NUDT5

nudix hydrolase 5, the group of Nudix hydrolase family

Basic information

Region (hg38): 10:12165330-12195891

Links

ENSG00000165609

∙ NCBI:11164 ∙ OMIM:609230 ∙ HGNC:8052 ∙ Uniprot:Q9UKK9 ∙ 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 NUDT5 gene.

not_specified (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014142.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT5	protein_coding	protein_coding	ENST00000491614	9	30820

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00140	0.968	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.523	113	130	0.871	0.00000735	1419
Missense in Polyphen		40	46.627	0.85787		499
Synonymous	0.0272	50	50.2	0.995	0.00000343	412
Loss of Function	1.90	7	14.9	0.468	7.18e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000545	0.0000544
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Enzyme that can either act as an ADP-sugar pyrophosphatase in absence of diphosphate or catalyze the synthesis of ATP in presence of diphosphate (PubMed:27257257). In absence of diphosphate, hydrolyzes with similar activities various modified nucleoside diphosphates such as ADP-ribose, ADP-mannose, ADP-glucose, 8-oxo-GDP and 8-oxo-dGDP (PubMed:10567213, PubMed:10722730, PubMed:19699693, PubMed:21389046, PubMed:17052728). Can also hydrolyze other nucleotide sugars with low activity (PubMed:19699693, PubMed:21389046). In presence of diphosphate, mediates the synthesis of ATP in the nucleus by catalyzing the conversion of ADP-ribose to ATP and ribose 5- phosphate. Nuclear ATP synthesis takes place when dephosphorylated at Thr-45 (PubMed:27257257). Nuclear ATP generation is required for extensive chromatin remodeling events that are energy- consuming (PubMed:27257257). Does not play a role in U8 snoRNA decapping activity (By similarity). Binds U8 snoRNA (By similarity). {ECO:0000250|UniProtKB:Q9JKX6, ECO:0000269|PubMed:10567213, ECO:0000269|PubMed:10722730, ECO:0000269|PubMed:17052728, ECO:0000269|PubMed:19699693, ECO:0000269|PubMed:21389046, ECO:0000269|PubMed:27257257}.;
Pathway: Purine metabolism - Homo sapiens (human);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Nucleobase catabolism;Metabolism of nucleotides;Metabolism;Purine nucleotides nucleosides metabolism;Phosphate bond hydrolysis by NUDT proteins;Purine catabolism (Consensus)

Recessive Scores

pRec: 0.142

Intolerance Scores

loftool: 0.604
rvis_EVS: -0.07
rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

pHI: 0.498
hipred: N
hipred_score: 0.394
ghis: 0.594

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.742

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Nudt5
Phenotype

Gene ontology

Biological process: chromatin remodeling;nucleoside phosphate metabolic process;nucleotide metabolic process;ribonucleoside diphosphate catabolic process;D-ribose catabolic process;ribose phosphate metabolic process;nucleobase-containing small molecule catabolic process;ATP generation from poly-ADP-D-ribose
Cellular component: nucleus;cytosol;extracellular exosome
Molecular function: magnesium ion binding;protein binding;nucleotidyltransferase activity;ADP-sugar diphosphatase activity;snoRNA binding;protein homodimerization activity;8-oxo-dGDP phosphatase activity;ADP-ribose diphosphatase activity;m7G(5')pppN diphosphatase activity