NUDT16

nudix hydrolase 16, the group of Nudix hydrolase family

Basic information

Region (hg38): 3:131381671-131388830

Links

ENSG00000198585 ∙ NCBI:131870 ∙ OMIM:617381 ∙ HGNC:26442 ∙ Uniprot:Q96DE0 ∙ 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 NUDT16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT16 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			15		1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1	1	7
Total	0	0	20	2	2

Variants in NUDT16

This is a list of pathogenic ClinVar variants found in the NUDT16 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-131381811-G-A		not specified	Uncertain significance (Nov 17, 2022)
3-131381814-G-A		not specified	Uncertain significance (Nov 06, 2023)
3-131381817-C-T		not specified	Uncertain significance (Mar 03, 2025)
3-131381836-A-G		not specified	Uncertain significance (Mar 15, 2024)
3-131381838-G-A		not specified	Uncertain significance (Feb 21, 2024)
3-131381841-C-A		not specified	Uncertain significance (Aug 09, 2021)
3-131381874-C-G		not specified	Uncertain significance (Feb 23, 2023)
3-131381893-C-G		not specified	Uncertain significance (Nov 14, 2024)
3-131381923-C-T		not specified	Uncertain significance (May 15, 2024)
3-131382112-C-G			Benign (Nov 03, 2017)
3-131382140-G-A		not specified	Uncertain significance (Aug 21, 2024)
3-131382170-T-C		not specified	Uncertain significance (Oct 10, 2023)
3-131382184-A-C		not specified	Uncertain significance (May 17, 2023)
3-131382223-G-A		not specified	Uncertain significance (Jul 30, 2024)
3-131382247-C-A		not specified	Uncertain significance (Nov 07, 2024)
3-131382349-A-G		not specified	Uncertain significance (Jul 02, 2024)
3-131382379-C-G		not specified	Uncertain significance (Dec 04, 2024)
3-131382458-G-T		not specified	Likely benign (Jul 09, 2024)
3-131382494-G-A			Benign (Aug 16, 2018)
3-131382517-C-T		not specified	Uncertain significance (Sep 02, 2024)
3-131382533-A-G		not specified	Uncertain significance (Sep 22, 2023)
3-131382559-A-G		not specified	Likely benign (Dec 11, 2024)
3-131382566-T-C		not specified	Uncertain significance (Jul 12, 2023)
3-131383311-T-G		not specified	Uncertain significance (Jul 31, 2024)
3-131383324-A-T		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT16	protein_coding	protein_coding	ENST00000502852	2	7160

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00462	0.460	124517	0	4	124521	0.0000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.301	121	131	0.926	0.00000586	1422
Missense in Polyphen		29	39.751	0.72954		420
Synonymous	0.787	49	56.5	0.867	0.00000256	503
Loss of Function	-0.305	3	2.48	1.21	1.07e-7	22

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000126
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000110
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000111	0.000110
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal- dependent manner. Part of the U8 snoRNP complex that is required for the accumulation of mature 5.8S and 28S rRNA. Has diphosphatase activity and removes m7G and/or m227G caps from U8 snoRNA and leaves a 5'monophosphate on the RNA. Catalyzes also the cleavage of the cap structure on mRNAs. Does not hydrolyze cap analog structures like 7-methylguanosine nucleoside triphosphate (m7GpppG). Also hydrolysis m7G- and m227G U3-capped RNAs but with less efficiencies. Has broad substrate specificity with manganese or cobalt as cofactor and can act on various RNA species. Binds to the U8 snoRNA; metal is not required for RNA-binding. May play a role in the regulation of snoRNAs and mRNAs degradation. Acts also as a phosphatase; hydrolyzes the non-canonical purine nucleotides inosine diphosphate (IDP) and deoxyinosine diphosphate (dITP) as well as guanosine diphosphate (GDP), deoxyguanosine diphosphate (dGDP), xanthine diphosphate (XDP), inosine triphosphate (ITP) and deoxyinosine triphosphate (ITP) to their respective monophosphate derivatives and does not distinguish between the deoxy- and ribose forms (PubMed:20385596, PubMed:26121039). The order of activity with different substrates is IDP > dIDP >> GDP = dGDP > XDP = ITP = dITP (PubMed:20385596). Binds strongly to GTP, ITP and XTP. Participates in the hydrolysis of dIDP/IDP and probably excludes non-canonical purines from RNA and DNA precursor pools, thus preventing their incorporation into RNA and DNA and avoiding chromosomal lesions (PubMed:20385596). {ECO:0000269|PubMed:15053875, ECO:0000269|PubMed:17567574, ECO:0000269|PubMed:18820299, ECO:0000269|PubMed:20385596, ECO:0000269|PubMed:21070968, ECO:0000269|PubMed:21337011, ECO:0000269|PubMed:26121039}.
• Pathway: RNA degradation - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Nucleobase catabolism;Metabolism of nucleotides;Metabolism;Phosphate bond hydrolysis by NUDT proteins;Purine catabolism (Consensus)

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.153
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.316

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt16

Gene ontology

• Biological process: adenosine to inosine editing;mRNA catabolic process;proteolysis;positive regulation of cell population proliferation;snoRNA catabolic process;dephosphorylation;nucleobase-containing small molecule catabolic process;dITP catabolic process;IDP catabolic process;positive regulation of cell cycle process;RNA phosphodiester bond hydrolysis, endonucleolytic;XDP catabolic process;negative regulation of rRNA processing;positive regulation of double-strand break repair
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm
• Molecular function: magnesium ion binding;mRNA binding;GTP binding;metalloexopeptidase activity;manganese ion binding;snoRNA binding;chloride ion binding;dITP diphosphatase activity;identical protein binding;protein homodimerization activity;m7G(5')pppN diphosphatase activity;cobalt ion binding;dIDP diphosphatase activity;nucleotide phosphatase activity, acting on free nucleotides;XTP binding;ITP binding;IDP phosphatase activity;phosphodiesterase decapping endonuclease activity