RTKN2

rhotekin 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 10:62183035-62268844

Previous symbols: [ "PLEKHK1" ]

Links

ENSG00000182010 ∙ NCBI:219790 ∙ OMIM:618450 ∙ HGNC:19364 ∙ Uniprot:Q8IZC4 ∙ 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 RTKN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTKN2 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	1	0

Variants in RTKN2

This is a list of pathogenic ClinVar variants found in the RTKN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-62197946-T-A		not specified	Uncertain significance (Jan 22, 2024)
10-62197946-T-C		not specified	Uncertain significance (Jan 26, 2023)
10-62197955-T-C		not specified	Uncertain significance (Sep 06, 2022)
10-62197996-T-C		not specified	Likely benign (Aug 08, 2022)
10-62198062-G-A		not specified	Uncertain significance (Dec 02, 2022)
10-62198066-C-T		not specified	Uncertain significance (Feb 09, 2023)
10-62198081-G-C		not specified	Uncertain significance (May 26, 2023)
10-62198093-T-C		not specified	Uncertain significance (Jul 14, 2023)
10-62198144-T-C		not specified	Uncertain significance (Jun 29, 2022)
10-62198242-C-T		not specified	Uncertain significance (Sep 14, 2022)
10-62199778-C-T		not specified	Uncertain significance (Dec 05, 2022)
10-62199815-C-T		not specified	Uncertain significance (May 23, 2024)
10-62199846-C-T		not specified	Uncertain significance (Sep 26, 2023)
10-62204934-G-T		not specified	Uncertain significance (Jan 31, 2024)
10-62204943-T-C		not specified	Uncertain significance (Oct 27, 2023)
10-62204944-G-C		not specified	Uncertain significance (Jun 21, 2021)
10-62205000-T-C		not specified	Uncertain significance (Mar 16, 2022)
10-62217166-C-A		not specified	Uncertain significance (Jul 12, 2023)
10-62217185-T-TA		Interstitial lung disease 2	Uncertain significance (May 06, 2018)
10-62217189-G-A		not specified	Uncertain significance (Mar 24, 2023)
10-62217245-A-G		not specified	Uncertain significance (Oct 12, 2021)
10-62218265-A-G		not specified	Uncertain significance (Oct 29, 2021)
10-62223261-T-C		not specified	Uncertain significance (Aug 10, 2021)
10-62223288-T-C		not specified	Uncertain significance (Oct 12, 2022)
10-62223327-A-T		not specified	Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTKN2	protein_coding	protein_coding	ENST00000373789	12	85673

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.46e-15	0.324	124915	10	822	125747	0.00331

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0227	308	307	1.00	0.0000143	4017
Missense in Polyphen		97	95.983	1.0106		1342
Synonymous	0.364	98	103	0.954	0.00000470	1105
Loss of Function	1.36	27	35.8	0.754	0.00000238	386

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00267	0.00258
Ashkenazi Jewish	0.00	0.00
East Asian	0.00463	0.00452
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000465	0.000413
Middle Eastern	0.00463	0.00452
South Asian	0.0214	0.0211
Other	0.00150	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in lymphopoiesis. {ECO:0000269|PubMed:15504364}.

Recessive Scores

• pRec: 0.0911

Intolerance Scores

• loftool: 0.909
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.78

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.264
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.386

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtkn2

Gene ontology

• Biological process: signal transduction;positive regulation of cell population proliferation;hemopoiesis;positive regulation of NF-kappaB transcription factor activity;positive regulation of NIK/NF-kappaB signaling;negative regulation of intrinsic apoptotic signaling pathway
• Cellular component: nucleus;cytoplasm