DDX46

DEAD-box helicase 46, the group of DEAD-box helicases|Spliceosomal A complex

Basic information

Region (hg38): 5:134758771-134855133

Links

ENSG00000145833 ∙ NCBI:9879 ∙ OMIM:617848 ∙ HGNC:18681 ∙ Uniprot:Q7L014 ∙ 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 DDX46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX46 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			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	0

Variants in DDX46

This is a list of pathogenic ClinVar variants found in the DDX46 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-134766939-G-T		not specified	Uncertain significance (Dec 06, 2022)
5-134766941-C-G		not specified	Uncertain significance (Aug 08, 2022)
5-134773780-G-A		not specified	Uncertain significance (May 02, 2024)
5-134777621-G-A		not specified	Uncertain significance (Nov 08, 2024)
5-134777721-A-G		not specified	Uncertain significance (Aug 12, 2021)
5-134781146-C-T		not specified	Uncertain significance (Apr 20, 2024)
5-134782962-T-A		not specified	Uncertain significance (Mar 21, 2023)
5-134794857-G-A		not specified	Uncertain significance (Dec 08, 2023)
5-134796006-A-G		not specified	Uncertain significance (Nov 17, 2022)
5-134796012-T-C		not specified	Uncertain significance (Jan 26, 2022)
5-134796048-G-C		not specified	Uncertain significance (Sep 12, 2023)
5-134811332-A-C		not specified	Uncertain significance (Feb 12, 2024)
5-134811338-T-A		not specified	Uncertain significance (Jan 10, 2023)
5-134817701-A-G		6 conditions	Uncertain significance (Oct 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX46	protein_coding	protein_coding	ENST00000354283	23	96355

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	6.35e-8	125732	0	6	125738	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	5.48	193	557	0.347	0.0000297	6773
Missense in Polyphen		27	215.85	0.12509		2661
Synonymous	-0.129	182	180	1.01	0.00000900	1902
Loss of Function	6.92	4	63.5	0.0630	0.00000412	734

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000108	0.000106
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000187	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an essential role in splicing, either prior to, or during splicing A complex formation. {ECO:0000269|PubMed:12234937}.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.241
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.72

Haploinsufficiency Scores

• pHI: 0.717
• hipred: Y
• hipred_score: 0.775
• ghis: 0.705

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx46

Zebrafish Information Network

• Gene name: ddx46
• Affected structure: hematopoietic stem cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: fibrillar center;nucleus;nucleoplasm;Cajal body;membrane;nuclear speck
• Molecular function: RNA binding;helicase activity;ATP binding