KMO

protein-coding

kynurenine 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

NM_003679.5

Inheritance

AR

ClinVar variants

U:46B:7

Top phenotype

KMO-related congenital malformation syndrome

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr1:241,532,134-241,595,642

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~63.5 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

pellagraLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019975

Submitter: PanelApp Australia

pellagraNO_KNOWN

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

4 Conditions Cataloged
not specifiedTotal: 44
not providedTotal: 5
KMO-related congenital malformation syndromeTotal: 2
KMO-related disorderTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
44
clinvar
5
clinvar
1
clinvar
50
nonsense
0
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total00465253
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003679.5RefSeqNP_003670.215MANE Select
ENST00000366559.9EnsemblENSP00000355517.415MANE Select
NM_001410944.1RefSeqNP_001397873.115Standard
ENST00000366555.5EnsemblENSP00000355513.57Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
kmoDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.831802630.6830.00001293218
Missense (PolyPhen)5592.7290.593131131
Synonymous-1.4010790.11.190.00000465880
Loss of Function2.791227.90.4310.00000142334

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00160.0016notable
Latino/Admixed American0.0000880.000087rare
Ashkenazi Jewish00.0absent
East Asian0.0000550.000054rare
Finnish00.0absent
European (Non-Finnish)0.000200.00020rare
South Asian0.000430.00042rare
Other0.000170.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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