NUDT12

protein-coding

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

Gene summary

Nucleotides are involved in numerous biochemical reactions and pathways within the cell as substrates, cofactors, and effectors. Nudix hydrolases, such as NUDT12, regulate the concentrations of individual nucleotides and of nucleotide ratios in response to changing circumstances (Abdelraheim et al., 2003 [PubMed 12790796]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_031438.4

Inheritance

—

ClinVar variants

U:72B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr5:103,548,855-103,562,790

External References & Databases

Ensembl (ENSG00000112874)

Transcript & Mutation Effects

hg38 • Region Span ~13.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NUDT12 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 66

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031438.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			70 clinvar	1 clinvar		71
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	72	2	0	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031438.4	RefSeq	NP_113626.1	6	MANE Select
ENST00000230792.7	Ensembl	ENSP00000230792.2	6	MANE Select
NM_001300741.2	RefSeq	NP_001287670.1	6	Standard
ENST00000507423.1	Ensembl	ENSP00000424521.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nicotinate and nicotinamide metabolism - Homo sapiens (human)
Peroxisome - Homo sapiens (human)
Nicotinate and Nicotinamide Metabolism
Vitamin B3 (nicotinate and nicotinamide) metabolism
Metabolism

Biological Process

NADH metabolic process
NADP catabolic process
NAD catabolic process
NAD biosynthesis via nicotinamide riboside salvage pathway

Molecular Function

NAD+ diphosphatase activity
protein binding
hydrolase activity
NADH pyrophosphatase activity
metal ion binding

Cellular Component

nucleus
peroxisome
peroxisomal matrix
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000230792
Coding exons: 6
Length: 13939
Individuals with no LoFs: 125670
Homozygous LoFs: 0
Heterozygous LoFs: 73
Defined: 125743
p: 0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.478	247	227	1.09	0.0000104	3014
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00046	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00018	0.00016	rare
Finnish	0.00088	0.00088	rare
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00027	0.00026	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

LoFtool: 0.895
RVIS EVS: 0.29
RVIS percentile EVS: 71.5

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.215

Gene Damage Prediction

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