NUDT3
nudix hydrolase 3, the group of Nudix hydrolase family
Basic information
Region (hg38): 6:34279679-34392669
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT3 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in NUDT3
This is a list of pathogenic ClinVar variants found in the NUDT3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-34288761-T-A | not specified | Uncertain significance (Apr 06, 2022) | ||
| 6-34288764-C-A | not specified | Uncertain significance (Jul 16, 2024) | ||
| 6-34288899-C-T | not specified | Uncertain significance (Jun 25, 2024) | ||
| 6-34392298-G-C | not specified | Uncertain significance (Oct 27, 2022) | ||
| 6-34392346-G-A | not specified | Uncertain significance (Jan 29, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUDT3 | protein_coding | protein_coding | ENST00000607016 | 5 | 112996 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.425 | 0.568 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.32 | 63 | 100 | 0.629 | 0.00000529 | 1113 |
| Missense in Polyphen | 19 | 48.545 | 0.39139 | 527 | ||
| Synonymous | -1.27 | 50 | 39.8 | 1.26 | 0.00000241 | 323 |
| Loss of Function | 2.27 | 2 | 9.60 | 0.208 | 4.04e-7 | 124 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000298 | 0.0000298 |
| Ashkenazi Jewish | 0.000198 | 0.000198 |
| East Asian | 0.0000586 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.0000586 | 0.0000544 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Cleaves a beta-phosphate from the diphosphate groups in PP-InsP5 (diphosphoinositol pentakisphosphate) and [PP]2-InsP4 (bisdiphosphoinositol tetrakisphosphate), suggesting that it may play a role in signal transduction. InsP6 (inositol hexakisphophate) is not a substrate. Acts as a negative regulator of the ERK1/2 pathway. Also able to catalyze the hydrolysis of dinucleoside oligophosphates, with Ap6A and Ap5A being the preferred substrates. The major reaction products are ADP and p4a from Ap6A and ADP and ATP from Ap5A. Also able to hydrolyze 5- phosphoribose 1-diphosphate. {ECO:0000269|PubMed:9822604}.;
- Pathway
- Inositol Phosphate Metabolism;Metabolism;Synthesis of pyrophosphates in the cytosol;Inositol phosphate metabolism
(Consensus)
Recessive Scores
- pRec
- 0.163
Intolerance Scores
- loftool
- 0.157
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.26
Haploinsufficiency Scores
- pHI
- 0.378
- hipred
- Y
- hipred_score
- 0.728
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.961
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nudt3
- Phenotype
Gene ontology
- Biological process
- cell-cell signaling;diadenosine polyphosphate catabolic process;inositol phosphate metabolic process;diphosphoinositol polyphosphate metabolic process;diphosphoinositol polyphosphate catabolic process;diadenosine pentaphosphate catabolic process;diadenosine hexaphosphate catabolic process;adenosine 5'-(hexahydrogen pentaphosphate) catabolic process
- Cellular component
- nucleus;cytoplasm;cytosol
- Molecular function
- magnesium ion binding;endopolyphosphatase activity;diphosphoinositol-polyphosphate diphosphatase activity;bis(5'-adenosyl)-hexaphosphatase activity;bis(5'-adenosyl)-pentaphosphatase activity;m7G(5')pppN diphosphatase activity;inositol diphosphate tetrakisphosphate diphosphatase activity;inositol bisdiphosphate tetrakisphosphate diphosphatase activity;inositol diphosphate pentakisphosphate diphosphatase activity;inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity;inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity;inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity;inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity;inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity;inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity