DDX47

DEAD-box helicase 47, the group of DEAD-box helicases|SSU processome

Basic information

Region (hg38): 12:12813316-12829981

Links

ENSG00000213782 ∙ NCBI:51202 ∙ OMIM:615428 ∙ HGNC:18682 ∙ Uniprot:Q9H0S4 ∙ 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 DDX47 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX47 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			37			37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	0	0

Variants in DDX47

This is a list of pathogenic ClinVar variants found in the DDX47 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-12813380-G-A		not specified	Uncertain significance (Oct 22, 2021)
12-12813387-A-G		not specified	Uncertain significance (May 29, 2024)
12-12813411-A-C		not specified	Uncertain significance (Aug 09, 2021)
12-12821211-G-A		not specified	Uncertain significance (Jul 21, 2021)
12-12821255-G-A		not specified	Uncertain significance (Jan 02, 2024)
12-12821300-C-T		not specified	Uncertain significance (Oct 29, 2024)
12-12821330-C-T		not specified	Uncertain significance (Jun 29, 2022)
12-12821702-G-A		not specified	Uncertain significance (Apr 01, 2024)
12-12821997-A-G		not specified	Uncertain significance (Feb 15, 2023)
12-12822076-A-C		not specified	Uncertain significance (Nov 27, 2023)
12-12822694-C-T		not specified	Uncertain significance (Dec 01, 2022)
12-12822721-A-G		not specified	Uncertain significance (Mar 05, 2024)
12-12823203-G-A		not specified	Uncertain significance (May 20, 2024)
12-12823249-C-T		not specified	Uncertain significance (Aug 30, 2022)
12-12823251-G-A		not specified	Uncertain significance (Mar 07, 2023)
12-12823933-A-G		not specified	Uncertain significance (Dec 03, 2024)
12-12823939-A-G		not specified	Uncertain significance (Nov 15, 2021)
12-12823948-C-G		not specified	Uncertain significance (Jan 30, 2024)
12-12823973-A-G		not specified	Uncertain significance (Jun 07, 2023)
12-12824013-T-A		not specified	Uncertain significance (Aug 20, 2024)
12-12824546-C-T		not specified	Uncertain significance (May 27, 2022)
12-12824582-C-T		not specified	Uncertain significance (Dec 22, 2023)
12-12824583-G-A		not specified	Uncertain significance (Apr 18, 2024)
12-12824594-C-A		not specified	Uncertain significance (Dec 17, 2023)
12-12824613-G-C		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX47	protein_coding	protein_coding	ENST00000358007	12	16666

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-10	0.784	125658	0	89	125747	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.395	250	268	0.932	0.0000153	2962
Missense in Polyphen		54	73.386	0.73584		806
Synonymous	0.621	88	95.7	0.919	0.00000517	915
Loss of Function	1.63	20	29.6	0.677	0.00000202	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000874	0.000874
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000326	0.000325
Middle Eastern	0.000707	0.000707
South Asian	0.000556	0.000555
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in apoptosis. May have a role in rRNA processing and mRNA splicing. Associates with pre-rRNA precursors. {ECO:0000269|PubMed:15977068, ECO:0000269|PubMed:16963496}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.979
• rvis_EVS: -0.91
• rvis_percentile_EVS: 9.96

Haploinsufficiency Scores

• pHI: 0.327
• hipred: N
• hipred_score: 0.350
• ghis: 0.484

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.514

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx47

Gene ontology

• Biological process: rRNA processing;mRNA processing;RNA splicing;extrinsic apoptotic signaling pathway via death domain receptors
• Cellular component: nucleoplasm;nucleolus;membrane
• Molecular function: RNA binding;helicase activity;protein binding;ATP binding