DDX54

DEAD-box helicase 54, the group of DEAD-box helicases|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:113157173-113185479

Links

ENSG00000123064 ∙ NCBI:79039 ∙ OMIM:611665 ∙ HGNC:20084 ∙ Uniprot:Q8TDD1 ∙ 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 DDX54 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX54 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	4
missense			83	6	5	94
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region					3	3
non coding						0
Total	0	0	83	8	8

Variants in DDX54

This is a list of pathogenic ClinVar variants found in the DDX54 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-113158890-C-T		not specified	Uncertain significance (Aug 22, 2023)
12-113158891-G-A		not specified	Uncertain significance (Jan 02, 2024)
12-113158899-C-T		not specified	Uncertain significance (Oct 17, 2024)
12-113158920-C-T		not specified	Uncertain significance (Aug 01, 2024)
12-113158930-C-A		not specified	Uncertain significance (Dec 12, 2023)
12-113158932-C-A		not specified	Uncertain significance (Feb 15, 2023)
12-113158939-G-C		not specified	Uncertain significance (Jul 30, 2024)
12-113158953-C-T		DDX54-related disorder	Likely benign (Jul 08, 2022)
12-113158984-G-C		not specified	Uncertain significance (Sep 14, 2022)
12-113158986-C-A		DDX54-related Neurodevelopmental Disorder	Uncertain significance (Feb 11, 2020)
12-113158992-C-T		not specified	Uncertain significance (Nov 18, 2022)
12-113158993-G-A		not specified	Uncertain significance (Apr 08, 2024)
12-113159000-G-T		not specified	Uncertain significance (Sep 08, 2024)
12-113159020-G-A		not specified	Uncertain significance (Jun 30, 2024)
12-113159023-G-A		See cases	Uncertain significance (May 05, 2020)
12-113159040-T-C		not specified	Uncertain significance (Mar 14, 2023)
12-113159061-G-A		DDX54-related disorder	Benign (Nov 11, 2019)
12-113159065-G-A		not specified	Uncertain significance (Dec 04, 2024)
12-113159070-C-T		not specified	Uncertain significance (Oct 06, 2021)
12-113159100-C-T		not specified	Likely benign (Oct 29, 2021)
12-113159109-C-T		not specified	Uncertain significance (Sep 29, 2023)
12-113161276-C-T		DDX54-related disorder	Likely benign (Oct 30, 2019)
12-113161279-G-A		not specified	Uncertain significance (Sep 17, 2021)
12-113161314-C-T		not specified	Uncertain significance (Jan 31, 2023)
12-113161315-G-A		not specified	Uncertain significance (Jan 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX54	protein_coding	protein_coding	ENST00000314045	20	28306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.74e-9	1.00	125657	0	91	125748	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.676	547	593	0.922	0.0000424	5599
Missense in Polyphen		167	204.65	0.81603		1913
Synonymous	0.173	241	244	0.986	0.0000162	1847
Loss of Function	3.41	22	47.3	0.465	0.00000274	486

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000685	0.000684
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.00114	0.00102
European (Non-Finnish)	0.000277	0.000273
Middle Eastern	0.000490	0.000489
South Asian	0.000233	0.000229
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has RNA-dependent ATPase activity. Represses the transcriptional activity of nuclear receptors. {ECO:0000269|PubMed:12466272}.
• Pathway: Validated nuclear estrogen receptor alpha network;Validated nuclear estrogen receptor beta network (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.849
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.73

Haploinsufficiency Scores

• pHI: 0.167
• hipred: Y
• hipred_score: 0.694
• ghis: 0.566

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx54
• Phenotype: growth/size/body region phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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: ddx54
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: RNA processing;RNA metabolic process;intracellular estrogen receptor signaling pathway;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleolus;Golgi apparatus;membrane
• Molecular function: transcription corepressor activity;RNA binding;ATP-dependent RNA helicase activity;signaling receptor binding;ATP binding;estrogen receptor binding