ECT2
epithelial cell transforming 2, the group of Dbl family Rho GEFs
Basic information
Region (hg38): 3:172750682-172821474
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 ECT2 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 | 1 | |||||
| missense | 30 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 30 | 0 | 1 |
Variants in ECT2
This is a list of pathogenic ClinVar variants found in the ECT2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-172754634-T-G | not specified | Uncertain significance (Jun 22, 2024) | ||
| 3-172757001-G-A | not specified | Uncertain significance (Sep 08, 2024) | ||
| 3-172758990-T-G | not specified | Uncertain significance (Oct 29, 2021) | ||
| 3-172759014-C-T | not specified | Uncertain significance (Oct 31, 2022) | ||
| 3-172759020-T-C | not specified | Uncertain significance (Aug 02, 2023) | ||
| 3-172760160-G-T | not specified | Uncertain significance (Oct 26, 2022) | ||
| 3-172760208-T-G | not specified | Uncertain significance (Jul 19, 2022) | ||
| 3-172761635-T-A | not specified | Uncertain significance (Jul 11, 2023) | ||
| 3-172762455-T-G | not specified | Uncertain significance (Apr 09, 2024) | ||
| 3-172762458-A-T | not specified | Uncertain significance (Aug 05, 2024) | ||
| 3-172762732-C-G | not specified | Uncertain significance (Dec 10, 2024) | ||
| 3-172762750-A-G | not specified | Uncertain significance (Dec 19, 2023) | ||
| 3-172762773-A-T | not specified | Uncertain significance (May 11, 2022) | ||
| 3-172764311-A-G | not specified | Uncertain significance (Apr 17, 2023) | ||
| 3-172764351-G-A | not specified | Uncertain significance (Dec 11, 2023) | ||
| 3-172764365-A-G | not specified | Uncertain significance (Oct 20, 2023) | ||
| 3-172764383-A-G | not specified | Uncertain significance (Feb 17, 2022) | ||
| 3-172764395-G-A | not specified | Likely benign (Oct 07, 2024) | ||
| 3-172764413-C-T | not specified | Uncertain significance (Jun 06, 2023) | ||
| 3-172764446-A-G | not specified | Uncertain significance (Jun 22, 2023) | ||
| 3-172764488-A-G | not specified | Uncertain significance (Mar 21, 2024) | ||
| 3-172764495-A-G | not specified | Uncertain significance (Jun 06, 2023) | ||
| 3-172769064-A-C | not specified | Uncertain significance (Oct 26, 2021) | ||
| 3-172769066-T-C | not specified | Uncertain significance (Nov 15, 2024) | ||
| 3-172769103-C-G | not specified | Uncertain significance (Aug 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ECT2 | protein_coding | protein_coding | ENST00000392692 | 24 | 70793 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 8.08e-10 | 1.00 | 125695 | 0 | 52 | 125747 | 0.000207 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.74 | 360 | 466 | 0.773 | 0.0000233 | 6012 |
| Missense in Polyphen | 114 | 195.14 | 0.58419 | 2442 | ||
| Synonymous | -0.680 | 161 | 150 | 1.07 | 0.00000712 | 1684 |
| Loss of Function | 3.54 | 24 | 51.4 | 0.467 | 0.00000285 | 657 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000461 | 0.000431 |
| Ashkenazi Jewish | 0.000103 | 0.0000992 |
| East Asian | 0.000111 | 0.000109 |
| Finnish | 0.000416 | 0.000416 |
| European (Non-Finnish) | 0.000234 | 0.000229 |
| Middle Eastern | 0.000111 | 0.000109 |
| South Asian | 0.000236 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Guanine nucleotide exchange factor (GEF) that catalyzes the exchange of GDP for GTP. Promotes guanine nucleotide exchange on the Rho family members of small GTPases, like RHOA, RHOC, RAC1 and CDC42. Required for signal transduction pathways involved in the regulation of cytokinesis. Component of the centralspindlin complex that serves as a microtubule-dependent and Rho-mediated signaling required for the myosin contractile ring formation during the cell cycle cytokinesis. Regulates the translocation of RHOA from the central spindle to the equatorial region. Plays a role in the control of mitotic spindle assembly; regulates the activation of CDC42 in metaphase for the process of spindle fibers attachment to kinetochores before chromosome congression. Involved in the regulation of epithelial cell polarity; participates in the formation of epithelial tight junctions in a polarity complex PARD3-PARD6-protein kinase PRKCQ-dependent manner. Plays a role in the regulation of neurite outgrowth. Inhibits phenobarbital (PB)- induced NR1I3 nuclear translocation. Stimulates the activity of RAC1 through its association with the oncogenic PARD6A-PRKCI complex in cancer cells, thereby acting to coordinately drive tumor cell proliferation and invasion. Also stimulates genotoxic stress-induced RHOB activity in breast cancer cells leading to their cell death. {ECO:0000269|PubMed:10579713, ECO:0000269|PubMed:14645260, ECO:0000269|PubMed:15254234, ECO:0000269|PubMed:15545273, ECO:0000269|PubMed:15642749, ECO:0000269|PubMed:16103226, ECO:0000269|PubMed:16170345, ECO:0000269|PubMed:16236794, ECO:0000269|PubMed:16495035, ECO:0000269|PubMed:19129481, ECO:0000269|PubMed:19468300, ECO:0000269|PubMed:19617897, ECO:0000269|PubMed:21189248, ECO:0000269|PubMed:21373644}.;
- Pathway
- Gastric Cancer Network 1;Signaling by GPCR;Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases;NRAGE signals death through JNK;Death Receptor Signalling;p75 NTR receptor-mediated signalling;G alpha (12/13) signalling events;GPCR downstream signalling;PLK1 signaling events;Cell death signalling via NRAGE, NRIF and NADE;Regulation of RhoA activity
(Consensus)
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- loftool
- 0.699
- rvis_EVS
- -0.87
- rvis_percentile_EVS
- 10.8
Haploinsufficiency Scores
- pHI
- 0.507
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.690
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.850
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ect2
- 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype;
Zebrafish Information Network
- Gene name
- ect2
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- curved dorsal
Gene ontology
- Biological process
- mitotic cytokinesis;cell morphogenesis;G protein-coupled receptor signaling pathway;protein transport;activation of protein kinase activity;positive regulation of cytokinesis;regulation of Rho protein signal transduction;intracellular signal transduction;positive regulation of protein import into nucleus;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;positive regulation of GTPase activity;positive regulation of neuron differentiation;regulation of protein kinase activity;regulation of small GTPase mediated signal transduction;protein homooligomerization;regulation of attachment of spindle microtubules to kinetochore;cellular response to hydrogen peroxide;bicellular tight junction assembly;cellular response to calcium ion;cellular response to ionizing radiation;activation of GTPase activity;regulation of cytokinesis, actomyosin contractile ring assembly
- Cellular component
- nucleus;cytoplasm;cytosol;cell-cell junction;bicellular tight junction;midbody;cleavage furrow;mitotic spindle;centralspindlin complex
- Molecular function
- guanyl-nucleotide exchange factor activity;Rho guanyl-nucleotide exchange factor activity;GTPase activator activity;protein binding;protein homodimerization activity