KMO
Basic information
Region (hg38): 1:241532134-241595642
Links
Phenotypes
GenCC
Source:
- pellagra (No Known Disease Relationship), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (40 variants)
- not_provided (5 variants)
- KMO-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the KMO gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003679.5. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 37 | 43 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 38 | 5 | 2 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
KMO | protein_coding | protein_coding | ENST00000366559 | 15 | 63511 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000478 | 0.999 | 125671 | 0 | 67 | 125738 | 0.000266 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.83 | 180 | 263 | 0.683 | 0.0000129 | 3218 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00171 | 0.00169 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000546 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000203 | 0.000202 |
Middle Eastern | 0.0000546 | 0.0000544 |
South Asian | 0.000426 | 0.000425 |
Other | 0.000166 | 0.000163 |
dbNSFP
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}.;
- Pathway
- Tryptophan metabolism - Homo sapiens (human);Tryptophan Metabolism;Selenium Micronutrient Network;NAD Biosynthesis II (from tryptophan);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;Tryptophan metabolism;NAD <i>de novo</i> biosynthesis;Tryptophan degradation;superpathway of tryptophan utilization;tryptophan degradation
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.708
- rvis_EVS
- 0.66
- rvis_percentile_EVS
- 84.55
Haploinsufficiency Scores
- pHI
- 0.0692
- hipred
- N
- hipred_score
- 0.475
- ghis
- 0.402
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.613
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Kmo
- Phenotype
- homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- kmo
- Affected structure
- podocyte
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- tryptophan catabolic process;aging;response to salt stress;NAD metabolic process;quinolinate biosynthetic process;kynurenic acid biosynthetic process;'de novo' NAD biosynthetic process from tryptophan;anthranilate metabolic process;oxidation-reduction process;kynurenine metabolic process;cellular response to lipopolysaccharide;cellular response to interleukin-1;L-kynurenine metabolic process;positive regulation of neuron death;positive regulation of glutamate secretion, neurotransmission
- Cellular component
- extracellular space;mitochondrion;mitochondrial outer membrane;cytosol;integral component of membrane
- Molecular function
- kynurenine 3-monooxygenase activity;NAD(P)H oxidase activity;flavin adenine dinucleotide binding;FAD binding