DDX41
Basic information
Region (hg38): 5:177511577-177516961
Links
Phenotypes
GenCC
Source:
- DDX41-related hematologic malignancy predisposition syndrome (Strong), mode of inheritance: AD
- DDX41-related hematologic malignancy predisposition syndrome (Strong), mode of inheritance: AD
- DDX41-related hematologic malignancy predisposition syndrome (Definitive), mode of inheritance: AD
- DDX41-related hematologic malignancy predisposition syndrome (Definitive), mode of inheritance: AD
- DDX41-related hematologic malignancy predisposition syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Familial myeloproliferative/lymphoproliferative neoplasms, multiple types, susceptibility to | AD | Oncologic | Among other findings, individuals have been described with hematologic malignancies, and awareness may allow early detection and management | Allergy/Immunology/Infectious; Oncologic | 25920683; 26712909 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (27 variants)
- DDX41-related hematologic malignancy predisposition syndrome (13 variants)
- DDX41-related disorder (5 variants)
- Acute myeloid leukemia (2 variants)
- Inherited acute myeloid leukemia (1 variants)
- Myelodysplasia (1 variants)
- Myelodysplastic syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX41 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 | 11 | 106 | 118 | |||
missense | 232 | 244 | ||||
nonsense | 11 | 17 | ||||
start loss | 2 | |||||
frameshift | 17 | 12 | 30 | |||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 4 | |||||
splice region | 1 | 22 | 19 | 3 | 45 | |
non coding | 18 | 80 | 20 | 123 | ||
Total | 30 | 34 | 263 | 190 | 22 |
Highest pathogenic variant AF is 0.0000394
Variants in DDX41
This is a list of pathogenic ClinVar variants found in the DDX41 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
5-177511597-T-C | not specified | Uncertain significance (Apr 20, 2020) | ||
5-177511610-G-C | not specified | Uncertain significance (Apr 03, 2018) | ||
5-177511694-G-A | Likely benign (Mar 27, 2019) | |||
5-177511717-G-A | not specified | Benign/Likely benign (Jun 21, 2019) | ||
5-177511728-A-G | not specified | Uncertain significance (Oct 24, 2019) | ||
5-177511788-G-A | not specified • DDX41-related disorder | Benign/Likely benign (Apr 22, 2022) | ||
5-177511790-C-T | DDX41-related disorder | Likely benign (Jan 30, 2023) | ||
5-177511792-C-T | Uncertain significance (Dec 04, 2022) | |||
5-177511793-A-T | Uncertain significance (Apr 08, 2024) | |||
5-177511806-G-A | Likely benign (Sep 22, 2023) | |||
5-177511808-T-C | DDX41-related hematologic malignancy predisposition syndrome | Uncertain significance (Aug 09, 2024) | ||
5-177511810-T-C | DDX41-related disorder • DDX41-related hematologic malignancy predisposition syndrome | Uncertain significance (Apr 16, 2024) | ||
5-177511817-G-A | Likely benign (Dec 10, 2024) | |||
5-177511824-C-T | Likely benign (Oct 09, 2023) | |||
5-177511832-C-T | Uncertain significance (Sep 21, 2022) | |||
5-177511833-G-A | not specified • Inborn genetic diseases | Likely benign (Dec 08, 2024) | ||
5-177511848-C-CATAGCAACATATG | Uncertain significance (Apr 07, 2024) | |||
5-177511866-G-A | Likely benign (Jan 20, 2025) | |||
5-177511871-T-C | Uncertain significance (Sep 23, 2022) | |||
5-177511901-C-A | DDX41-related hematologic malignancy predisposition syndrome | Uncertain significance (Dec 22, 2020) | ||
5-177511905-G-A | Inborn genetic diseases | Likely benign (Nov 18, 2024) | ||
5-177511920-G-A | Inborn genetic diseases | Likely benign (Jan 31, 2025) | ||
5-177511921-C-T | Uncertain significance (Oct 28, 2024) | |||
5-177511930-G-A | Inborn genetic diseases | Uncertain significance (Jan 20, 2025) | ||
5-177511930-G-T | Uncertain significance (Sep 27, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DDX41 | protein_coding | protein_coding | ENST00000507955 | 17 | 5893 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
5.59e-8 | 0.998 | 125659 | 0 | 89 | 125748 | 0.000354 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.28 | 272 | 401 | 0.679 | 0.0000253 | 4056 |
Missense in Polyphen | 67 | 112.95 | 0.59317 | 1189 | ||
Synonymous | -2.77 | 199 | 155 | 1.28 | 0.0000102 | 1201 |
Loss of Function | 2.81 | 18 | 36.3 | 0.496 | 0.00000190 | 408 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000547 | 0.000547 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000544 | 0.000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000481 | 0.000466 |
Middle Eastern | 0.000544 | 0.000544 |
South Asian | 0.000327 | 0.000327 |
Other | 0.000816 | 0.000815 |
dbNSFP
Source:
- Function
- FUNCTION: Probable ATP-dependent RNA helicase. Is required during post-transcriptional gene expression. May be involved in pre-mRNA splicing. {ECO:0000269|PubMed:25920683}.;
- Disease
- DISEASE: Myeloproliferative/lymphoproliferative neoplasms, familial (MPLPF) [MIM:616871]: A familial cancer predisposition syndrome with incomplete penetrance, characterized by increased susceptibility to myeloid neoplasms and rarely to lymphoid malignancies. MPLPF inheritance is autosomal dominant. {ECO:0000269|PubMed:25920683, ECO:0000269|PubMed:26712909}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- STING mediated induction of host immune responses;Regulation of innate immune responses to cytosolic DNA;Innate Immune System;Immune System;IRF3-mediated induction of type I IFN;Cytosolic sensors of pathogen-associated DNA
(Consensus)
Recessive Scores
- pRec
- 0.258
Intolerance Scores
- loftool
- rvis_EVS
- -1.09
- rvis_percentile_EVS
- 7.05
Haploinsufficiency Scores
- pHI
- 0.225
- hipred
- Y
- hipred_score
- 0.603
- ghis
- 0.638
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.733
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ddx41
- Phenotype
- 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
- ddx41
- Affected structure
- positive regulation of NIK/NF-kappaB signaling
- Phenotype tag
- abnormal
- Phenotype quality
- disrupted
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;apoptotic process;cell population proliferation;cell differentiation;positive regulation of type I interferon production;cellular response to interferon-beta;positive regulation of transcription by RNA polymerase II;defense response to virus
- Cellular component
- nucleus;spliceosomal complex;endoplasmic reticulum;cytosol;membrane;catalytic step 2 spliceosome
- Molecular function
- DNA binding;RNA binding;helicase activity;protein binding;ATP binding;metal ion binding