DDX4

DEAD-box helicase 4, the group of DEAD-box helicases

Basic information

Region (hg38): 5:55738016-55817157

Links

ENSG00000152670 ∙ NCBI:54514 ∙ OMIM:605281 ∙ HGNC:18700 ∙ Uniprot:Q9NQI0 ∙ 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 DDX4 gene.

• Inborn genetic diseases (19 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX4 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			19		1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	19	0	3

Variants in DDX4

This is a list of pathogenic ClinVar variants found in the DDX4 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-55739013-A-G		not specified	Uncertain significance (Dec 14, 2021)
5-55746183-A-G		not specified	Uncertain significance (Aug 30, 2021)
5-55763225-G-A		not specified	Uncertain significance (Dec 18, 2023)
5-55764062-G-A		not specified	Uncertain significance (Jan 18, 2023)
5-55767889-A-T		not specified	Uncertain significance (Apr 11, 2023)
5-55767910-A-G		not specified	Uncertain significance (Aug 09, 2021)
5-55767921-A-C		not specified	Uncertain significance (Oct 17, 2023)
5-55779987-G-A		not specified	Uncertain significance (Feb 02, 2024)
5-55780003-A-G		not specified	Uncertain significance (Nov 21, 2022)
5-55781089-T-C		not specified	Uncertain significance (Feb 05, 2024)
5-55781973-G-A		not specified	Uncertain significance (Aug 02, 2021)
5-55785747-T-C		not specified	Uncertain significance (Aug 15, 2023)
5-55785849-A-G		not specified	Uncertain significance (Aug 02, 2023)
5-55786561-T-C		not specified	Uncertain significance (Feb 21, 2024)
5-55786564-C-T		not specified	Uncertain significance (Oct 03, 2023)
5-55786630-G-A		not specified	Uncertain significance (Mar 11, 2024)
5-55787886-A-T		not specified	Uncertain significance (Jan 10, 2023)
5-55787904-G-A		not specified	Uncertain significance (Dec 13, 2021)
5-55787916-T-C		not specified	Uncertain significance (Jul 09, 2021)
5-55787961-T-C		not specified	Uncertain significance (Mar 16, 2022)
5-55788009-A-G			Benign (Aug 08, 2017)
5-55790582-T-G		not specified	Uncertain significance (Oct 12, 2022)
5-55790684-G-A		not specified	Uncertain significance (Mar 29, 2023)
5-55792658-C-G		not specified	Uncertain significance (Nov 14, 2023)
5-55792682-T-G			Benign (Jan 30, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX4	protein_coding	protein_coding	ENST00000505374	21	79141

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00174	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	280	395	0.709	0.0000203	4738
Missense in Polyphen		67	164.76	0.40666		1968
Synonymous	0.490	116	123	0.944	0.00000599	1361
Loss of Function	5.39	6	45.0	0.133	0.00000259	520

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP-dependent RNA helicase required during spermatogenesis (PubMed:10920202, PubMed:21034600). Required to repress transposable elements and preventing their mobilization, which is essential for the germline integrity (By similarity). Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons (By similarity). Involved in the secondary piRNAs metabolic process, the production of piRNAs in fetal male germ cells through a ping- pong amplification cycle (By similarity). Required for PIWIL2 slicing-triggered piRNA biogenesis: helicase activity enables utilization of one of the slice cleavage fragments generated by PIWIL2 and processing these pre-piRNAs into piRNAs (By similarity). {ECO:0000250|UniProtKB:Q61496, ECO:0000269|PubMed:10920202, ECO:0000269|PubMed:21034600}.
• Pathway: Gene expression (Transcription);PIWI-interacting RNA (piRNA) biogenesis;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.320
• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.15

Haploinsufficiency Scores

• pHI: 0.686
• hipred: Y
• hipred_score: 0.575
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.828

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx4
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Zebrafish Information Network

• Gene name: ddx4
• Affected structure: primordial germ cell
• Phenotype tag: abnormal
• Phenotype quality: increased amount

Gene ontology

• Biological process: male meiotic nuclear division;male meiosis I;multicellular organism development;spermatogenesis;negative regulation of transposition;cell differentiation;flagellated sperm motility;gene silencing by RNA;piRNA metabolic process;DNA methylation involved in gamete generation;piRNA biosynthetic process
• Cellular component: cytoplasm;perinuclear region of cytoplasm;pi-body;piP-body
• Molecular function: nucleic acid binding;helicase activity;ATP binding;ATPase activity