DDX5
DEAD-box helicase 5, the group of DEAD-box helicases|MicroRNA protein coding host genes
Basic information
Region (hg38): 17:64498254-64508199
Previous symbols: [ "HLR1", "G17P1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX5 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 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 13 | 0 | 1 |
Variants in DDX5
This is a list of pathogenic ClinVar variants found in the DDX5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-64499993-G-A | not specified | Uncertain significance (Apr 29, 2024) | ||
| 17-64500026-A-C | not specified | Uncertain significance (Dec 10, 2024) | ||
| 17-64500143-T-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 17-64500197-C-T | not specified | Uncertain significance (Apr 29, 2024) | ||
| 17-64500212-G-A | not specified | Uncertain significance (Apr 25, 2022) | ||
| 17-64500287-C-G | not specified | Uncertain significance (Oct 20, 2024) | ||
| 17-64500311-C-T | not specified | Uncertain significance (May 25, 2022) | ||
| 17-64500642-T-C | not specified | Uncertain significance (Mar 30, 2024) | ||
| 17-64500648-T-C | not specified | Uncertain significance (Jul 17, 2023) | ||
| 17-64502478-C-T | not specified | Uncertain significance (Jun 29, 2022) | ||
| 17-64502943-G-C | not specified | Uncertain significance (Aug 09, 2021) | ||
| 17-64502953-A-G | not specified | Uncertain significance (Oct 05, 2022) | ||
| 17-64502977-T-C | not specified | Uncertain significance (Dec 13, 2021) | ||
| 17-64503070-G-A | Global developmental delay | Uncertain significance (Jan 01, 2020) | ||
| 17-64503094-T-A | not specified | Uncertain significance (Feb 14, 2024) | ||
| 17-64503194-T-C | Benign (Oct 10, 2018) | |||
| 17-64503565-C-T | not specified | Uncertain significance (Jun 09, 2022) | ||
| 17-64504048-G-A | not specified | Uncertain significance (Jul 17, 2024) | ||
| 17-64504098-A-G | not specified | Uncertain significance (Mar 13, 2023) | ||
| 17-64504116-G-A | not specified | Uncertain significance (Sep 22, 2022) | ||
| 17-64506081-G-C | not specified | Uncertain significance (Jul 14, 2024) | ||
| 17-64507101-G-A | not specified | Uncertain significance (Dec 01, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DDX5 | protein_coding | protein_coding | ENST00000225792 | 13 | 8584 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000211 | 125735 | 0 | 3 | 125738 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.76 | 200 | 344 | 0.582 | 0.0000173 | 4051 |
| Missense in Polyphen | 28 | 126.2 | 0.22187 | 1560 | ||
| Synonymous | -3.69 | 162 | 112 | 1.44 | 0.00000560 | 1152 |
| Loss of Function | 5.10 | 0 | 30.3 | 0.00 | 0.00000136 | 375 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000177 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the alternative regulation of pre-mRNA splicing; its RNA helicase activity is necessary for increasing tau exon 10 inclusion and occurs in a RBM4-dependent manner. Binds to the tau pre-mRNA in the stem-loop region downstream of exon 10. The rate of ATP hydrolysis is highly stimulated by single-stranded RNA. Involved in transcriptional regulation; the function is independent of the RNA helicase activity. Transcriptional coactivator for androgen receptor AR but probably not ESR1. Synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and involved in skeletal muscle differentiation. Transcriptional coactivator for p53/TP53 and involved in p53/TP53 transcriptional response to DNA damage and p53/TP53-dependent apoptosis. Transcriptional coactivator for RUNX2 and involved in regulation of osteoblast differentiation. Acts as transcriptional repressor in a promoter-specific manner; the function probably involves association with histone deacetylases, such as HDAC1. As component of a large PER complex is involved in the inhibition of 3' transcriptional termination of circadian target genes such as PER1 and NR1D1 and the control of the circadian rhythms. {ECO:0000269|PubMed:12527917, ECO:0000269|PubMed:15298701, ECO:0000269|PubMed:15660129, ECO:0000269|PubMed:17011493, ECO:0000269|PubMed:17960593, ECO:0000269|PubMed:18829551, ECO:0000269|PubMed:19718048, ECO:0000269|PubMed:21343338}.;
- Pathway
- Proteoglycans in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Spliceosome - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;Signal Transduction;Metabolism of RNA;mRNA Splicing - Major Pathway;AndrogenReceptor;akap95 role in mitosis and chromosome dynamics;Signaling by Nuclear Receptors;Direct p53 effectors;Estrogen-dependent gene expression;ESR-mediated signaling;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.260
Intolerance Scores
- loftool
- 0.311
- rvis_EVS
- -0.71
- rvis_percentile_EVS
- 14.5
Haploinsufficiency Scores
- pHI
- 0.995
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.616
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ddx5
- Phenotype
- cellular phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;alternative mRNA splicing, via spliceosome;regulation of alternative mRNA splicing, via spliceosome;mRNA splicing, via spliceosome;nuclear-transcribed mRNA catabolic process;epithelial to mesenchymal transition;regulation of transcription by RNA polymerase II;mRNA transcription;BMP signaling pathway;intracellular estrogen receptor signaling pathway;androgen receptor signaling pathway;positive regulation of DNA damage response, signal transduction by p53 class mediator;regulation of viral genome replication;myoblast differentiation;regulation of osteoblast differentiation;rhythmic process;regulation of androgen receptor signaling pathway;pri-miRNA transcription by RNA polymerase II;intrinsic apoptotic signaling pathway by p53 class mediator;regulation of pri-miRNA transcription by RNA polymerase II;positive regulation of production of miRNAs involved in gene silencing by miRNA;regulation of skeletal muscle cell differentiation
- Cellular component
- nucleus;nucleoplasm;nucleolus;membrane;extracellular exosome;catalytic step 2 spliceosome;ribonucleoprotein complex
- Molecular function
- RNA binding;RNA helicase activity;mRNA 3'-UTR binding;ATP-dependent RNA helicase activity;protein binding;calmodulin binding;ATP binding;enzyme binding;MH2 domain binding;pre-mRNA binding;ribonucleoprotein complex binding;SMAD binding;calcium-dependent protein binding;androgen receptor binding;R-SMAD binding;primary miRNA binding;promoter-specific chromatin binding