DDX39B

DExD-box helicase 39B, the group of DEAD-box helicases|Spliceosomal E complex|Transcription and export complex 1 subunits|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 6:31530218-31542448

Previous symbols: [ "BAT1" ]

Links

ENSG00000198563 ∙ NCBI:7919 ∙ OMIM:142560 ∙ HGNC:13917 ∙ Uniprot:Q13838 ∙ 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 DDX39B gene.

• Neurodevelopmental disorder (5 variants)
• Inborn genetic diseases (4 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX39B 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					2	2
non coding						0
Total	0	0	9	0	1

Variants in DDX39B

This is a list of pathogenic ClinVar variants found in the DDX39B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31531137-T-C			Benign (Dec 31, 2019)
6-31532784-T-C		not specified	Uncertain significance (Aug 17, 2022)
6-31536546-A-C		not specified	Uncertain significance (Dec 06, 2023)
6-31536684-C-A		Neurodevelopmental disorder	Uncertain significance (Mar 01, 2023)
6-31536689-G-A			Benign (Jan 09, 2019)
6-31538827-C-T		Neurodevelopmental disorder	Uncertain significance (Mar 01, 2023)
6-31539211-C-T		Neurodevelopmental disorder	Uncertain significance (Mar 01, 2023)
6-31539278-A-G			Benign (Jun 15, 2018)
6-31540352-C-A		not specified	Uncertain significance (Jan 04, 2022)
6-31540401-G-C		Neurodevelopmental disorder	Uncertain significance (Mar 01, 2023)
6-31540424-C-A		Neurodevelopmental disorder	Uncertain significance (Mar 01, 2023)
6-31540441-G-A		not specified	Uncertain significance (Dec 31, 2023)
6-31540442-C-G		not specified	Uncertain significance (Jun 16, 2023)
6-31540468-G-C		not specified	Uncertain significance (Nov 07, 2022)
6-31540469-C-G		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX39B	protein_coding	protein_coding	ENST00000396172	10	12230

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00275	125689	0	1	125690	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.56	55	264	0.209	0.0000157	2853
Missense in Polyphen		9	65.633	0.13713		733
Synonymous	1.38	78	95.1	0.820	0.00000517	803
Loss of Function	4.12	1	21.7	0.0460	0.00000128	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in nuclear export of spliced and unspliced mRNA. Assembling component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription- independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. May undergo several rounds of ATP hydrolysis during assembly of TREX to drive subsequent loading of components such as ALYREF/THOC and CHTOP onto mRNA. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. Also associates with pre-mRNA independent of ALYREF/THOC4 and the THO complex. Involved in the nuclear export of intronless mRNA; the ATP-bound form is proposed to recruit export adapter ALYREF/THOC4 to intronless mRNA; its ATPase activity is cooperatively stimulated by RNA and ALYREF/THOC4 and ATP hydrolysis is thought to trigger the dissociation from RNA to allow the association of ALYREF/THOC4 and the NXF1-NXT1 heterodimer. Involved in transcription elongation and genome stability.
• Pathway: Influenza A - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);Spliceosome - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.600
• hipred: Y
• hipred_score: 0.655
• ghis: 0.628

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddx39b

Gene ontology

• Biological process: spliceosomal complex assembly;mRNA splicing, via spliceosome;liver development;RNA export from nucleus;mRNA export from nucleus;RNA splicing;RNA secondary structure unwinding;mRNA 3'-end processing;positive regulation of DNA-templated transcription, elongation;positive regulation of translation;viral mRNA export from host cell nucleus;positive regulation of cell growth involved in cardiac muscle cell development;positive regulation of vascular smooth muscle cell proliferation;negative regulation of DNA damage checkpoint;positive regulation of DNA biosynthetic process
• Cellular component: transcription export complex;nucleus;nucleoplasm;spliceosomal complex;U4 snRNP;U6 snRNP;cytoplasm;nuclear matrix;nuclear speck
• Molecular function: RNA binding;ATP-dependent RNA helicase activity;protein binding;ATP binding;RNA-dependent ATPase activity;ATPase activity;U6 snRNA binding;U4 snRNA binding;identical protein binding;ATP-dependent protein binding;protein-containing complex binding