RTKN
Basic information
Region (hg38): 2:74425834-74442422
Links
Phenotypes
GenCC
Source:
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 RTKN 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 | 43 | 44 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 43 | 0 | 1 |
Variants in RTKN
This is a list of pathogenic ClinVar variants found in the RTKN region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-74426271-G-A | not specified | Uncertain significance (Oct 13, 2023) | ||
2-74426310-C-T | not specified | Uncertain significance (Jan 23, 2024) | ||
2-74426325-G-C | not specified | Uncertain significance (Aug 01, 2022) | ||
2-74426325-G-T | not specified | Uncertain significance (Dec 06, 2022) | ||
2-74426338-G-A | not specified | Uncertain significance (Apr 19, 2023) | ||
2-74426370-T-A | not specified | Uncertain significance (Feb 27, 2023) | ||
2-74426517-C-A | not specified | Uncertain significance (Aug 16, 2022) | ||
2-74426524-G-A | not specified | Uncertain significance (Jun 01, 2023) | ||
2-74426535-A-G | not specified | Uncertain significance (Dec 28, 2022) | ||
2-74426536-T-C | not specified | Uncertain significance (May 14, 2024) | ||
2-74426572-T-C | not specified | Uncertain significance (Apr 25, 2023) | ||
2-74427462-C-T | not specified | Uncertain significance (Jul 25, 2023) | ||
2-74427478-G-A | not specified | Uncertain significance (Feb 07, 2023) | ||
2-74427549-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
2-74427561-T-G | not specified | Uncertain significance (Apr 20, 2024) | ||
2-74427580-G-A | not specified | Uncertain significance (Mar 25, 2024) | ||
2-74428327-G-A | not specified | Uncertain significance (Mar 11, 2024) | ||
2-74428336-A-C | not specified | Uncertain significance (Jun 17, 2024) | ||
2-74428372-C-G | not specified | Uncertain significance (Dec 07, 2021) | ||
2-74428631-C-G | Uncertain significance (Aug 01, 2018) | |||
2-74428692-C-T | not specified | Uncertain significance (May 02, 2024) | ||
2-74428693-G-C | not specified | Uncertain significance (Apr 07, 2023) | ||
2-74428702-C-T | not specified | Uncertain significance (Aug 15, 2023) | ||
2-74428877-C-T | not specified | Uncertain significance (Feb 28, 2024) | ||
2-74428934-C-T | not specified | Uncertain significance (Dec 26, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RTKN | protein_coding | protein_coding | ENST00000272430 | 12 | 16587 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000270 | 0.996 | 125693 | 0 | 55 | 125748 | 0.000219 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.02 | 296 | 350 | 0.846 | 0.0000210 | 3617 |
Missense in Polyphen | 97 | 129.59 | 0.74851 | 1332 | ||
Synonymous | 0.369 | 130 | 135 | 0.960 | 0.00000732 | 1197 |
Loss of Function | 2.58 | 14 | 29.0 | 0.483 | 0.00000156 | 289 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000887 | 0.000883 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.0000464 | 0.0000462 |
European (Non-Finnish) | 0.000221 | 0.000220 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000360 | 0.000359 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates Rho signaling to activate NF-kappa-B and may confer increased resistance to apoptosis to cells in gastric tumorigenesis. May play a novel role in the organization of septin structures. {ECO:0000269|PubMed:10940294, ECO:0000269|PubMed:15480428, ECO:0000269|PubMed:16007136}.;
- Pathway
- G13 Signaling Pathway;Signal Transduction;Alpha6Beta4Integrin;RHO GTPases Activate Rhotekin and Rhophilins;RHO GTPase Effectors;Signaling by Rho GTPases
(Consensus)
Recessive Scores
- pRec
- 0.103
Intolerance Scores
- loftool
- 0.935
- rvis_EVS
- -0.84
- rvis_percentile_EVS
- 11.36
Haploinsufficiency Scores
- pHI
- 0.164
- hipred
- Y
- hipred_score
- 0.598
- ghis
- 0.611
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.759
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rtkn
- Phenotype
Gene ontology
- Biological process
- mitotic cytokinesis;actomyosin contractile ring assembly;apoptotic process;signal transduction;Rho protein signal transduction;cortical cytoskeleton organization;septin ring organization;negative regulation of GTPase activity;regulation of apoptotic process;protein localization to mitotic actomyosin contractile ring
- Cellular component
- cellular_component;actomyosin contractile ring;cytosol
- Molecular function
- GTPase inhibitor activity;protein binding;GTP binding;GTP-Rho binding