NME3

protein-coding

NME/NM23 nucleoside diphosphate kinase 3, the group of NME/NM23 family

Gene summary

Enables several functions, including mitochondrion-mitochondrion outer membrane tether activity; nucleoside diphosphate kinase activity; and purine ribonucleotide binding activity. Involved in several processes, including dTTP biosynthetic process; mitochondrial outer membrane fusion; and protein hexamerization. Located in cytoplasm. Is active in mitochondrial outer membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_002513.3

Inheritance

ClinVar variants

U:41B:4

Top phenotype

NME3-related condition

gnomAD constraint

pLI —, LoF o/e 1.68

Max pathogenic AF

—

Genomic locus

chr16:1,770,320-1,771,561

External References & Databases

Ensembl (ENSG00000103024)

Transcript & Mutation Effects

hg38 • Region Span ~1.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

inherited neurodegenerative disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0024237

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NME3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 39

not providedTotal: 3

NME3-related conditionTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002513.3. 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				1 clinvar		1
missense			39 clinvar	1 clinvar	1 clinvar	41
nonsense				1 clinvar		1
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	41	3	1	45

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002513.3	RefSeq	NP_002504.2	5	MANE Select
ENST00000219302.8	Ensembl	ENSP00000219302.3	5	MANE Select
ENST00000563498.1	Ensembl	ENSP00000455435.1	3	Standard
ENST00000563498.2	Ensembl	ENSP00000455435.1	3	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
nme3	Danio rerio	Structure: whole organism Quality: decreased amount abnormal

Gene / Model

Organism

Observed Phenotype

nme3

Danio rerio

Structure: whole organism

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pyrimidine metabolism - Homo sapiens (human)
Drug metabolism - other enzymes - Homo sapiens (human)
Purine metabolism - Homo sapiens (human)
Pyrimidine metabolism
pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis

Biological Process

nucleoside diphosphate phosphorylation
GTP biosynthetic process
UTP biosynthetic process
CTP biosynthetic process
apoptotic process

Molecular Function

nucleoside diphosphate kinase activity
protein binding
ATP binding
metal ion binding

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000219302
Coding exons: 5
Length: 1445
Individuals with no LoFs: 121544
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 121571
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.686	106	87.9	1.21	0.00000420	1043
Missense (PolyPhen)		45	39.009	1.1536		451
Synonymous	-1.76	53	39.0	1.36	0.00000209	339
Loss of Function	-1.45	9	5.37	1.68	2.30e-7	74

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000070	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00010	rare
South Asian	0.00045	0.00043	rare
Other	0.00019	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Probably has a role in normal hematopoiesis by inhibition of granulocyte differentiation and induction of apoptosis.;

Recessive Scores

pRec: 0.185

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.711

Gene Damage Prediction

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