RTKN

rhotekin, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 2:74425835-74442422

Links

ENSG00000114993 ∙ NCBI:6242 ∙ OMIM:602288 ∙ HGNC:10466 ∙ Uniprot:Q9BST9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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		1	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: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rtkn

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