DDX6
Basic information
Region (hg38): 11:118747763-118791164
Previous symbols: [ "HLR2" ]
Links
Phenotypes
GenCC
Source:
- syndromic intellectual disability (Supportive), mode of inheritance: AD
- intellectual developmental disorder with impaired language and dysmorphic facies (Strong), mode of inheritance: AD
- intellectual developmental disorder with impaired language and dysmorphic facies (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Intellectual developmental disorder with impaired language and dysmorphic facies | AD | Cardiovascular | The condition can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Neurologic | 31422817 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (25 variants)
- Inborn_genetic_diseases (25 variants)
- Intellectual_developmental_disorder_with_impaired_language_and_dysmorphic_facies (22 variants)
- not_specified (7 variants)
- DDX6-related_disorder (4 variants)
- Teratoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDX6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004397.6. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | |||||
| missense | 42 | 55 | ||||
| nonsense | 4 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 5 | 4 | 49 | 7 | 0 |
Highest pathogenic variant AF is 6.8435963e-7
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DDX6 | protein_coding | protein_coding | ENST00000264018 | 12 | 41825 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000357 | 121730 | 0 | 1 | 121731 | 0.00000411 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.78 | 89 | 261 | 0.341 | 0.0000133 | 3188 |
| Missense in Polyphen | 5 | 80.843 | 0.061848 | 938 | ||
| Synonymous | 0.239 | 86 | 88.9 | 0.968 | 0.00000443 | 907 |
| Loss of Function | 4.65 | 1 | 27.2 | 0.0368 | 0.00000156 | 305 |
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 | 0.0000484 | 0.0000484 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: In the process of mRNA degradation, plays a role in mRNA decapping (PubMed:16364915). Blocks autophagy in nutrient-rich conditions by repressing the expression of ATG-related genes through degration of their transcripts (PubMed:26098573). {ECO:0000269|PubMed:16364915, ECO:0000269|PubMed:26098573}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving DDX6 may be a cause of hematopoietic tumors such as B-cell lymphomas. Translocation t(11;14)(q23;q32).;
- Pathway
- RNA degradation - Homo sapiens (human);Metabolism of RNA;EGFR1;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay
(Consensus)
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- loftool
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.58
Haploinsufficiency Scores
- pHI
- 0.571
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.513
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.964
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ddx6
- Phenotype
Zebrafish Information Network
- Gene name
- ddx6
- Affected structure
- trunk vasculature
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- viral RNA genome packaging;stem cell population maintenance;cytoplasmic mRNA processing body assembly;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;negative regulation of neuron differentiation;spermatid differentiation
- Cellular component
- heterochromatin;P-body;outer dense fiber;nucleus;nucleolus;cytoplasm;mitochondrion;cytosol;cell-cell adherens junction;cytoplasmic stress granule;membrane;RISC complex;chromatoid body;cytoplasmic ribonucleoprotein granule;perinuclear region of cytoplasm;concave side of sperm head;sperm annulus
- Molecular function
- RNA binding;RNA helicase activity;helicase activity;protein binding;ATP binding;protein domain specific binding;cadherin binding