GeneBe

NUDT1

nudix hydrolase 1, the group of Nudix hydrolase family

Basic information

Region (hg38): 7:2242226-2251146

Previous symbols: [ "MTH1" ]

Links

ENSG00000106268 ∙ NCBI:4521 ∙ OMIM:600312 ∙ HGNC:8048 ∙ Uniprot:P36639 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUDT1 gene.

  • not_specified (28 variants)
  • not_provided (1 variants)

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. These statistics are base on transcript: NM_000002452.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
26
clinvar
2
clinvar
 28
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 26 3 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NUDT1protein_codingprotein_codingENST00000397049 48925
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
7.45e-120.0052912564711001257480.000402
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6071271091.160.000006841189
Missense in Polyphen3533.3641.049377
Synonymous-0.4474844.21.090.00000314334
Loss of Function-1.63148.791.595.56e-781

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001210.00121
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001090.000109
Finnish0.00009250.0000924
European (Non-Finnish)0.0002250.000220
Middle Eastern0.0001090.000109
South Asian0.001110.00108
Other0.0002140.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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