RIOX2
protein-codingribosomal oxygenase 2, the group of Iron (II) and 2-oxoglutarate dependent oxygenases
Gene summary
MINA is a c-Myc (MYC; MIM 190080) target gene that may play a role in cell proliferation or regulation of cell growth. (Tsuneoka et al., 2002 [PubMed 12091391]; Zhang et al., 2005 [PubMed 15897898]).[supplied by OMIM, May 2008]
- MINA
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~30.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RIOX2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_153182.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 90 | 4 | 94 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 90 | 4 | 0 | 94 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_694822.2 | 9 | MANE Select | |
| Ensembl | ENSP00000377748.2 | 9 | MANE Select | |
| RefSeq | NP_001035998.1 | 9 | Standard | |
| RefSeq | NP_001248758.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- HDMs demethylate histones
- Chromatin modifying enzymes
- Chromatin organization
- Validated targets of C-MYC transcriptional activation
Biological Process
- histone demethylation
- ribosome biogenesis
- oxidation-reduction process
Molecular Function
- histone demethylase activity
- identical protein binding
- metal ion binding
- dioxygenase activity
Cellular Component
- nucleus
- nucleoplasm
- transcription factor complex
- nucleolus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000333396
- Coding exons
- 9
- Length
- 30640
- Individuals with no LoFs
- 125536
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 210
- Defined
- 125748
- p
- 0.000843
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0546 | 253 | 255 | 0.990 | 0.0000139 | 3033 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.0021 | 0.0020 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00092 | 0.00091 | rare |
| South Asian | 0.00067 | 0.00059 | rare |
| Other | 0.0011 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- 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}.;
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- RVIS EVS
- 0.0000761
- RVIS percentile EVS
- 53.98
Essentials
- Essential (gene trap)
- N