVS: 96.61

Haploinsufficiency Scores

• pHI: 0.184
• hipred: N
• hipred_score: 0.437
• ghis: 0.414

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx20
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism 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); reproductive system phenotype; embryo phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;spliceosomal tri-snRNP complex assembly;spliceosomal snRNP assembly;RNA processing;negative regulation of cell population proliferation;positive regulation of apoptotic process;oogenesis;regulation of steroid biosynthetic process;import into nucleus
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;cytoskeleton;membrane;SMN complex;SMN-Sm protein complex;RNA polymerase II transcription repressor complex;Gemini of coiled bodies
• Molecular function: DNA binding;ATP-dependent RNA helicase activity;protein binding;ATP binding;protein domain specific binding;protein binding, bridging;histone deacetylase binding;repressing transcription factor binding