RIOK1

RIO kinase 1, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 6:7389793-7418037

Links

ENSG00000124784 ∙ NCBI:83732 ∙ OMIM:617753 ∙ HGNC:18656 ∙ Uniprot:Q9BRS2 ∙ 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 RIOK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIOK1 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				2		2
missense			30	1		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	3	0

Variants in RIOK1

This is a list of pathogenic ClinVar variants found in the RIOK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-7390024-A-G		not specified	Uncertain significance (May 04, 2023)
6-7393142-C-T			Likely benign (May 01, 2022)
6-7393212-G-A		not specified	Likely benign (Jul 26, 2022)
6-7393228-T-A		not specified	Uncertain significance (Dec 17, 2023)
6-7393243-G-C		not specified	Uncertain significance (Aug 12, 2021)
6-7393265-G-T		not specified	Uncertain significance (Aug 02, 2022)
6-7393286-G-A		not specified	Uncertain significance (Dec 26, 2023)
6-7395140-T-A		not specified	Uncertain significance (Feb 27, 2023)
6-7398705-A-G		not specified	Uncertain significance (Sep 29, 2022)
6-7398709-A-G		not specified	Uncertain significance (Oct 25, 2022)
6-7400998-T-C		not specified	Uncertain significance (Nov 15, 2021)
6-7402610-T-C		not specified	Uncertain significance (Feb 12, 2024)
6-7402846-C-T		not specified	Uncertain significance (Jan 04, 2024)
6-7402888-A-G		not specified	Uncertain significance (Oct 05, 2021)
6-7403993-G-A		not specified	Uncertain significance (Jul 25, 2023)
6-7404480-A-C		not specified	Uncertain significance (Feb 28, 2024)
6-7404494-A-G		not specified	Uncertain significance (Nov 29, 2023)
6-7404934-G-A		not specified	Uncertain significance (Mar 31, 2024)
6-7404968-A-G		not specified	Uncertain significance (Mar 25, 2024)
6-7404993-C-G		not specified	Uncertain significance (Jun 02, 2024)
6-7405018-A-G		not specified	Uncertain significance (Dec 21, 2022)
6-7405257-A-G		not specified	Uncertain significance (Aug 17, 2022)
6-7405275-G-A			Likely benign (Jun 01, 2024)
6-7405280-G-A		not specified	Uncertain significance (Mar 18, 2024)
6-7405285-T-C		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIOK1	protein_coding	protein_coding	ENST00000379834	17	28542

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.25e-14	0.213	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.509	284	309	0.918	0.0000156	3819
Missense in Polyphen		98	109.69	0.89341		1345
Synonymous	1.04	91	104	0.871	0.00000567	952
Loss of Function	1.13	25	31.9	0.784	0.00000149	425

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000438	0.000437
Ashkenazi Jewish	0.00	0.00
East Asian	0.000602	0.000598
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000389	0.000378
Middle Eastern	0.000602	0.000598
South Asian	0.000426	0.000425
Other	0.000692	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the final steps of cytoplasmic maturation of the 40S ribosomal subunit. Involved in processing of 18S-E pre- rRNA to the mature 18S rRNA. Required for the recycling of NOB1 and PNO1 from the late 40S precursor (PubMed:22072790). The association with the very late 40S subunit intermediate may involve a translation-like checkpoint point cycle preceeding the binding to the 60S ribosomal subunit (By similarity). Despite the protein kinase domain is proposed to act predominantly as an ATPase (By similarity). The catalytic activity regulates its dynamic association with the 40S subunit (By similarity). In addition to its role in ribosomal biogenesis acts as an adapter protein by recruiting NCL/nucleolin the to PRMT5 complex for its symmetrical methylation (PubMed:21081503). {ECO:0000250|UniProtKB:G0S3J5, ECO:0000250|UniProtKB:Q12196, ECO:0000269|PubMed:21081503, ECO:0000269|PubMed:22072790}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.21

Haploinsufficiency Scores

• pHI: 0.0743
• hipred: N
• hipred_score: 0.289
• ghis: 0.538

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Riok1

Gene ontology

• Biological process: protein phosphorylation;maturation of SSU-rRNA;ribosomal small subunit biogenesis;positive regulation of rRNA processing
• Cellular component: nucleoplasm;cytosol;preribosome, small subunit precursor;methyltransferase complex
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;hydrolase activity;metal ion binding