DDX39A

DExD-box helicase 39A, the group of DEAD-box helicases|Transcription and export complex 1 subunits

Basic information

Region (hg38): 19:14408798-14419383

Previous symbols: [ "DDX39" ]

Links

ENSG00000123136 ∙ NCBI:10212 ∙ OMIM:619906 ∙ HGNC:17821 ∙ Uniprot:O00148 ∙ 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 DDX39A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX39A 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	14			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	14	0	1

Variants in DDX39A

This is a list of pathogenic ClinVar variants found in the DDX39A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-14408950-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-14409052-C-T		not specified	Uncertain significance (Jun 06, 2023)
19-14409128-G-T		not specified	Uncertain significance (Jun 28, 2024)
19-14409567-C-T		not specified	Uncertain significance (Dec 07, 2024)
19-14409570-T-C		not specified	Uncertain significance (Feb 28, 2023)
19-14409575-G-A		not specified	Uncertain significance (Dec 21, 2023)
19-14409611-A-G		not specified	Uncertain significance (Oct 29, 2024)
19-14409769-A-T		not specified	Uncertain significance (Nov 23, 2024)
19-14409783-G-A		not specified	Uncertain significance (Jun 02, 2023)
19-14410242-G-C		not specified	Uncertain significance (Jun 01, 2023)
19-14410271-A-T			Likely pathogenic (-)
19-14410311-T-C		not specified	Uncertain significance (Dec 18, 2023)
19-14410325-C-T		not specified	Uncertain significance (Dec 22, 2023)
19-14410996-C-A		not specified	Uncertain significance (Feb 13, 2024)
19-14411063-C-T		not specified	Uncertain significance (Jun 25, 2024)
19-14411112-A-G		not specified	Uncertain significance (Nov 06, 2023)
19-14413109-A-G		not specified	Uncertain significance (Jun 29, 2022)
19-14413149-C-A		not specified	Uncertain significance (Aug 12, 2021)
19-14413176-T-C			Benign (Mar 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDX39A	protein_coding	protein_coding	ENST00000242776	10	10562

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.602	0.398	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.94	142	280	0.507	0.0000185	2832
Missense in Polyphen		17	67.071	0.25346		721
Synonymous	0.0118	114	114	0.999	0.00000815	798
Loss of Function	3.35	4	20.3	0.197	9.48e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform 1: Involved in pre-mRNA splicing. Required for the export of mRNA out of the nucleus. {ECO:0000269|PubMed:15047853, ECO:0000269|PubMed:17548965}.
• Pathway: 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)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.59

Haploinsufficiency Scores

• pHI: 0.193
• hipred: Y
• hipred_score: 0.685
• ghis: 0.661

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• 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: Ddx39

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA export from nucleus;mRNA export from nucleus;mRNA 3'-end processing
• Cellular component: nucleus;nucleoplasm;cytoplasm;membrane;nuclear speck
• Molecular function: RNA binding;helicase activity;protein binding;ATP binding;ATPase activity;identical protein binding