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.

not_specified (68 variants)
not_provided (4 variants)

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. These statistics are base on transcript: NM_000018343.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			65 clinvar	2 clinvar	2 clinvar	69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	3	3

Loading clinvar variants...

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