IDO2

indoleamine 2,3-dioxygenase 2

Basic information

Region (hg38): 8:39934613-40016392

Previous symbols: [ "INDOL1" ]

Links

ENSG00000188676 ∙ NCBI:169355 ∙ OMIM:612129 ∙ HGNC:27269 ∙ Uniprot:Q6ZQW0 ∙ 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 IDO2 gene.

• Inborn genetic diseases (28 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IDO2 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				1		1
missense			27	1	2	30
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	3

Variants in IDO2

This is a list of pathogenic ClinVar variants found in the IDO2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-39949242-G-C		not specified	Uncertain significance (May 31, 2023)
8-39949247-C-A		not specified	Uncertain significance (Mar 13, 2023)
8-39949256-G-C		not specified	Uncertain significance (Jul 14, 2023)
8-39963617-C-T		not specified	Uncertain significance (Sep 14, 2022)
8-39963629-A-G		not specified	Uncertain significance (Aug 03, 2022)
8-39963651-A-G		not specified	Uncertain significance (Aug 04, 2023)
8-39963668-A-T		not specified	Uncertain significance (May 03, 2023)
8-39963689-G-C		not specified	Uncertain significance (Aug 12, 2021)
8-39963700-C-G		not specified	Uncertain significance (Oct 03, 2022)
8-39979103-C-T		not specified	Uncertain significance (Jul 26, 2022)
8-39979113-G-T		not specified	Uncertain significance (Nov 17, 2022)
8-39979155-T-C		not specified	Uncertain significance (May 26, 2022)
8-39982702-G-T		not specified	Uncertain significance (Jun 16, 2023)
8-39982715-A-G			Benign (Apr 30, 2021)
8-39982769-G-A		not specified	Likely benign (May 17, 2023)
8-39985511-C-G		not specified	Uncertain significance (Apr 25, 2022)
8-39985512-C-A		not specified	Uncertain significance (Dec 26, 2023)
8-39987884-A-G		not specified	Uncertain significance (May 26, 2022)
8-39987902-G-A		not specified	Uncertain significance (Aug 02, 2021)
8-39987925-A-G		not specified	Uncertain significance (Apr 26, 2023)
8-39987935-G-T		not specified	Uncertain significance (Dec 27, 2022)
8-39989811-A-C		not specified	Uncertain significance (Dec 14, 2023)
8-39989823-T-G		not specified	Uncertain significance (Oct 26, 2021)
8-40005338-C-A		not specified	Uncertain significance (Oct 04, 2022)
8-40005342-A-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IDO2	protein_coding	protein_coding	ENST00000502986	11	81778

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.14e-9	0.309	74801	6915	42939	124655	0.225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.456	234	215	1.09	0.0000107	2704
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.417	0.414
Ashkenazi Jewish	0.162	0.162
East Asian	0.378	0.378
Finnish	0.207	0.207
European (Non-Finnish)	0.212	0.211
Middle Eastern	0.378	0.378
South Asian	0.231	0.229
Other	0.209	0.206

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: 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;tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde;Metabolism;L-kynurenine degradation;NAD <i>de novo</i> biosynthesis;superpathway of tryptophan utilization;tryptophan degradation (Consensus)

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.131

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Ido2
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: immune system process;tryptophan catabolic process;tryptophan catabolic process to kynurenine;'de novo' NAD biosynthetic process from tryptophan;oxidation-reduction process
• Cellular component: cytoplasm;cytosol
• Molecular function: tryptophan 2,3-dioxygenase activity;heme binding;indoleamine 2,3-dioxygenase activity;metal ion binding