TPX2
TPX2 microtubule nucleation factor
Basic information
Region (hg38): 20:31739271-31801805
Previous symbols: [ "C20orf2", "C20orf1" ]
Links
Phenotypes
GenCC
Source:
- Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (77 variants)
- not_provided (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TPX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012112.5. 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 | 5 | |||||
| missense | 73 | 78 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 73 | 7 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TPX2 | protein_coding | protein_coding | ENST00000300403 | 16 | 62535 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000185 | 125731 | 0 | 14 | 125745 | 0.0000557 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.490 | 355 | 382 | 0.929 | 0.0000189 | 4883 |
| Missense in Polyphen | 79 | 112.05 | 0.70502 | 1522 | ||
| Synonymous | 0.302 | 130 | 134 | 0.967 | 0.00000656 | 1381 |
| Loss of Function | 5.45 | 4 | 42.2 | 0.0949 | 0.00000235 | 525 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000148 | 0.000148 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000465 | 0.0000462 |
| European (Non-Finnish) | 0.0000620 | 0.0000615 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Spindle assembly factor required for normal assembly of mitotic spindles. Required for normal assembly of microtubules during apoptosis. Required for chromatin and/or kinetochore dependent microtubule nucleation. Mediates AURKA localization to spindle microtubules (PubMed:18663142, PubMed:19208764). Activates AURKA by promoting its autophosphorylation at 'Thr-288' and protects this residue against dephosphorylation (PubMed:18663142, PubMed:19208764). TPX2 is inactivated upon binding to importin- alpha (PubMed:26165940). At the onset of mitosis, GOLGA2 interacts with importin-alpha, liberating TPX2 from importin-alpha, allowing TPX2 to activates AURKA kinase and stimulates local microtubule nucleation (PubMed:26165940). {ECO:0000269|PubMed:18663142, ECO:0000269|PubMed:19208764, ECO:0000269|PubMed:26165940}.;
- Pathway
- Gastric Cancer Network 1;Gene expression (Transcription);role of ran in mitotic spindle regulation;Generic Transcription Pathway;RNA Polymerase II Transcription;Aurora A signaling;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle;Cell Cycle, Mitotic;PLK1 signaling events
(Consensus)
Recessive Scores
- pRec
- 0.0968
Intolerance Scores
- loftool
- 0.0807
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.88
Haploinsufficiency Scores
- pHI
- 0.928
- hipred
- Y
- hipred_score
- 0.792
- ghis
- 0.678
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.561
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tpx2
- 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); immune system phenotype; embryo phenotype; neoplasm; 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); hematopoietic system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- mitotic cell cycle;apoptotic process;cell population proliferation;regulation of G2/M transition of mitotic cell cycle;activation of protein kinase activity;cell division;regulation of mitotic spindle organization;mitotic spindle assembly;regulation of signal transduction by p53 class mediator
- Cellular component
- spindle pole;nucleus;nucleoplasm;microtubule organizing center;spindle;cytosol;microtubule;microtubule cytoskeleton;axon hillock;intercellular bridge;mitotic spindle
- Molecular function
- protein binding;ATP binding;GTP binding;protein kinase binding;importin-alpha family protein binding