DDX5

DEAD-box helicase 5, the group of DEAD-box helicases|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:64498253-64508199

Previous symbols: [ "HLR1", "G17P1" ]

Links

ENSG00000108654 ∙ NCBI:1655 ∙ OMIM:180630 ∙ HGNC:2746 ∙ Uniprot:P17844 ∙ 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 DDX5 gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

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	1
missense			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	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
17-64500143-T-C		not specified	Uncertain significance (Oct 06, 2021)
17-64500212-G-A		not specified	Uncertain significance (Apr 25, 2022)
17-64500311-C-T		not specified	Uncertain significance (May 25, 2022)
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)
17-64504098-A-G		not specified	Uncertain significance (Mar 13, 2023)
17-64504116-G-A		not specified	Uncertain significance (Sep 22, 2022)
17-64507101-G-A		not specified	Uncertain significance (Dec 01, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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