DYNC1LI1
dynein cytoplasmic 1 light intermediate chain 1, the group of Dynein 1 complex subunits
Basic information
Region (hg38): 3:32525974-32570858
Previous symbols: [ "DNCLI1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (51 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DYNC1LI1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016141.4. 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 | 0 | |||||
| missense | 51 | 52 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 51 | 1 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DYNC1LI1 | protein_coding | protein_coding | ENST00000273130 | 13 | 44904 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.963 | 0.0365 | 125729 | 0 | 17 | 125746 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 221 | 269 | 0.822 | 0.0000125 | 3361 |
| Missense in Polyphen | 47 | 72.026 | 0.65254 | 950 | ||
| Synonymous | 0.657 | 94 | 102 | 0.917 | 0.00000521 | 1039 |
| Loss of Function | 4.20 | 4 | 27.9 | 0.143 | 0.00000142 | 360 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000116 | 0.000109 |
| Finnish | 0.0000499 | 0.0000462 |
| European (Non-Finnish) | 0.000108 | 0.000105 |
| Middle Eastern | 0.000116 | 0.000109 |
| South Asian | 0.0000821 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. Cytoplasmic dynein 1 acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. May play a role in binding dynein to membranous organelles or chromosomes. Probably involved in the microtubule-dependent transport of pericentrin. Is required for progress through the spindle assembly checkpoint. The phosphorylated form appears to be involved in the selective removal of MAD1L1 and MAD1L2 but not BUB1B from kinetochores. {ECO:0000269|PubMed:19229290}.;
- Pathway
- Salmonella infection - Homo sapiens (human);Phagosome - Homo sapiens (human);Vasopressin-regulated water reabsorption - Homo sapiens (human);Neutrophil degranulation;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Innate Immune System;Immune System;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Mitotic Prometaphase;COPI-mediated anterograde transport;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;ER to Golgi Anterograde Transport;Cell Cycle, Mitotic;Intra-Golgi and retrograde Golgi-to-ER traffic
(Consensus)
Intolerance Scores
- loftool
- 0.319
- rvis_EVS
- 0.51
- rvis_percentile_EVS
- 80.2
Haploinsufficiency Scores
- pHI
- 0.810
- hipred
- Y
- hipred_score
- 0.640
- ghis
- 0.489
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.913
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dync1li1
- Phenotype
- cellular phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- dync1li1
- Affected structure
- cell
- Phenotype tag
- abnormal
- Phenotype quality
- broken
Gene ontology
- Biological process
- microtubule cytoskeleton organization;endoplasmic reticulum to Golgi vesicle-mediated transport;microtubule-based movement;cell cycle;viral process;antigen processing and presentation of exogenous peptide antigen via MHC class II;neutrophil degranulation;cell division;positive regulation of mitotic cell cycle spindle assembly checkpoint
- Cellular component
- kinetochore;condensed chromosome kinetochore;spindle pole;centrosome;cytosol;cytoplasmic dynein complex;microtubule;plasma membrane;membrane;secretory granule membrane;ficolin-1-rich granule membrane
- Molecular function
- RNA binding;microtubule motor activity;protein binding;ATP binding;GTP binding;GDP binding;dynein heavy chain binding