NUDT1
nudix hydrolase 1, the group of Nudix hydrolase family
Basic information
Region (hg38): 7:2242226-2251146
Previous symbols: [ "MTH1" ]
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 NUDT1 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 | 1 | |||||
| missense | 12 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 2 | 0 |
Variants in NUDT1
This is a list of pathogenic ClinVar variants found in the NUDT1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-2244624-G-A | not specified | Uncertain significance (Feb 12, 2024) | ||
| 7-2244656-G-A | not specified | Uncertain significance (Jun 10, 2022) | ||
| 7-2244659-G-A | not specified | Uncertain significance (Jun 05, 2023) | ||
| 7-2244662-G-A | not specified | Uncertain significance (Mar 29, 2023) | ||
| 7-2244681-G-T | not specified | Uncertain significance (Apr 04, 2023) | ||
| 7-2249911-G-C | not specified | Likely benign (Oct 27, 2021) | ||
| 7-2249927-G-A | not specified | Uncertain significance (Dec 09, 2023) | ||
| 7-2249933-G-A | not specified | Uncertain significance (Jan 07, 2022) | ||
| 7-2249967-C-T | not specified | Uncertain significance (Jul 28, 2021) | ||
| 7-2249973-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
| 7-2249989-C-T | Likely benign (Oct 01, 2022) | |||
| 7-2249990-G-A | not specified | Uncertain significance (Jul 26, 2022) | ||
| 7-2250930-C-A | not specified | Uncertain significance (Mar 21, 2024) | ||
| 7-2250973-A-G | not specified | Uncertain significance (Nov 07, 2022) | ||
| 7-2250981-C-T | not specified | Uncertain significance (Jul 17, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUDT1 | protein_coding | protein_coding | ENST00000397049 | 4 | 8925 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 7.45e-12 | 0.00529 | 125647 | 1 | 100 | 125748 | 0.000402 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.607 | 127 | 109 | 1.16 | 0.00000684 | 1189 |
| Missense in Polyphen | 35 | 33.364 | 1.049 | 377 | ||
| Synonymous | -0.447 | 48 | 44.2 | 1.09 | 0.00000314 | 334 |
| Loss of Function | -1.63 | 14 | 8.79 | 1.59 | 5.56e-7 | 81 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00121 | 0.00121 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.0000925 | 0.0000924 |
| European (Non-Finnish) | 0.000225 | 0.000220 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00111 | 0.00108 |
| Other | 0.000214 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Antimutagenic (PubMed:8226881, PubMed:7713500, PubMed:10608900). Plays a redundant role in sanitizing oxidized nucleotide pools, such as 8-oxo-dGTP pools (PubMed:28679043). Acts as a sanitizing enzyme for oxidized nucleotide pools, thus suppressing cell dysfunction and death induced by oxidative stress (PubMed:12857738, PubMed:24695224, PubMed:24695225). Hydrolyzes 8- oxo-dGTP, 8-oxo-dATP and 2-OH-dATP, thus preventing misincorporation of oxidized purine nucleoside triphosphates into DNA and subsequently preventing A:T to C:G and G:C to T:A transversions (PubMed:8226881, PubMed:10373420, PubMed:10608900, PubMed:11756418, PubMed:12857738, PubMed:16607562, PubMed:24695224, PubMed:24695225, PubMed:26999531, PubMed:28035004). Able to hydrolyze also the corresponding ribonucleotides, 2-OH-ATP, 8-oxo-GTP and 8-oxo-ATP (PubMed:10373420, PubMed:11139615). Does not play a role in U8 snoRNA decapping activity. Binds U8 snoRNA (By similarity). {ECO:0000250|UniProtKB:P53368, ECO:0000269|PubMed:10373420, ECO:0000269|PubMed:10608900, ECO:0000269|PubMed:11139615, ECO:0000269|PubMed:11756418, ECO:0000269|PubMed:12857738, ECO:0000269|PubMed:16607562, ECO:0000269|PubMed:22556419, ECO:0000269|PubMed:24695224, ECO:0000269|PubMed:24695225, ECO:0000269|PubMed:26999531, ECO:0000269|PubMed:28035004, ECO:0000269|PubMed:28679043, ECO:0000269|PubMed:7713500, ECO:0000269|PubMed:8226881}.;
- Pathway
- Nucleobase catabolism;Metabolism of nucleotides;Metabolism;oxidized GTP and dGTP detoxification;Phosphate bond hydrolysis by NUDT proteins;Purine catabolism
(Consensus)
Recessive Scores
- pRec
- 0.180
Intolerance Scores
- loftool
- 0.997
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.92
Haploinsufficiency Scores
- pHI
- 0.426
- hipred
- N
- hipred_score
- 0.177
- ghis
- 0.599
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.987
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nudt1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype;
Gene ontology
- Biological process
- purine nucleotide catabolic process;dGTP catabolic process;DNA repair;response to oxidative stress;aging;male gonad development;nucleobase-containing small molecule catabolic process;DNA protection;dATP catabolic process;response to cadmium ion
- Cellular component
- acrosomal vesicle;extracellular space;nucleus;cytoplasm;mitochondrion;mitochondrial matrix;cytosol;plasma membrane;nuclear membrane
- Molecular function
- GTPase activity;protein binding;8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity;snoRNA binding;8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity;GTP diphosphatase activity;2-hydroxy-adenosine triphosphate pyrophosphatase activity;2-hydroxy-(deoxy)adenosine-triphosphate pyrophosphatase activity;metal ion binding;ATP diphosphatase activity;m7G(5')pppN diphosphatase activity