DDX50

DExD-box helicase 50, the group of DEAD-box helicases

Basic information

Region (hg38): 10:68901285-68946847

Links

ENSG00000107625 ∙ NCBI:79009 ∙ OMIM:610373 ∙ HGNC:17906 ∙ Uniprot:Q9BQ39 ∙ 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 DDX50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX50 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			40		1	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	0	2

Variants in DDX50

This is a list of pathogenic ClinVar variants found in the DDX50 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-68901404-G-C		not specified	Uncertain significance (Jan 04, 2022)
10-68901431-C-T		not specified	Uncertain significance (Jun 14, 2023)
10-68901439-G-A		not specified	Uncertain significance (Feb 10, 2023)
10-68901452-A-C		not specified	Uncertain significance (May 12, 2024)
10-68901455-A-T		not specified	Uncertain significance (May 12, 2024)
10-68901457-A-G		not specified	Uncertain significance (Sep 23, 2023)
10-68906734-C-A		not specified	Uncertain significance (Oct 12, 2022)
10-68906745-C-T		Malignant tumor of prostate	Uncertain significance (-)
10-68906787-A-C		not specified	Uncertain significance (Oct 26, 2022)
10-68906788-C-G		not specified	Uncertain significance (Dec 22, 2023)
10-68906820-T-C		not specified	Uncertain significance (Nov 22, 2023)
10-68906852-G-C		not specified	Uncertain significance (Feb 21, 2024)
10-68906925-T-C		not specified	Uncertain significance (Sep 14, 2022)
10-68906973-C-G		not specified	Uncertain significance (Nov 28, 2023)
10-68910329-A-G		not specified	Uncertain significance (Oct 26, 2022)
10-68910335-C-A		not specified	Uncertain significance (Apr 19, 2023)
10-68910335-C-G		not specified	Uncertain significance (Jul 27, 2021)
10-68911139-A-G		not specified	Uncertain significance (Mar 14, 2023)
10-68911151-C-T		not specified	Uncertain significance (Aug 17, 2021)
10-68911235-C-T		not specified	Uncertain significance (Jul 13, 2021)
10-68911239-C-T		not specified	Uncertain significance (Jan 03, 2022)
10-68913172-T-C		not specified	Uncertain significance (May 21, 2024)
10-68913180-A-G		not specified	Uncertain significance (Dec 20, 2022)
10-68913222-A-G		not specified	Uncertain significance (May 08, 2023)
10-68913239-C-T			Benign (Jul 04, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX50	protein_coding	protein_coding	ENST00000373585	15	45570

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.75e-7	1.00	125711	0	35	125746	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	280	396	0.708	0.0000209	4768
Missense in Polyphen		35	89.083	0.39289		1137
Synonymous	-0.0318	131	131	1.00	0.00000614	1426
Loss of Function	3.62	18	43.9	0.410	0.00000269	494

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000221	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000146	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.776
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.784
• hipred: Y
• hipred_score: 0.675
• ghis: 0.680

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• 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: Ddx50

Gene ontology

• Cellular component: nucleolus;plasma membrane;membrane
• Molecular function: RNA binding;helicase activity;ATP binding