DDX55

DEAD-box helicase 55, the group of Small nucleolar RNA protein coding host genes|DEAD-box helicases

Basic information

Region (hg38): 12:123602077-123620943

Links

ENSG00000111364 ∙ NCBI:57696 ∙ OMIM:620176 ∙ HGNC:20085 ∙ Uniprot:Q8NHQ9 ∙ 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 DDX55 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX55 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						0
missense			43	3		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	3	0

Variants in DDX55

This is a list of pathogenic ClinVar variants found in the DDX55 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-123602164-G-C		not specified	Uncertain significance (Aug 10, 2024)
12-123602171-C-T		not specified	Uncertain significance (Apr 15, 2024)
12-123602200-C-G		not specified	Uncertain significance (Apr 24, 2023)
12-123602200-C-T		not specified	Uncertain significance (Nov 23, 2022)
12-123605934-G-A		not specified	Uncertain significance (Sep 11, 2024)
12-123605938-C-T		not specified	Uncertain significance (Mar 07, 2024)
12-123606119-A-G		not specified	Uncertain significance (Oct 05, 2023)
12-123607465-C-G		not specified	Uncertain significance (Dec 28, 2023)
12-123607481-A-G		not specified	Uncertain significance (Nov 12, 2024)
12-123607483-G-A		not specified	Uncertain significance (Feb 10, 2023)
12-123607502-C-G		not specified	Uncertain significance (Apr 28, 2023)
12-123608736-C-A		not specified	Uncertain significance (Jul 27, 2021)
12-123608789-G-C		not specified	Uncertain significance (Jun 17, 2024)
12-123608820-T-G		not specified	Uncertain significance (Oct 25, 2024)
12-123610031-C-T		not specified	Uncertain significance (Jun 17, 2022)
12-123610072-G-A		not specified	Uncertain significance (Dec 14, 2023)
12-123610075-G-A		not specified	Uncertain significance (Nov 07, 2024)
12-123610091-C-T		not specified	Uncertain significance (Jan 22, 2024)
12-123610108-C-T		not specified	Uncertain significance (Dec 28, 2023)
12-123610114-G-A		not specified	Uncertain significance (Dec 06, 2024)
12-123613173-T-G		not specified	Uncertain significance (Oct 26, 2021)
12-123613203-G-A		not specified	Uncertain significance (Mar 30, 2024)
12-123613207-A-G		not specified	Uncertain significance (Oct 04, 2024)
12-123615187-C-T		not specified	Uncertain significance (Mar 21, 2022)
12-123615257-T-G		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX55	protein_coding	protein_coding	ENST00000238146	14	18865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.11e-8	0.970	125548	0	200	125748	0.000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.653	304	338	0.900	0.0000187	3950
Missense in Polyphen		106	133.24	0.79556		1496
Synonymous	0.264	124	128	0.970	0.00000728	1123
Loss of Function	2.11	17	29.3	0.580	0.00000148	357

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00239	0.00238
Ashkenazi Jewish	0.00218	0.00199
East Asian	0.00165	0.00163
Finnish	0.000582	0.000508
European (Non-Finnish)	0.000673	0.000668
Middle Eastern	0.00165	0.00163
South Asian	0.000166	0.000163
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable ATP-binding RNA helicase.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.963
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.57

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.647
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx55
• 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); 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)

Zebrafish Information Network

• Gene name: ddx55
• Affected structure: ceratohyal cartilage
• Phenotype tag: abnormal
• Phenotype quality: bent

Gene ontology

• Cellular component: nucleus;nucleolus;cytosol;membrane
• Molecular function: RNA binding;helicase activity;protein binding;ATP binding