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GeneBe

RTKN

rhotekin, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 2:74425834-74442422

Links

ENSG00000114993NCBI:6242OMIM:602288HGNC:10466Uniprot:Q9BST9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RTKN gene.

  • Inborn genetic diseases (33 variants)
  • not provided (2 variants)

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
34
clinvar
1
clinvar
35
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 34 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)3156851
2-74426310-C-T not specified Uncertain significance (Jan 23, 2024)3156850
2-74426325-G-C not specified Uncertain significance (Aug 01, 2022)2304409
2-74426325-G-T not specified Uncertain significance (Dec 06, 2022)2333750
2-74426338-G-A not specified Uncertain significance (Apr 19, 2023)2569875
2-74426370-T-A not specified Uncertain significance (Feb 27, 2023)2489742
2-74426517-C-A not specified Uncertain significance (Aug 16, 2022)2209434
2-74426524-G-A not specified Uncertain significance (Jun 01, 2023)2555192
2-74426535-A-G not specified Uncertain significance (Dec 28, 2022)2340040
2-74426572-T-C not specified Uncertain significance (Apr 25, 2023)2511836
2-74427462-C-T not specified Uncertain significance (Jul 25, 2023)2613561
2-74427478-G-A not specified Uncertain significance (Feb 07, 2023)2481512
2-74427549-C-T not specified Uncertain significance (Oct 12, 2021)2254205
2-74428327-G-A not specified Uncertain significance (Mar 11, 2024)3156849
2-74428372-C-G not specified Uncertain significance (Dec 07, 2021)2401295
2-74428631-C-G Uncertain significance (Aug 01, 2018)808782
2-74428693-G-C not specified Uncertain significance (Apr 07, 2023)2569951
2-74428702-C-T not specified Uncertain significance (Aug 15, 2023)2592761
2-74428877-C-T not specified Uncertain significance (Feb 28, 2024)3156857
2-74428934-C-T not specified Uncertain significance (Dec 26, 2023)3156856
2-74428935-G-A not specified Uncertain significance (May 22, 2023)2549369
2-74429895-G-A not specified Uncertain significance (Mar 11, 2022)2412029
2-74429900-C-T not specified Uncertain significance (Feb 28, 2023)3156855
2-74429958-C-T not specified Uncertain significance (Jul 06, 2021)2401319
2-74429991-C-T not specified Uncertain significance (Jun 30, 2023)2609215

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RTKNprotein_codingprotein_codingENST00000272430 1216587
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000002700.9961256930551257480.000219
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.022963500.8460.00002103617
Missense in Polyphen97129.590.748511332
Synonymous0.3691301350.9600.000007321197
Loss of Function2.581429.00.4830.00000156289

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008870.000883
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004640.0000462
European (Non-Finnish)0.0002210.000220
Middle Eastern0.00005440.0000544
South Asian0.0003600.000359
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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