NUDT17

protein-coding

nudix hydrolase 17, the group of Nudix hydrolase family

Gene summary

Predicted to enable 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity and NADH pyrophosphatase activity. Predicted to be involved in NAD+ catabolic process; NADP+ catabolic process; and RNA decapping. Predicted to be active in peroxisome. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001012758.3

Inheritance

—

ClinVar variants

U:58B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr1:145,845,630-145,848,954

External References & Databases

Ensembl (ENSG00000186364)

Transcript & Mutation Effects

hg38 • Region Span ~3.3 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 NUDT17 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 56

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001012758.3. 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			2 clinvar			2
missense			54 clinvar	3 clinvar		57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	58	3	0	61

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001012758.3	RefSeq	NP_001012776.1	8	MANE Select
ENST00000334513.6	Ensembl	ENSP00000334437.5	8	MANE Select
ENST00000867824.1	Ensembl	ENSP00000537883.1	6	Standard
ENST00000867825.1	Ensembl	ENSP00000537884.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

NADH metabolic process
NADP catabolic process
NAD catabolic process

Molecular Function

hydrolase activity
NADH pyrophosphatase activity
metal ion binding

Cellular Component

peroxisome
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000334513
Coding exons: 8
Length: 3325
Individuals with no LoFs: 125665
Homozygous LoFs: 0
Heterozygous LoFs: 83
Defined: 125748
p: 0.000330

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.730	205	178	1.15	0.00000867	2020
Missense (PolyPhen)		63	56.87	1.1078		702
Synonymous	-1.19	87	74.0	1.18	0.00000373	709
Loss of Function	1.01	13	17.6	0.739	9.11e-7	166

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00025	rare
Latino/Admixed American	0.00044	0.00043	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00044	0.00044	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00033	0.00031	rare
South Asian	0.00059	0.00059	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probably mediates the hydrolysis of some nucleoside diphosphate derivatives. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.455
RVIS EVS: -0.23
RVIS percentile EVS: 37.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 6.91e-7

Gene Damage Prediction

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