DDX60

DExD/H-box helicase 60, the group of Ski2 like RNA helicases

Basic information

Region (hg38): 4:168216291-168318883

Links

ENSG00000137628 ∙ NCBI:55601 ∙ OMIM:613974 ∙ HGNC:25942 ∙ Uniprot:Q8IY21 ∙ 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 DDX60 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX60 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			50	8	2	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	50	10	3

Variants in DDX60

This is a list of pathogenic ClinVar variants found in the DDX60 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-168216988-A-G		not specified	Uncertain significance (Nov 27, 2023)
4-168221770-A-G		not specified	Uncertain significance (Dec 19, 2023)
4-168221839-C-T		not specified	Uncertain significance (Jun 29, 2022)
4-168221856-T-C			Benign (Jan 19, 2018)
4-168224265-A-G		not specified	Uncertain significance (Feb 06, 2023)
4-168224338-T-A		not specified	Uncertain significance (Apr 01, 2024)
4-168225588-C-T		not specified	Uncertain significance (Dec 12, 2022)
4-168236370-G-A		not specified	Uncertain significance (Jan 18, 2022)
4-168237369-T-C		not specified	Uncertain significance (Jun 01, 2023)
4-168237436-C-G			Benign (Jan 19, 2018)
4-168246437-G-A		not specified	Uncertain significance (Mar 22, 2022)
4-168246470-C-T		not specified	Uncertain significance (Feb 28, 2023)
4-168246489-T-C		not specified	Uncertain significance (Nov 30, 2022)
4-168246573-C-T		not specified	Uncertain significance (Aug 16, 2022)
4-168251016-T-A		not specified	Uncertain significance (Jan 09, 2024)
4-168252564-T-C		not specified	Uncertain significance (Jan 24, 2023)
4-168252625-C-T		not specified	Likely benign (Jan 10, 2022)
4-168252633-G-T		not specified	Likely benign (Oct 10, 2023)
4-168255724-T-G		not specified	Uncertain significance (Sep 13, 2023)
4-168255757-T-C		not specified	Uncertain significance (Aug 11, 2022)
4-168255781-C-T		not specified	Uncertain significance (Jan 04, 2022)
4-168255793-G-A		not specified	Uncertain significance (Nov 17, 2023)
4-168255844-C-T		not specified	Uncertain significance (Nov 22, 2022)
4-168260952-T-C		not specified	Uncertain significance (Oct 03, 2022)
4-168262089-A-C		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX60	protein_coding	protein_coding	ENST00000393743	37	102515

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.21e-16	1.00	125646	0	102	125748	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	750	853	0.879	0.0000431	11303
Missense in Polyphen		155	235.65	0.65776		3225
Synonymous	0.319	297	304	0.977	0.0000158	3074
Loss of Function	4.88	42	92.6	0.453	0.00000500	1206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000825	0.000815
Ashkenazi Jewish	0.00	0.00
East Asian	0.000713	0.000707
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000436	0.000431
Middle Eastern	0.000713	0.000707
South Asian	0.000298	0.000294
Other	0.000832	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Positively regulates DDX58/RIG-I- and IFIH1/MDA5- dependent type I interferon and interferon inducible gene expression in response to viral infection. Binds ssRNA, dsRNA and dsDNA and can promote the binding of DDX58/RIG-I to dsRNA. Exhibits antiviral activity against hepatitis C virus and vesicular stomatitis virus (VSV). {ECO:0000269|PubMed:21478870, ECO:0000269|PubMed:21791617}.

Recessive Scores

• pRec: 0.0908

Intolerance Scores

• loftool: 0.945
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.69

Haploinsufficiency Scores

• pHI: 0.125
• hipred: Y
• hipred_score: 0.526
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.364

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx60
• Phenotype: immune 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); normal phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to virus;innate immune response;defense response to virus;positive regulation of MDA-5 signaling pathway;positive regulation of RIG-I signaling pathway
• Cellular component: cytoplasm;cytosol;intermediate filament cytoskeleton
• Molecular function: double-stranded DNA binding;double-stranded RNA binding;single-stranded RNA binding;helicase activity;protein binding;ATP binding