DDX10

DEAD-box helicase 10, the group of DEAD-box helicases|SSU processome

Basic information

Region (hg38): 11:108665057-108940999

Links

ENSG00000178105 ∙ NCBI:1662 ∙ OMIM:601235 ∙ HGNC:2735 ∙ Uniprot:Q13206 ∙ 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 DDX10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX10 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				4	2	6
missense			46	3	1	50
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	46	8	3

Variants in DDX10

This is a list of pathogenic ClinVar variants found in the DDX10 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-108665248-A-T		not specified	Uncertain significance (May 30, 2024)
11-108665284-C-G		DDX10-related disorder	Benign/Likely benign (Jul 08, 2019)
11-108673520-A-G		DDX10-related disorder	Likely benign (Nov 18, 2019)
11-108675644-C-T		not specified	Uncertain significance (May 17, 2023)
11-108675733-A-G		DDX10-related disorder	Benign (Nov 26, 2019)
11-108677085-G-A		not specified	Uncertain significance (Mar 15, 2024)
11-108677093-A-C		not specified	Uncertain significance (Nov 09, 2021)
11-108677103-C-T		not specified	Uncertain significance (Jun 02, 2024)
11-108677104-G-A		not specified	Uncertain significance (Mar 07, 2024)
11-108677152-C-G		not specified	Uncertain significance (Apr 13, 2022)
11-108677184-G-T		not specified	Uncertain significance (Oct 20, 2021)
11-108678379-T-G		not specified	Uncertain significance (Jul 12, 2022)
11-108679403-G-C		not specified	Uncertain significance (Feb 03, 2022)
11-108679448-A-G		not specified	Uncertain significance (Feb 27, 2023)
11-108679451-C-T		not specified	Uncertain significance (Dec 16, 2023)
11-108679558-T-C			Benign/Likely benign (Apr 01, 2023)
11-108689034-G-A		not specified	Uncertain significance (Jun 22, 2021)
11-108691886-T-G		not specified	Uncertain significance (Mar 20, 2023)
11-108691910-G-A		not specified	Uncertain significance (Jun 21, 2022)
11-108692000-C-T		not specified	Uncertain significance (Aug 11, 2022)
11-108692021-T-C		not specified	Uncertain significance (Oct 05, 2023)
11-108693512-G-A		DDX10-related disorder	Likely benign (Dec 27, 2019)
11-108693547-T-G		not specified	Uncertain significance (Mar 27, 2023)
11-108693570-C-T		not specified	Uncertain significance (Apr 06, 2024)
11-108715890-A-G		not specified • DDX10-related disorder	Benign/Likely benign (Dec 09, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX10	protein_coding	protein_coding	ENST00000322536	18	275906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.46e-17	0.621	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.304	441	459	0.960	0.0000233	5815
Missense in Polyphen		164	173.88	0.94317		2165
Synonymous	-0.677	174	163	1.07	0.00000847	1558
Loss of Function	1.83	32	45.3	0.707	0.00000226	588

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00148	0.00147
Ashkenazi Jewish	0.00	0.00
East Asian	0.000275	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000427	0.000422
Middle Eastern	0.000275	0.000272
South Asian	0.000297	0.000294
Other	0.000174	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative ATP-dependent RNA helicase.

Recessive Scores

• pRec: 0.0983

Intolerance Scores

• loftool: 0.921
• rvis_EVS: -0.48
• rvis_percentile_EVS: 22.78

Haploinsufficiency Scores

• pHI: 0.407
• hipred: N
• hipred_score: 0.484
• ghis: 0.583

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx10
• Phenotype: digestive/alimentary phenotype; skeleton phenotype; craniofacial phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: anterior head development
• Molecular function: RNA binding;RNA helicase activity;ATP binding