NUDT7
protein-codingnudix hydrolase 7, the group of Nudix hydrolase family
Gene summary
The protein encoded by this gene is a member of the Nudix hydrolase family. Nudix hydrolases eliminate potentially toxic nucleotide metabolites from the cell and regulate the concentrations and availability of many different nucleotide substrates, cofactors, and signaling molecules. Alternatively spliced transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~19.8 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 NUDT7 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001105663.3. 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 | 0 | |||||
| missense | 52 | 3 | 55 | |||
| nonsense | 1 | 1 | 2 | |||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 55 | 3 | 1 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001099133.1 | 4 | MANE Select | |
| Ensembl | ENSP00000268533.5 | 4 | MANE Select | |
| RefSeq | NP_001230586.1 | 5 | Standard | |
| RefSeq | NP_001230589.1 | 4 | 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
- nucleoside diphosphate metabolic process
- coenzyme A catabolic process
Molecular Function
- magnesium ion binding
- molecular_function
- acetyl-CoA hydrolase activity
- signaling receptor binding
- CoA hydrolase activity
Cellular Component
- peroxisome
- peroxisomal matrix
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000268533
- Coding exons
- 4
- Length
- 19747
- Individuals with no LoFs
- 124503
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 289
- Defined
- 124793
- p
- 0.00116
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.825 | 164 | 137 | 1.20 | 0.00000754 | 1540 |
| Missense (PolyPhen) | 53 | 49.152 | 1.0783 | 550 | ||
| Synonymous | -1.82 | 68 | 51.4 | 1.32 | 0.00000264 | 471 |
| Loss of Function | -0.877 | 8 | 5.73 | 1.40 | 2.46e-7 | 82 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0.00056 | 0.00055 | rare |
| Ashkenazi Jewish | 0.0016 | 0.0016 | notable |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.0014 | 0.0014 | notable |
| European (Non-Finnish) | 0.0019 | 0.0019 | notable |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0.00099 | 0.00099 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Coenzyme A diphosphatase which mediates the cleavage of CoA, CoA esters and oxidized CoA with similar efficiencies, yielding 3',5'-ADP and the corresponding 4'-phosphopantetheine derivative as products. CoA into 3',5'-ADP and 4'- phosphopantetheine. Has no activity toward NDP-sugars, CDP- alcohols, (deoxy)nucleoside 5'-triphosphates, nucleoside 5'-di or monophosphates, diadenosine polyphosphates, NAD, NADH, NADP, NADPH or thymidine-5'-monophospho-p-nitrophenyl ester. May be required to eliminate oxidized CoA from peroxisomes, or regulate CoA and acyl-CoA levels in this organelle in response to metabolic demand. Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0950
Intolerance Scores
- LoFtool
- 0.780
- RVIS EVS
- 0.33
- RVIS percentile EVS
- 73.41
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.228
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |