DDX56

DEAD-box helicase 56, the group of DEAD-box helicases

Basic information

Region (hg38): 7:44565804-44575051

Links

ENSG00000136271 ∙ NCBI:54606 ∙ OMIM:608023 ∙ HGNC:18193 ∙ Uniprot:Q9NY93 ∙ 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 DDX56 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX56 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	2	3
missense			36	1	1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	2	3

Variants in DDX56

This is a list of pathogenic ClinVar variants found in the DDX56 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-44566039-T-C		not specified	Likely benign (Sep 23, 2023)
7-44566068-G-T			Likely benign (Mar 01, 2024)
7-44566464-G-A		not specified	Uncertain significance (Jan 31, 2024)
7-44566470-G-A		not specified	Uncertain significance (May 27, 2022)
7-44566490-G-C		not specified	Uncertain significance (Nov 21, 2022)
7-44566501-C-G		not specified	Uncertain significance (Jun 26, 2024)
7-44566510-G-A		not specified	Uncertain significance (Jun 23, 2023)
7-44568148-G-A		not specified	Uncertain significance (Sep 12, 2023)
7-44568958-C-T		not specified	Uncertain significance (Sep 20, 2023)
7-44569135-A-C		not specified	Uncertain significance (Jun 13, 2024)
7-44569167-C-T		not specified	Uncertain significance (Oct 29, 2024)
7-44569186-G-A			Benign (May 11, 2017)
7-44569878-T-C		not specified	Uncertain significance (Sep 07, 2022)
7-44569886-T-C		not specified	Uncertain significance (Nov 13, 2024)
7-44570079-C-T		not specified	Uncertain significance (Oct 06, 2021)
7-44570088-A-C		not specified	Uncertain significance (Aug 21, 2024)
7-44570108-C-T		not specified	Uncertain significance (Dec 26, 2023)
7-44570856-G-C		not specified	Uncertain significance (Jul 09, 2024)
7-44570876-A-G		not specified	Uncertain significance (Oct 29, 2021)
7-44571498-C-T		not specified	Uncertain significance (Oct 31, 2023)
7-44571499-G-A		not specified	Uncertain significance (Apr 11, 2023)
7-44571510-T-G		not specified	Uncertain significance (Mar 20, 2024)
7-44571516-T-C		not specified	Uncertain significance (May 20, 2024)
7-44571552-A-G		not specified	Uncertain significance (Feb 13, 2024)
7-44571585-T-C		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX56	protein_coding	protein_coding	ENST00000258772	14	9635

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.21e-8	0.979	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.230	333	321	1.04	0.0000186	3491
Missense in Polyphen		86	96.793	0.8885		1100
Synonymous	-0.0769	122	121	1.01	0.00000593	1141
Loss of Function	2.17	16	28.5	0.561	0.00000145	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000311	0.000308
Middle Eastern	0.000272	0.000272
South Asian	0.000359	0.000359
Other	0.000334	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.663
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.647
• ghis: 0.610

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.971

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx56

Zebrafish Information Network

• Gene name: ddx56
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased width

Gene ontology

• Biological process: rRNA processing;positive regulation of neuron projection development
• Cellular component: nucleolus;membrane
• Molecular function: RNA binding;ATP-dependent RNA helicase activity;ATP binding