NUDT12

nudix hydrolase 12, the group of Ankyrin repeat domain containing|Nudix hydrolase family

Basic information

Region (hg38): 5:103548855-103562790

Links

ENSG00000112874 ∙ NCBI:83594 ∙ OMIM:609232 ∙ HGNC:18826 ∙ Uniprot:Q9BQG2 ∙ 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 NUDT12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUDT12 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			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	1	0

Variants in NUDT12

This is a list of pathogenic ClinVar variants found in the NUDT12 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-103550923-G-T		not specified	Uncertain significance (Jan 18, 2022)
5-103550947-T-C		not specified	Uncertain significance (Feb 21, 2025)
5-103550962-C-T		not specified	Uncertain significance (Oct 06, 2024)
5-103550968-G-C		not specified	Likely benign (Feb 16, 2023)
5-103552237-G-A		not specified	Uncertain significance (Sep 03, 2024)
5-103552248-A-G		not specified	Uncertain significance (Feb 12, 2024)
5-103552263-A-C		not specified	Uncertain significance (Jul 25, 2023)
5-103552299-C-G		not specified	Uncertain significance (Dec 04, 2024)
5-103552305-A-T		not specified	Uncertain significance (Nov 17, 2022)
5-103552319-C-T		not specified	Uncertain significance (Jun 03, 2024)
5-103552368-C-A		not specified	Uncertain significance (Jul 17, 2024)
5-103554775-C-T		not specified	Uncertain significance (May 04, 2023)
5-103554850-G-A		not specified	Uncertain significance (Jun 21, 2023)
5-103554851-G-C		not specified	Uncertain significance (Jul 11, 2023)
5-103555963-T-C		not specified	Uncertain significance (Feb 05, 2024)
5-103556072-G-A		not specified	Uncertain significance (Jan 10, 2023)
5-103558928-A-T		not specified	Uncertain significance (Mar 01, 2025)
5-103558936-A-G		not specified	Uncertain significance (Jun 28, 2024)
5-103558947-C-G		not specified	Uncertain significance (Jul 27, 2024)
5-103558971-A-G		not specified	Uncertain significance (Feb 15, 2025)
5-103558984-C-T		not specified	Uncertain significance (Oct 26, 2022)
5-103558986-A-G		not specified	Uncertain significance (Feb 21, 2024)
5-103558993-A-C		not specified	Uncertain significance (Aug 20, 2024)
5-103559029-C-A		not specified	Uncertain significance (Jun 27, 2022)
5-103559067-A-T		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUDT12	protein_coding	protein_coding	ENST00000230792	6	13939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.00e-11	0.123	125670	0	73	125743	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.478	247	227	1.09	0.0000104	3014
Missense in Polyphen		91	93.555	0.97269		1238
Synonymous	0.0281	77	77.3	0.996	0.00000354	874
Loss of Function	0.462	17	19.2	0.886	9.58e-7	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000715	0.000711
Ashkenazi Jewish	0.00	0.00
East Asian	0.000179	0.000163
Finnish	0.000879	0.000878
European (Non-Finnish)	0.000180	0.000176
Middle Eastern	0.000179	0.000163
South Asian	0.000270	0.000261
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes NAD(P)H to NMNH and AMP (2',5'-ADP), and diadenosine diphosphate to AMP. Has also activity towards NAD(P)(+), ADP-ribose and diadenosine triphosphate. May act to regulate the concentration of peroxisomal nicotinamide nucleotide cofactors required for oxidative metabolism in this organelle. {ECO:0000269|PubMed:12790796}.
• Pathway: Nicotinate and nicotinamide metabolism - Homo sapiens (human);Peroxisome - Homo sapiens (human);Nicotinate and Nicotinamide Metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Nicotinamide salvaging;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Metabolism of vitamins and cofactors (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.895
• rvis_EVS: 0.29
• rvis_percentile_EVS: 71.5

Haploinsufficiency Scores

• pHI: 0.0779
• hipred: N
• hipred_score: 0.350
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.215

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nudt12

Gene ontology

• Biological process: NADH metabolic process;NADP catabolic process;NAD catabolic process;NAD biosynthesis via nicotinamide riboside salvage pathway
• Cellular component: nucleus;peroxisome;peroxisomal matrix;cytosol
• Molecular function: NAD+ diphosphatase activity;protein binding;hydrolase activity;NADH pyrophosphatase activity;metal ion binding