DDX23

DEAD-box helicase 23, the group of DEAD-box helicases|U5 small nuclear ribonucleoprotein

Basic information

Region (hg38): 12:48829756-48852842

Links

ENSG00000174243 ∙ NCBI:9416 ∙ OMIM:612172 ∙ HGNC:17347 ∙ Uniprot:Q9BUQ8 ∙ 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 DDX23 gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX23 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	1
missense	1	3	53	2		59
nonsense						0
start loss						0
frameshift			1			1
inframe indel	1		3			4
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	2	3	58	2	1

Variants in DDX23

This is a list of pathogenic ClinVar variants found in the DDX23 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-48830495-G-A		Congenital bilateral perisylvian syndrome	Likely pathogenic (Dec 01, 2023)
12-48830526-C-G			Uncertain significance (Mar 03, 2023)
12-48830604-G-T		Inborn genetic diseases	Uncertain significance (Jun 10, 2024)
12-48830630-G-A		Inborn genetic diseases	Uncertain significance (Mar 23, 2022)
12-48830648-C-T			Uncertain significance (May 01, 2024)
12-48830668-G-A			Conflicting classifications of pathogenicity (Nov 10, 2020)
12-48831190-G-C		DDX23-related disorder	Uncertain significance (Jan 18, 2024)
12-48831199-T-C		Inborn genetic diseases	Uncertain significance (May 11, 2022)
12-48831248-CTTGAGG-C			Pathogenic (Oct 28, 2022)
12-48831250-T-C			Likely pathogenic (Oct 28, 2022)
12-48831253-G-A		Inborn genetic diseases	Uncertain significance (May 25, 2022)
12-48831312-T-C		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
12-48832465-G-A		Neurodevelopmental disorder	Likely pathogenic (Sep 02, 2022)
12-48832491-A-C		Fetal growth restriction;Motor delay;Failure to thrive;Abnormal facial shape	Conflicting classifications of pathogenicity (Jul 20, 2021)
12-48832501-C-T			Uncertain significance (May 01, 2024)
12-48832565-C-A			Uncertain significance (Aug 10, 2020)
12-48833358-G-T			Pathogenic (Apr 17, 2024)
12-48833434-T-A			Uncertain significance (Aug 10, 2020)
12-48833495-A-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2023)
12-48833497-C-T		Intellectual disability	Uncertain significance (Aug 10, 2020)
12-48833498-G-A			Uncertain significance (Aug 10, 2020)
12-48834399-G-A		Inborn genetic diseases	Uncertain significance (May 11, 2022)
12-48834494-G-C		Inborn genetic diseases	Uncertain significance (Aug 13, 2021)
12-48836142-G-A		DDX23-related Neurodevelopmental disorder	Uncertain significance (Jul 20, 2022)
12-48836190-CCAGTCT-C			Uncertain significance (Apr 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX23	protein_coding	protein_coding	ENST00000308025	16	23079

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.542	0.458	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.62	218	513	0.425	0.0000353	5365
Missense in Polyphen		22	143.64	0.15316		1654
Synonymous	0.901	156	171	0.912	0.00000878	1604
Loss of Function	5.15	11	50.5	0.218	0.00000378	504

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation. {ECO:0000269|PubMed:18425142}.
• Pathway: Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing - Minor Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.135

Intolerance Scores

• loftool: 0.445
• rvis_EVS: -0.98
• rvis_percentile_EVS: 8.75

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.694
• ghis: 0.580

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx23

Gene ontology

• Biological process: cis assembly of pre-catalytic spliceosome;RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleus;nucleoplasm;U5 snRNP;nucleolus;extracellular exosome;catalytic step 2 spliceosome
• Molecular function: RNA binding;ATP-dependent RNA helicase activity;protein binding;ATP binding;ATP-dependent helicase activity