DDX59

DEAD-box helicase 59, the group of DEAD-box helicases|Zinc fingers HIT-type

Basic information

Region (hg38): 1:200623896-200669907

Links

ENSG00000118197 ∙ NCBI:83479 ∙ OMIM:615464 ∙ HGNC:25360 ∙ Uniprot:Q5T1V6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• orofaciodigital syndrome V (Strong), mode of inheritance: AR
• orofaciodigital syndrome V (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Orofaciodigital syndrome V	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	23972372

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DDX59 gene.

• not provided (1 variants)
• Orofaciodigital syndrome V (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX59 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	21	5	27
missense		1	33	12	5	51
nonsense	1		1			2
start loss						0
frameshift	1		1			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region		1		1	1	3
non coding				1	11	12
Total	2	2	37	34	21

Highest pathogenic variant AF is 0.00000657

Variants in DDX59

This is a list of pathogenic ClinVar variants found in the DDX59 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-200641221-A-C		DDX59-related disorder	Likely benign (Sep 02, 2020)
1-200644255-C-A		Orofaciodigital syndrome V	Pathogenic (Jan 07, 2022)
1-200644288-A-T		Inborn genetic diseases	Uncertain significance (Oct 25, 2023)
1-200644311-T-G			Likely benign (Feb 01, 2024)
1-200644351-T-C		Inborn genetic diseases	Uncertain significance (Apr 22, 2024)
1-200644427-G-A			Uncertain significance (Jan 28, 2022)
1-200644448-G-C			Uncertain significance (Jun 29, 2023)
1-200644457-AATT-A		Orofaciodigital syndrome V	Likely pathogenic (Sep 26, 2019)
1-200644480-G-A		Inborn genetic diseases	Uncertain significance (Jun 25, 2024)
1-200644481-C-T			Uncertain significance (Dec 25, 2021)
1-200644482-T-C			Benign (Dec 19, 2023)
1-200644514-C-T		Orofaciodigital syndrome V	Uncertain significance (Mar 17, 2024)
1-200644517-T-C		Inborn genetic diseases	Likely benign (Dec 16, 2023)
1-200644523-A-C		Orofaciodigital syndrome V	Likely pathogenic (Oct 01, 2021)
1-200648405-G-T			Benign (May 11, 2021)
1-200648492-T-C		Inborn genetic diseases	Uncertain significance (Nov 22, 2023)
1-200648497-C-T		DDX59-related disorder	Benign (Jan 02, 2024)
1-200648508-T-C			Likely benign (Jul 16, 2018)
1-200648515-C-T		Inborn genetic diseases	Uncertain significance (Jun 04, 2024)
1-200648553-T-C			Likely benign (Jun 01, 2023)
1-200648579-A-C			Benign (Oct 03, 2023)
1-200649110-T-C		Orofaciodigital syndrome V	Benign (Jan 31, 2024)
1-200649110-T-T			Benign (Jan 29, 2024)
1-200649118-T-C			Benign/Likely benign (Oct 01, 2024)
1-200649150-A-G			Likely benign (Jan 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX59	protein_coding	protein_coding	ENST00000331314	7	46074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.85e-7	0.970	125639	0	109	125748	0.000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.779	282	321	0.878	0.0000155	4055
Missense in Polyphen		104	125.94	0.82581		1555
Synonymous	0.0760	114	115	0.991	0.00000582	1194
Loss of Function	2.04	14	25.0	0.560	0.00000138	317

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000980	0.000980
Ashkenazi Jewish	0.00	0.00
East Asian	0.000513	0.000489
Finnish	0.000648	0.000647
European (Non-Finnish)	0.000415	0.000413
Middle Eastern	0.000513	0.000489
South Asian	0.000263	0.000261
Other	0.00100	0.000978

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Orofaciodigital syndrome 5 (OFD5) [MIM:174300]: A form of orofaciodigital syndrome, a group of heterogeneous disorders characterized by malformations of the oral cavity, face and digits, and associated phenotypic abnormalities that lead to the delineation of various subtypes. OFD5 patients show the core features of cleft palate, lobulated tongue, and polydactyly. Additional features include frontal bossing and intellectual disability. {ECO:0000269|PubMed:23972372}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.453
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.67

Haploinsufficiency Scores

• pHI: 0.0563
• hipred: N
• hipred_score: 0.492
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.962

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx59
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation 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)

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding;helicase activity;ATP binding;metal ion binding