NUDT2

nudix hydrolase 2, the group of Nudix hydrolase family

Basic information

Region (hg38): 9:34329506-34343713

Previous symbols: [ "APAH1" ]

Links

ENSG00000164978 ∙ NCBI:318 ∙ OMIM:602852 ∙ HGNC:8049 ∙ Uniprot:P50583 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual developmental disorder with or without peripheral neuropathy (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder with or without peripheral neuropathy	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	27431290; 30059600; 33058507

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUDT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT2 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		1	6			7
nonsense		1				1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	3	6	0	2

Variants in NUDT2

This is a list of pathogenic ClinVar variants found in the NUDT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-34338895-C-G			Benign (May 14, 2021)
9-34339073-C-T		Intellectual developmental disorder with or without peripheral neuropathy	Likely pathogenic (Mar 17, 2024)
9-34339107-C-T		not specified	Uncertain significance (Sep 13, 2023)
9-34342932-G-A			Benign (May 14, 2021)
9-34343170-G-T		Intellectual developmental disorder with or without peripheral neuropathy	Likely pathogenic (May 11, 2023)
9-34343180-GA-G		NUDT2-associated condition • Intellectual disability • Intellectual developmental disorder with or without peripheral neuropathy • Complex neurodevelopmental disorder	Pathogenic/Likely pathogenic (Jul 16, 2024)
9-34343187-G-T			Uncertain significance (Sep 01, 2024)
9-34343210-A-G		not specified	Uncertain significance (Jul 14, 2024)
9-34343276-T-C		not specified	Uncertain significance (Jul 26, 2022)
9-34343285-G-C		not specified	Uncertain significance (Aug 14, 2023)
9-34343303-G-A			Uncertain significance (Jul 22, 2022)
9-34343313-G-C		not specified	Uncertain significance (Mar 20, 2024)
9-34343339-C-T			Uncertain significance (Jul 22, 2022)
9-34343368-G-C			Likely benign (Aug 01, 2024)
9-34343402-CAAG-C		Intellectual developmental disorder with or without peripheral neuropathy	Uncertain significance (Dec 31, 2024)
9-34343436-C-T		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT2	protein_coding	protein_coding	ENST00000379158	2	14206

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00575	0.741	125710	0	37	125747	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.485	68	80.2	0.848	0.00000407	953
Missense in Polyphen		28	31.863	0.87877		401
Synonymous	-0.177	33	31.7	1.04	0.00000164	281
Loss of Function	0.818	4	6.20	0.645	3.47e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000281	0.000281
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Asymmetrically hydrolyzes Ap4A to yield AMP and ATP. Plays a major role in maintaining homeostasis.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);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;Detoxification of Reactive Oxygen Species;Folate metabolism;Cellular responses to stress;Cellular responses to external stimuli;Purine nucleotides nucleosides metabolism (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.671
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.346
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.754

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt2

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;apoptotic process;cellular response to oxidative stress
• Cellular component: mitochondrial matrix
• Molecular function: bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity;protein binding;GTP binding;bis(5'-nucleosyl)-tetraphosphatase (symmetrical) activity