NUDT16
nudix hydrolase 16, the group of Nudix hydrolase family
Basic information
Region (hg38): 3:131381671-131388830
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (37 variants)
- not_provided (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT16 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000152395.3. 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 | 0 | |||||
| missense | 25 | 28 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 2 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUDT16 | protein_coding | protein_coding | ENST00000502852 | 2 | 7160 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00462 | 0.460 | 124517 | 0 | 4 | 124521 | 0.0000161 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.301 | 121 | 131 | 0.926 | 0.00000586 | 1422 |
| Missense in Polyphen | 29 | 39.751 | 0.72954 | 420 | ||
| Synonymous | 0.787 | 49 | 56.5 | 0.867 | 0.00000256 | 503 |
| Loss of Function | -0.305 | 3 | 2.48 | 1.21 | 1.07e-7 | 22 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000128 | 0.000126 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000111 | 0.000110 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.000111 | 0.000110 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal- dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5'monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms (PubMed:20385596, PubMed:26121039). The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP (PubMed:20385596). Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions (PubMed:20385596). {ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574, ECO:0000269|PubMed:18820299, ECO:0000269|PubMed:20385596, ECO:0000269|PubMed:21070968, ECO:0000269|PubMed:21337011, ECO:0000269|PubMed:26121039}.;
- Pathway
- RNA degradation - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Nucleobase catabolism;Metabolism of nucleotides;Metabolism;Phosphate bond hydrolysis by NUDT proteins;Purine catabolism
(Consensus)
Haploinsufficiency Scores
- pHI
- 0.225
- hipred
- N
- hipred_score
- 0.153
- ghis
- 0.527
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.316
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nudt16
- Phenotype
Gene ontology
- Biological process
- adenosine to inosine editing;mRNA catabolic process;proteolysis;positive regulation of cell population proliferation;snoRNA catabolic process;dephosphorylation;nucleobase-containing small molecule catabolic process;dITP catabolic process;IDP catabolic process;positive regulation of cell cycle process;RNA phosphodiester bond hydrolysis, endonucleolytic;XDP catabolic process;negative regulation of rRNA processing;positive regulation of double-strand break repair
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytoplasm
- Molecular function
- magnesium ion binding;mRNA binding;GTP binding;metalloexopeptidase activity;manganese ion binding;snoRNA binding;chloride ion binding;dITP diphosphatase activity;identical protein binding;protein homodimerization activity;m7G(5')pppN diphosphatase activity;cobalt ion binding;dIDP diphosphatase activity;nucleotide phosphatase activity, acting on free nucleotides;XTP binding;ITP binding;IDP phosphatase activity;phosphodiesterase decapping endonuclease activity