IDO1

indoleamine 2,3-dioxygenase 1

Basic information

Region (hg38): 8:39902274-39928790

Previous symbols: [ "IDO", "INDO" ]

Links

ENSG00000131203 ∙ NCBI:3620 ∙ OMIM:147435 ∙ HGNC:6059 ∙ Uniprot:P14902 ∙ 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 IDO1 gene.

• Inborn genetic diseases (11 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IDO1 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			11		2	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	11	0	3

Variants in IDO1

This is a list of pathogenic ClinVar variants found in the IDO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-39913932-G-A			Benign (Dec 31, 2019)
8-39913935-A-G		not specified	Uncertain significance (Feb 03, 2022)
8-39917921-A-C		not specified	Uncertain significance (Dec 17, 2023)
8-39918168-G-A		not specified	Uncertain significance (Jul 05, 2023)
8-39918196-G-C		not specified	Uncertain significance (Jan 23, 2024)
8-39920101-C-A		not specified	Uncertain significance (Nov 07, 2022)
8-39920102-C-T			Benign (Dec 31, 2019)
8-39920111-A-G		not specified	Uncertain significance (Feb 14, 2023)
8-39922578-G-A		not specified	Uncertain significance (Feb 23, 2023)
8-39923526-G-C		not specified	Uncertain significance (Nov 22, 2022)
8-39925220-T-C			Likely benign (Aug 16, 2018)
8-39925267-G-T		not specified	Uncertain significance (Apr 05, 2023)
8-39925338-G-A		not specified	Uncertain significance (May 31, 2023)
8-39927922-C-G		not specified	Uncertain significance (Dec 21, 2023)
8-39927927-G-A			Benign (Apr 25, 2018)
8-39927956-T-G		not specified	Uncertain significance (Oct 10, 2023)
8-39927958-C-T		not specified	Uncertain significance (May 04, 2022)
8-39927959-G-A		not specified	Likely benign (Jan 23, 2024)
8-39928019-T-A		not specified	Uncertain significance (Jan 23, 2023)
8-39928021-G-A		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IDO1	protein_coding	protein_coding	ENST00000518237	10	26170

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000330	0.805	124625	0	27	124652	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.403	229	212	1.08	0.0000112	2617
Missense in Polyphen		94	80.938	1.1614		1015
Synonymous	-0.0732	77	76.2	1.01	0.00000391	763
Loss of Function	1.33	11	16.9	0.651	7.79e-7	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000514	0.000513
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000715	0.0000708
Middle Eastern	0.000111	0.000111
South Asian	0.0000982	0.0000980
Other	0.00	0.00

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 the peripheral immune tolerance, contributing to maintain homeostasis by preventing autoimmunity or immunopathology that would result from uncontrolled and overreacting immune responses (PubMed:25691885). Tryptophan shortage inhibits T lymphocytes division and accumulation of tryptophan catabolites induces T-cell apoptosis and differentiation of regulatory T-cells (PubMed:25691885). Acts as a suppressor of anti-tumor immunity (PubMed:23103127, PubMed:25157255, PubMed:14502282, PubMed:25691885). Limits the growth of intracellular pathogens by depriving tryptophan (PubMed:25691885). Protects the fetus from maternal immune rejection (PubMed:25691885). {ECO:0000269|PubMed:14502282, ECO:0000269|PubMed:17671174, ECO:0000303|PubMed:23103127, ECO:0000303|PubMed:25157255, ECO:0000303|PubMed:25691885}.
• Pathway: Tryptophan metabolism - Homo sapiens (human);African trypanosomiasis - Homo sapiens (human);Tryptophan Metabolism;NAD+ biosynthetic pathways;Tryptophan metabolism;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;Tryptophan degradation;superpathway of tryptophan utilization;tryptophan degradation (Consensus)

Recessive Scores

• pRec: 0.436

Intolerance Scores

• loftool: 0.732
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.493
• hipred: N
• hipred_score: 0.196

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.978

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ido1
• Phenotype: reproductive system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); immune system phenotype; renal/urinary system phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: immune system process;cytokine production involved in inflammatory response;positive regulation of T cell tolerance induction;positive regulation of chronic inflammatory response;positive regulation of type 2 immune response;tryptophan catabolic process;female pregnancy;tryptophan catabolic process to kynurenine;electron transport chain;response to lipopolysaccharide;negative regulation of interleukin-10 production;positive regulation of interleukin-12 production;multicellular organismal response to stress;kynurenic acid biosynthetic process;'de novo' NAD biosynthetic process from tryptophan;swimming behavior;negative regulation of T cell proliferation;regulation of activated T cell proliferation;negative regulation of T cell apoptotic process;positive regulation of T cell apoptotic process
• Cellular component: cytoplasm;cytosol;smooth muscle contractile fiber;stereocilium bundle
• Molecular function: tryptophan 2,3-dioxygenase activity;electron transfer activity;heme binding;indoleamine 2,3-dioxygenase activity;metal ion binding