NUDT13

protein-coding

nudix hydrolase 13, the group of Nudix hydrolase family

Gene summary

Predicted to enable NADH pyrophosphatase activity. Predicted to be involved in nucleobase-containing small molecule interconversion. Located in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015901.6

Inheritance

—

ClinVar variants

U:52B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr10:73,110,375-73,131,828

External References & Databases

Ensembl (ENSG00000166321)

Transcript & Mutation Effects

hg38 • Region Span ~21.5 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 NUDT13 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 51

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015901.6. 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			50 clinvar	2 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	52	2	0	54

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015901.6	RefSeq	NP_056985.3	8	MANE Select
ENST00000357321.9	Ensembl	ENSP00000349874.4	8	MANE Select
NM_001283014.2	RefSeq	NP_001269943.1	6	Standard
NM_001283015.2	RefSeq	NP_001269944.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of nucleotides
Interconversion of nucleotide di- and triphosphates
Metabolism

Biological Process

nucleobase-containing small molecule interconversion

Molecular Function

pyrophosphatase activity
metal ion binding

Cellular Component

mitochondrial matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357321
Coding exons: 8
Length: 21370
Individuals with no LoFs: 122061
Homozygous LoFs: 234
Heterozygous LoFs: 3451
Defined: 125746
p: 0.0148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.512	168	188	0.895	0.00000944	2274
Missense (PolyPhen)		50	70.365	0.71058		844
Synonymous	1.01	60	70.8	0.847	0.00000330	684
Loss of Function	0.284	18	19.4	0.930	9.93e-7	219

Population LoF Frequency

Population	CAF	p-value	Status
African	0.17	0.17	notable
Latino/Admixed American	0.0087	0.0087	notable
Ashkenazi Jewish	0.016	0.015	notable
East Asian	0.0011	0.0011	notable
Finnish	0.0021	0.0021	notable
European (Non-Finnish)	0.0050	0.0050	notable
South Asian	0.0025	0.0025	notable
Other	0.0083	0.0083	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.101

Intolerance Scores

LoFtool: 0.879
RVIS EVS: 0.91
RVIS percentile EVS: 89.47

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.410

Gene Damage Prediction

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