DDX42

DEAD-box helicase 42, the group of DEAD-box helicases

Basic information

Region (hg38): 17:63773602-63819317

Links

ENSG00000198231 ∙ NCBI:11325 ∙ OMIM:613369 ∙ HGNC:18676 ∙ Uniprot:Q86XP3 ∙ 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 DDX42 gene.

• Inborn genetic diseases (33 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX42 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			31	1		32
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	0

Variants in DDX42

This is a list of pathogenic ClinVar variants found in the DDX42 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63787114-G-A		not specified	Uncertain significance (May 26, 2023)
17-63787140-C-T		not specified	Uncertain significance (Jun 24, 2022)
17-63787170-G-T		not specified	Uncertain significance (Mar 29, 2023)
17-63787249-C-T		not specified	Uncertain significance (Jan 03, 2024)
17-63792446-G-A		not specified	Uncertain significance (Dec 12, 2023)
17-63792450-A-C		not specified	Uncertain significance (Jan 18, 2022)
17-63805105-A-G		not specified	Uncertain significance (Apr 18, 2023)
17-63805116-G-A		not specified	Uncertain significance (Oct 27, 2022)
17-63805174-G-A		not specified	Uncertain significance (Aug 04, 2023)
17-63806566-G-T		not specified	Uncertain significance (Sep 07, 2022)
17-63806600-T-TA			Uncertain significance (Sep 14, 2023)
17-63806602-T-C		not specified	Uncertain significance (Sep 15, 2021)
17-63808827-C-G		not specified	Uncertain significance (Apr 05, 2023)
17-63808863-G-A		not specified	Uncertain significance (May 04, 2022)
17-63809593-A-G		not specified	Uncertain significance (May 27, 2022)
17-63810546-G-A		not specified	Uncertain significance (Dec 21, 2022)
17-63812007-C-A		not specified	Uncertain significance (Mar 11, 2022)
17-63812088-A-G		not specified	Uncertain significance (Jan 10, 2023)
17-63812206-C-T		not specified	Uncertain significance (May 08, 2023)
17-63813257-A-G		not specified	Uncertain significance (Aug 04, 2021)
17-63813366-A-G		not specified	Uncertain significance (Dec 12, 2023)
17-63813421-C-T		not specified	Likely benign (Jun 06, 2023)
17-63813449-A-G		not specified	Uncertain significance (Dec 13, 2022)
17-63813449-A-T		not specified	Uncertain significance (May 24, 2023)
17-63815609-A-T		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX42	protein_coding	protein_coding	ENST00000578681	17	45715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000115	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.29	329	545	0.604	0.0000316	6224
Missense in Polyphen		76	213.43	0.35609		2396
Synonymous	0.600	174	184	0.944	0.0000102	1798
Loss of Function	6.08	2	46.9	0.0426	0.00000295	504

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATP-dependent RNA helicase. Binds to partially double- stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm. {ECO:0000269|PubMed:16397294, ECO:0000269|PubMed:19377511}.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.324
• rvis_EVS: -1
• rvis_percentile_EVS: 8.47

Haploinsufficiency Scores

• pHI: 0.322
• hipred: Y
• hipred_score: 0.783
• ghis: 0.675

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx42
• Phenotype: hematopoietic system 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); immune system phenotype

Gene ontology

• Biological process: mRNA splicing, via spliceosome;protein localization;regulation of apoptotic process
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;Cajal body;membrane;nuclear speck
• Molecular function: RNA binding;helicase activity;protein binding;ATP binding