IDO2
protein-codingindoleamine 2,3-dioxygenase 2
Gene summary
Along with the enzymes encoded by the INDO (MIM 147435) and TDO2 (MIM 191070) genes, the enzyme encoded by the INDOL1 gene metabolizes tryptophan in the kynurenine pathway (Ball et al., 2007 [PubMed 17499941]).[supplied by OMIM, Feb 2011]
- INDOL1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~81.8 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 IDO2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_194294.5. 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 | 1 | 1 | 2 | |||
| missense | 62 | 3 | 65 | |||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 65 | 4 | 0 | 69 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_919270.3 | 10 | MANE Select | |
| Ensembl | ENSP00000443432.2 | 10 | MANE Select | |
| RefSeq | NP_001382135.1 | 10 | Standard | |
| Ensembl | ENSP00000538866.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tryptophan metabolism - Homo sapiens (human)
- African trypanosomiasis - Homo sapiens (human)
- Tryptophan catabolism
- Histidine, lysine, phenylalanine, tyrosine, proline and tryptophan catabolism
- Metabolism of amino acids and derivatives
Biological Process
- immune system process
- tryptophan catabolic process
- tryptophan catabolic process to kynurenine
- 'de novo' NAD biosynthetic process from tryptophan
- oxidation-reduction process
Molecular Function
- tryptophan 2,3-dioxygenase activity
- heme binding
- indoleamine 2,3-dioxygenase activity
- metal ion binding
Cellular Component
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000502986
- Coding exons
- 11
- Length
- 81778
- Individuals with no LoFs
- 74801
- Homozygous LoFs
- 6915
- Heterozygous LoFs
- 42939
- Defined
- 124655
- p
- 0.225
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.456 | 234 | 215 | 1.09 | 0.0000107 | 2704 |
| Missense (PolyPhen) | 76 | 73.776 | 1.0301 | 945 | ||
| Synonymous | -0.368 | 85 | 80.8 | 1.05 | 0.00000402 | 808 |
| Loss of Function | 0.750 | 15 | 18.5 | 0.812 | 8.64e-7 | 246 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.14 | 0.13 | notable |
| Latino/Admixed American | 0.28 | 0.28 | notable |
| Ashkenazi Jewish | 0.16 | 0.16 | notable |
| East Asian | 0.38 | 0.38 | notable |
| Finnish | 0.21 | 0.21 | notable |
| European (Non-Finnish) | 0.21 | 0.21 | notable |
| South Asian | 0.23 | 0.23 | notable |
| Other | 0.21 | 0.21 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the first and rate limiting step of the catabolism of the essential amino acid tryptophan along the kynurenine pathway (PubMed:17671174). Involved in immune regulation. May not play a significant role in tryptophan-related tumoral resistance (PubMed:25691885). {ECO:0000269|PubMed:17671174, ECO:0000303|PubMed:25691885}.;
Essentials
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |