NUDT1

nudix hydrolase 1, the group of Nudix hydrolase family

Basic information

Region (hg38): 7:2242225-2251146

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.

• Inborn genetic diseases (11 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.

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		1
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	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)
7-2250973-A-G		not specified	Uncertain significance (Nov 07, 2022)
7-2250981-C-T		not specified	Uncertain significance (Jul 17, 2023)

GnomAD

Source: gnomAD

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: 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

	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