NUDT19
protein-codingnudix hydrolase 19, the group of Nudix hydrolase family
Gene summary
Predicted to enable magnesium ion binding activity. Predicted to be involved in acyl-CoA metabolic process and coenzyme A catabolic process. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~22.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NUDT19 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001105570.2. 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 | 2 | 2 | ||||
| missense | 108 | 6 | 114 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 112 | 8 | 0 | 120 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001099040.1 | 3 | MANE Select | |
| Ensembl | ENSP00000380251.2 | 3 | MANE Select | |
| Ensembl | ENSP00000792494.1 | 2 | Standard | |
| Ensembl | ENSP00000811951.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Peroxisome - Homo sapiens (human)
- Metabolism of lipids
- Metabolism of proteins
- Peroxisomal lipid metabolism
- Metabolism
Biological Process
- protein targeting to peroxisome
- biological_process
- fatty acid catabolic process
Molecular Function
- signaling receptor binding
- metal ion binding
- acyl-CoA hydrolase activity
Cellular Component
- cellular_component
- peroxisomal matrix
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000397061
- Coding exons
- 3
- Length
- 21836
- Individuals with no LoFs
- 124624
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 181
- Defined
- 124805
- p
- 0.000725
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.53 | 270 | 176 | 1.54 | 0.00000933 | 2326 |
| Missense (PolyPhen) | 77 | 50.484 | 1.5252 | 657 | ||
| Synonymous | -3.30 | 114 | 77.1 | 1.48 | 0.00000416 | 790 |
| Loss of Function | -2.87 | 17 | 8.16 | 2.08 | 3.53e-7 | 106 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00090 | 0.00084 | rare |
| Latino/Admixed American | 0.00018 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00048 | 0.00045 | rare |
| Finnish | 0.00016 | 0.00014 | rare |
| European (Non-Finnish) | 0.0012 | 0.00096 | notable |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.00092 | 0.00082 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Coenzyme A diphosphatase that mediates the hydrolysis of a wide range of CoA esters, including choloyl-CoA and branched- chain fatty-acyl-CoA esters. At low substrate concentrations medium and long-chain fatty-acyl-CoA esters are the primary substrates (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.288
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.175
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |