RIOK3

RIO kinase 3, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 18:23453287-23486603

Previous symbols: [ "SUDD" ]

Links

ENSG00000101782 ∙ NCBI:8780 ∙ OMIM:603579 ∙ HGNC:11451 ∙ Uniprot:O14730 ∙ 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 RIOK3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIOK3 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	22	0	1

Variants in RIOK3

This is a list of pathogenic ClinVar variants found in the RIOK3 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-23463055-A-C		not specified	Uncertain significance (Sep 28, 2022)
18-23463063-G-A		not specified	Uncertain significance (Aug 02, 2022)
18-23463971-G-T		not specified	Uncertain significance (Jul 20, 2022)
18-23463986-A-G		not specified	Uncertain significance (Feb 22, 2023)
18-23464011-C-G		Inborn genetic diseases	Uncertain significance (Apr 13, 2023)
18-23464067-G-A		not specified	Uncertain significance (Dec 27, 2023)
18-23464230-G-A		not specified	Uncertain significance (Feb 13, 2024)
18-23464528-T-C		not specified	Uncertain significance (Aug 10, 2023)
18-23466245-G-A		not specified	Uncertain significance (Sep 20, 2023)
18-23466245-G-T		not specified	Uncertain significance (Mar 16, 2022)
18-23467517-A-G		not specified	Uncertain significance (Aug 17, 2022)
18-23473578-G-A		not specified	Uncertain significance (Feb 14, 2023)
18-23473590-G-A		not specified	Uncertain significance (Nov 15, 2023)
18-23474951-G-A		not specified	Uncertain significance (Jul 20, 2022)
18-23475036-C-T		not specified	Uncertain significance (Feb 28, 2024)
18-23475088-C-T		not specified	Uncertain significance (Apr 18, 2023)
18-23477016-A-G		not specified	Uncertain significance (Jan 24, 2024)
18-23477222-C-T		not specified	Uncertain significance (Jan 31, 2024)
18-23477245-C-T		not specified	Uncertain significance (Aug 15, 2023)
18-23479330-G-C		not specified	Uncertain significance (Jun 22, 2024)
18-23479343-A-C		not specified	Uncertain significance (Jan 17, 2023)
18-23479374-G-C		not specified	Uncertain significance (Mar 29, 2024)
18-23481163-T-C			Benign (Nov 15, 2018)
18-23481200-A-T		not specified	Uncertain significance (Jan 23, 2024)
18-23481269-A-G		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIOK3	protein_coding	protein_coding	ENST00000339486	13	33781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.77e-7	0.991	125691	0	56	125747	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	236	287	0.823	0.0000151	3466
Missense in Polyphen		55	86.839	0.63336		1132
Synonymous	1.61	74	93.9	0.788	0.00000483	910
Loss of Function	2.38	15	28.8	0.521	0.00000154	357

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000361
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000282	0.000273
Middle Eastern	0.000163	0.000163
South Asian	0.000169	0.000163
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in regulation of type I interferon (IFN)- dependent immune response which plays a critical role in the innate immune response against DNA and RNA viruses. May act as an adapter protein essential for the recruitment of TBK1 to IRF3 (PubMed:24807708). Phosphorylates IFIH1 on 'Ser-828' interfering with IFIH1 filament assembly on long dsRNA and resulting in attenuated IFIH1-signaling (PubMed:25865883). Can inhibit CASP10 isoform 7-mediated activation of the NF-kappaB signaling pathway (PubMed:19557502). May play a role in the biogenesis of the 40S ribosomal subunit. Involved in the processing of 21S pre-rRNA to the mature 18S rRNA (PubMed:22418843). {ECO:0000269|PubMed:19557502, ECO:0000269|PubMed:22418843, ECO:0000269|PubMed:24807708, ECO:0000269|PubMed:25865883}.
• Pathway: Hematopoietic Stem Cell Differentiation (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.896
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.528
• hipred: Y
• hipred_score: 0.538
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Riok3

Gene ontology

• Biological process: protein phosphorylation;chromosome segregation;maturation of SSU-rRNA;negative regulation of protein homooligomerization;positive regulation of interferon-beta production;negative regulation of MDA-5 signaling pathway;negative regulation of I-kappaB kinase/NF-kappaB signaling;innate immune response;positive regulation of innate immune response;defense response to virus;cellular response to dsRNA;cellular response to virus;cellular response to dsDNA
• Cellular component: cytosol;preribosome, small subunit precursor
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;metal ion binding;caspase binding