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.

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.

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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in NUDT5

This is a list of pathogenic ClinVar variants found in the NUDT5 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
10-12167731-G-A		not specified	Uncertain significance (Oct 03, 2023)
10-12172767-G-A		not specified	Uncertain significance (Mar 25, 2024)
10-12172829-T-C		not specified	Uncertain significance (Apr 15, 2024)
10-12172839-T-A		not specified	Uncertain significance (Dec 16, 2023)
10-12172840-T-G		not specified	Uncertain significance (Nov 10, 2024)
10-12172845-A-G		not specified	Uncertain significance (Nov 09, 2021)
10-12172848-C-T		not specified	Uncertain significance (Jan 04, 2024)
10-12172866-G-A		not specified	Uncertain significance (Oct 17, 2023)
10-12177808-T-C		not specified	Uncertain significance (Oct 12, 2022)
10-12177821-C-G		not specified	Uncertain significance (Aug 26, 2022)
10-12177826-G-A		not specified	Uncertain significance (Nov 27, 2023)
10-12179127-C-G		not specified	Uncertain significance (Jun 21, 2022)
10-12184892-G-A		not specified	Uncertain significance (Aug 14, 2024)
10-12184911-T-C		not specified	Uncertain significance (Apr 09, 2024)
10-12186272-G-A		not specified	Uncertain significance (Oct 21, 2024)

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

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