RIOX2

ribosomal oxygenase 2, the group of Iron (II) and 2-oxoglutarate dependent oxygenases

Basic information

Region (hg38): 3:97941818-97972457

Previous symbols: [ "MINA" ]

Links

ENSG00000170854 ∙ NCBI:84864 ∙ OMIM:612049 ∙ HGNC:19441 ∙ Uniprot:Q8IUF8 ∙ 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 RIOX2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RIOX2 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			45	3		48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	3	0

Variants in RIOX2

This is a list of pathogenic ClinVar variants found in the RIOX2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-97945197-A-C		not specified	Uncertain significance (Oct 06, 2022)
3-97945290-C-G		not specified	Uncertain significance (Nov 24, 2024)
3-97945314-T-C		not specified	Uncertain significance (Apr 04, 2023)
3-97945330-G-A		not specified	Uncertain significance (Jul 06, 2021)
3-97945332-A-C		not specified	Uncertain significance (Jan 22, 2024)
3-97945333-G-A		not specified	Uncertain significance (Nov 06, 2023)
3-97945342-A-C		not specified	Uncertain significance (Feb 17, 2024)
3-97945822-C-A		not specified	Uncertain significance (Dec 13, 2022)
3-97945831-C-G		not specified	Uncertain significance (Dec 16, 2023)
3-97947437-G-C		not specified	Uncertain significance (Apr 18, 2023)
3-97947443-T-C		not specified	Uncertain significance (Oct 03, 2023)
3-97949873-G-A		not specified	Likely benign (Oct 06, 2023)
3-97949876-G-A		not specified	Uncertain significance (Dec 16, 2021)
3-97949876-G-C		not specified	Uncertain significance (Feb 10, 2023)
3-97949883-G-A		not specified	Uncertain significance (Feb 22, 2023)
3-97949883-G-T		not specified	Uncertain significance (Dec 28, 2022)
3-97949901-T-C		not specified	Likely benign (Jan 24, 2024)
3-97949909-T-C		not specified	Uncertain significance (Aug 01, 2024)
3-97949919-C-T		not specified	Uncertain significance (May 30, 2023)
3-97949937-T-C		not specified	Uncertain significance (Feb 06, 2023)
3-97949952-G-A		not specified	Uncertain significance (Oct 26, 2024)
3-97949984-C-A		not specified	Uncertain significance (Dec 06, 2022)
3-97949984-C-T		not specified	Uncertain significance (Jul 25, 2023)
3-97949993-G-T		not specified	Uncertain significance (Jan 27, 2022)
3-97949994-C-A		not specified	Uncertain significance (Jan 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RIOX2	protein_coding	protein_coding	ENST00000333396	9	30640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.26e-8	0.701	125536	2	210	125748	0.000843

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0546	253	255	0.990	0.0000139	3033
Missense in Polyphen		75	75.673	0.99111		942
Synonymous	-0.177	107	105	1.02	0.00000608	899
Loss of Function	1.31	15	21.6	0.696	0.00000111	268

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00238	0.00238
Ashkenazi Jewish	0.00	0.00
East Asian	0.000436	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000917	0.000915
Middle Eastern	0.000436	0.000435
South Asian	0.000665	0.000588
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Oxygenase that can act as both a histone lysine demethylase and a ribosomal histidine hydroxylase. Is involved in the demethylation of trimethylated 'Lys-9' on histone H3 (H3K9me3), leading to an increase in ribosomal RNA expression. Also catalyzes the hydroxylation of 60S ribosomal protein L27a on 'His-39'. May play an important role in cell growth and survival. May be involved in ribosome biogenesis, most likely during the assembly process of pre-ribosomal particles. {ECO:0000269|PubMed:12091391, ECO:0000269|PubMed:14695334, ECO:0000269|PubMed:15534111, ECO:0000269|PubMed:15819408, ECO:0000269|PubMed:15897898, ECO:0000269|PubMed:17317935, ECO:0000269|PubMed:19502796, ECO:0000269|PubMed:23103944}.
• Pathway: HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• rvis_EVS: 0.0000761
• rvis_percentile_EVS: 53.98

Haploinsufficiency Scores

• pHI: 0.129
• hipred: Y
• hipred_score: 0.675
• ghis: 0.542

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Riox2
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype; respiratory system phenotype

Gene ontology

• Biological process: histone demethylation;ribosome biogenesis;oxidation-reduction process
• Cellular component: nucleus;nucleoplasm;transcription factor complex;nucleolus;cytosol
• Molecular function: histone demethylase activity;identical protein binding;metal ion binding;dioxygenase activity