DCTN2
dynactin subunit 2, the group of Dynactin subunits
Basic information
Region (hg38): 12:57529633-57547224
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCTN2 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 | 0 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 1 | 2 |
Variants in DCTN2
This is a list of pathogenic ClinVar variants found in the DCTN2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-57530703-T-G | Benign (May 01, 2024) | |||
| 12-57530711-C-T | not specified | Uncertain significance (Sep 26, 2024) | ||
| 12-57530751-G-C | Uncertain significance (Dec 01, 2017) | |||
| 12-57530760-G-A | not specified | Conflicting classifications of pathogenicity (Jan 01, 2024) | ||
| 12-57530768-G-T | not specified | Uncertain significance (Aug 11, 2024) | ||
| 12-57532008-C-T | Uncertain significance (Feb 01, 2024) | |||
| 12-57532803-A-G | Benign (Aug 01, 2022) | |||
| 12-57533300-C-T | Likely benign (Jul 01, 2022) | |||
| 12-57533974-G-C | not specified | Uncertain significance (Mar 28, 2024) | ||
| 12-57533976-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 12-57534050-G-A | not specified | Uncertain significance (Sep 23, 2023) | ||
| 12-57534059-T-G | not specified | Uncertain significance (Jul 14, 2021) | ||
| 12-57534313-T-A | See cases | Uncertain significance (-) | ||
| 12-57535097-G-A | Charcot-Marie-Tooth disease | Uncertain significance (Dec 14, 2015) | ||
| 12-57535502-T-A | not specified | Uncertain significance (Sep 29, 2022) | ||
| 12-57547045-C-A | Uncertain significance (Jul 01, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DCTN2 | protein_coding | protein_coding | ENST00000434715 | 16 | 17230 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.997 | 0.00347 | 124635 | 0 | 3 | 124638 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.90 | 139 | 218 | 0.637 | 0.0000116 | 2607 |
| Missense in Polyphen | 29 | 67.894 | 0.42714 | 796 | ||
| Synonymous | 0.570 | 76 | 82.6 | 0.920 | 0.00000425 | 798 |
| Loss of Function | 4.31 | 2 | 25.5 | 0.0784 | 0.00000108 | 321 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000293 | 0.0000293 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000928 | 0.0000464 |
| European (Non-Finnish) | 0.00000887 | 0.00000885 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Modulates cytoplasmic dynein binding to an organelle, and plays a role in prometaphase chromosome alignment and spindle organization during mitosis. Involved in anchoring microtubules to centrosomes. May play a role in synapse formation during brain development.;
- Pathway
- Vasopressin-regulated water reabsorption - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Vesicle-mediated transport;lissencephaly gene (lis1) in neuronal migration and development;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Regulation of PLK1 Activity at G2/M Transition;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;COPI-mediated anterograde transport;M Phase;Cell Cycle;ER to Golgi Anterograde Transport;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Intra-Golgi and retrograde Golgi-to-ER traffic;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.347
Intolerance Scores
- loftool
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.66
Haploinsufficiency Scores
- pHI
- 0.709
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.520
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.710
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dctn2
- 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
- dctn2
- Affected structure
- neuromast hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- G2/M transition of mitotic cell cycle;mitotic cell cycle;endoplasmic reticulum to Golgi vesicle-mediated transport;mitotic spindle organization;cell population proliferation;regulation of G2/M transition of mitotic cell cycle;antigen processing and presentation of exogenous peptide antigen via MHC class II;melanosome transport;protein localization to centrosome;ciliary basal body-plasma membrane docking
- Cellular component
- kinetochore;cytoplasm;centrosome;cytosol;dynactin complex;microtubule;membrane;dynein complex;growth cone;vesicle;extracellular exosome
- Molecular function
- motor activity;protein binding;protein kinase binding;spectrin binding;identical protein binding