KMO
protein-codingkynurenine 3-monooxygenase
Gene summary
This gene encodes a mitochondrion outer membrane protein that catalyzes the hydroxylation of L-tryptophan metabolite, L-kynurenine, to form L-3-hydroxykynurenine. Studies in yeast identified this gene as a therapeutic target for Huntington disease. [provided by RefSeq, Oct 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~63.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0019975
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0019975
Submitter: ClinGen
The gene *KMO* encodes kynurenine 3-monooxygenase, an enzyme that catalyzes the conversion of L-kynurenine to 3-hydroxykynurenine (3-HK) in the kynurenine pathway, the primary pathway for tryptophan degradation in the body. A case of pellagra with colitis was first associated with a deficiency in tryptophan metabolism at the level of kynurenine 3-monooxygenase in 1990 by Clayton et al. (PMID:1833200), though enzymatic testing of KMO and genetic analysis was not preformed. Since then, no further reports have associated pellagra with KMO, though pellagra has been associated with deficiencies in other enzymes in the kynurenine pathway and chronic alcoholism can induce pellagra via inhibition of the rate limiting enzyme in the hepatic kynurenine pathway, tryptophan 2,3-dioxygenase. However, to date, no individuals have been identified with variants in *KMO* resulting in pellagra or even a deficiency in KMO enzymatic activity. Support for a potential gene-disease relationship comes from the biochemical function of KMO (PMID:32148781) including its enzymatic function in the kynurenine pathway, which when rendered inactive, shunts the tryptophan degradation pathway towards either kynurenine acid (KYNA) catalyzed by kynurenine aminotransferase (KAT) or anthranilic acid (AA) catalyzed by KYNU. Additionally, at least two knock out *KMO* (-/-) mouse models have been described (PMIDs:28187857, 24189070). One mouse model showed evidence that KO *KMO* resulted in behavioral changes including impairments in contextual memory and increased anxiety-like behavior, though in both models, mice did not show evidence of pellagra. This result was to be expected given that mice were not fed a niacin restricted diet. Biallelic variants have been identified in other enzymes (HAOO and KYNU) in the kynurenine pathway resulting in NAD deficiency along with congenital malformations (PMID: 28792876). There is considerable evidence that phenotypes resulting from enzymatic deficiencies in the kynurenine pathway can be prevented by a diet that consists of sufficient niacin, a dietary source of NAD. Finally, impaired KMO function has been implicated in the pathophysiology of schizophrenia. In summary, there is insufficient genetic evidence to support a gene-disease relationship. A classification of No Known Disease Relationship was approved by the General IEM GCEP on 05/18/2023.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to KMO variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003679.5. 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 | ||||
| missense | 44 | 5 | 1 | 50 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 46 | 5 | 2 | 53 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003670.2 | 15 | MANE Select | |
| Ensembl | ENSP00000355517.4 | 15 | MANE Select | |
| RefSeq | NP_001397873.1 | 15 | Standard | |
| Ensembl | ENSP00000355513.5 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| kmo | Danio rerio | Structure: podocyte Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Tryptophan metabolism - Homo sapiens (human)
- Tryptophan Metabolism
- Selenium Micronutrient Network
- NAD Biosynthesis II (from tryptophan)
- Tryptophan catabolism
Biological Process
- tryptophan catabolic process
- aging
- response to salt stress
- NAD metabolic process
- quinolinate biosynthetic process
Molecular Function
- kynurenine 3-monooxygenase activity
- NAD(P)H oxidase activity
- flavin adenine dinucleotide binding
- FAD binding
Cellular Component
- extracellular space
- mitochondrion
- mitochondrial outer membrane
- cytosol
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000366559
- Coding exons
- 15
- Length
- 63511
- Individuals with no LoFs
- 125671
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 67
- Defined
- 125738
- p
- 0.000266
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.83 | 180 | 263 | 0.683 | 0.0000129 | 3218 |
| Missense (PolyPhen) | 55 | 92.729 | 0.59313 | 1131 | ||
| Synonymous | -1.40 | 107 | 90.1 | 1.19 | 0.00000465 | 880 |
| Loss of Function | 2.79 | 12 | 27.9 | 0.431 | 0.00000142 | 334 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0016 | notable |
| Latino/Admixed American | 0.000088 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00020 | 0.00020 | rare |
| South Asian | 0.00043 | 0.00042 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the hydroxylation of L-kynurenine (L-Kyn) to form 3-hydroxy-L-kynurenine (L-3OHKyn) (PubMed:29429898, PubMed:23575632, PubMed:26752518, PubMed:28604669, PubMed:29208702). Required for synthesis of quinolinic acid, a neurotoxic NMDA receptor antagonist and potential endogenous inhibitor of NMDA receptor signaling in axonal targeting, synaptogenesis and apoptosis during brain development. Quinolinic acid may also affect NMDA receptor signaling in pancreatic beta cells, osteoblasts, myocardial cells, and the gastrointestinal tract (Probable). {ECO:0000269|PubMed:23575632, ECO:0000269|PubMed:26752518, ECO:0000269|PubMed:28604669, ECO:0000269|PubMed:29208702, ECO:0000269|PubMed:29429898, ECO:0000305|PubMed:12402501}.;
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- LoFtool
- 0.708
- RVIS EVS
- 0.66
- RVIS percentile EVS
- 84.55
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.613
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |