DDX49

DEAD-box helicase 49, the group of DEAD-box helicases|SSU processome

Basic information

Region (hg38): 19:18919705-18929189

Links

ENSG00000105671 ∙ NCBI:54555 ∙ ∙ HGNC:18684 ∙ Uniprot:Q9Y6V7 ∙ 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 DDX49 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX49 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				2		2
missense			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	3	0

Variants in DDX49

This is a list of pathogenic ClinVar variants found in the DDX49 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18919847-A-G		not specified	Uncertain significance (Jan 22, 2024)
19-18920633-G-C		not specified	Uncertain significance (May 23, 2024)
19-18920635-C-T			Likely benign (May 01, 2022)
19-18921694-C-T		not specified	Uncertain significance (May 08, 2024)
19-18921728-G-T		not specified	Uncertain significance (Oct 03, 2023)
19-18921847-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-18921865-G-T		not specified	Uncertain significance (Jan 09, 2024)
19-18921914-G-A		not specified	Uncertain significance (Sep 12, 2024)
19-18921939-T-G		not specified	Uncertain significance (May 15, 2024)
19-18921957-G-C		not specified	Uncertain significance (Sep 01, 2021)
19-18922377-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-18922399-C-A		not specified	Uncertain significance (Mar 12, 2024)
19-18922399-C-T		not specified	Uncertain significance (Nov 20, 2023)
19-18922408-C-G		not specified	Uncertain significance (Mar 16, 2022)
19-18922512-C-T		not specified	Uncertain significance (Feb 14, 2023)
19-18922614-G-A		not specified	Uncertain significance (Aug 19, 2024)
19-18922621-A-T		not specified	Uncertain significance (May 08, 2024)
19-18922665-G-C		not specified	Uncertain significance (Apr 22, 2024)
19-18922707-G-A		not specified	Uncertain significance (Mar 19, 2024)
19-18924262-G-A		not specified	Uncertain significance (May 22, 2024)
19-18924271-G-C		not specified	Uncertain significance (Aug 09, 2021)
19-18924282-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-18924297-A-G		not specified	Uncertain significance (Jan 31, 2024)
19-18924638-G-A		not specified	Uncertain significance (Sep 11, 2024)
19-18924668-C-T		not specified	Uncertain significance (Sep 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX49	protein_coding	protein_coding	ENST00000247003	13	8953

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.25e-14	0.100	125667	0	81	125748	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.964	261	309	0.846	0.0000198	3085
Missense in Polyphen		88	125.49	0.70127		1217
Synonymous	0.776	123	134	0.915	0.00000902	982
Loss of Function	0.772	23	27.4	0.841	0.00000160	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000597	0.000583
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000599	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000285	0.000281
Middle Eastern	0.000599	0.000544
South Asian	0.00142	0.000817
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Pathway: rRNA processing;Metabolism of RNA;TCR;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.904
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.56

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.384
• ghis: 0.536

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx49

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleoplasm
• Molecular function: RNA binding;helicase activity;ATP binding