RIOK2

RIO kinase 2, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 5:97160867-97183247

Links

ENSG00000058729 ∙ NCBI:55781 ∙ OMIM:617754 ∙ HGNC:18999 ∙ Uniprot:Q9BVS4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RIOK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIOK2 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	1
missense			22	1	2	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	22	1	3

Variants in RIOK2

This is a list of pathogenic ClinVar variants found in the RIOK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-97163077-C-T		not specified	Uncertain significance (Mar 29, 2023)
5-97163122-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-97163136-T-C		not specified	Uncertain significance (Oct 03, 2023)
5-97163200-C-T			Benign (Apr 24, 2018)
5-97163231-A-G			Benign (Apr 24, 2018)
5-97165077-C-T		not specified	Uncertain significance (Jan 26, 2022)
5-97167473-G-A		not specified	Uncertain significance (Oct 04, 2022)
5-97167475-C-A		not specified	Uncertain significance (Mar 25, 2024)
5-97167500-A-G		not specified	Uncertain significance (Nov 07, 2022)
5-97167530-T-C		not specified	Uncertain significance (Nov 24, 2021)
5-97167551-A-G		not specified	Uncertain significance (Feb 28, 2023)
5-97167603-T-G		not specified	Uncertain significance (May 30, 2024)
5-97167645-C-T		not specified	Uncertain significance (Sep 17, 2021)
5-97167651-C-G		not specified	Uncertain significance (Jun 17, 2024)
5-97167887-A-G		not specified	Likely benign (Dec 28, 2023)
5-97167897-C-G		not specified	Uncertain significance (May 08, 2023)
5-97167978-G-C		not specified	Uncertain significance (Jun 22, 2021)
5-97171216-T-G		not specified	Uncertain significance (Dec 13, 2023)
5-97171313-C-T			Benign (Apr 10, 2018)
5-97177175-T-C		not specified	Uncertain significance (Mar 20, 2023)
5-97177183-T-C			Benign (Jun 18, 2018)
5-97177257-T-G		not specified	Uncertain significance (Feb 28, 2023)
5-97177271-C-G		not specified	Uncertain significance (Dec 18, 2023)
5-97177755-T-A		not specified	Uncertain significance (Aug 08, 2022)
5-97177761-C-A		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIOK2	protein_coding	protein_coding	ENST00000283109	10	22394

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000134	0.998	125691	0	55	125746	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.850	246	287	0.859	0.0000147	3646
Missense in Polyphen		63	81.197	0.77589		946
Synonymous	0.389	92	96.9	0.950	0.00000485	979
Loss of Function	2.75	11	26.2	0.420	0.00000124	360

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000252	0.000249
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000551	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000337	0.000334
Middle Eastern	0.0000551	0.0000544
South Asian	0.000264	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase involved in the final steps of cytoplasmic maturation of the 40S ribosomal subunit. Involved in export of the 40S pre-ribosome particles (pre-40S) from the nucleus to the cytoplasm. Its kinase activity is required for the release of NOB1, PNO1 and LTV1 from the late pre-40S and the processing of 18S-E pre-rRNA to the mature 18S rRNA (PubMed:19564402). Regulates the timing of the metaphase-anaphase transition during mitotic progression, and its phosphorylation, most likely by PLK1, regulates this function (PubMed:21880710). {ECO:0000269|PubMed:16037817, ECO:0000269|PubMed:19564402, ECO:0000269|PubMed:21880710}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0917

Intolerance Scores

• loftool: 0.985
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.61

Haploinsufficiency Scores

• pHI: 0.640
• hipred: Y
• hipred_score: 0.622
• ghis: 0.504

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.813

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Riok2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: cell cycle;regulation of mitotic metaphase/anaphase transition;maturation of SSU-rRNA;ribosomal small subunit biogenesis;protein autophosphorylation;positive regulation of ribosomal small subunit export from nucleus;positive regulation of rRNA processing
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;preribosome, small subunit precursor
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;metal ion binding