NME9

protein-coding

NME/NM23 family member 9, the group of NME/NM23 family|Thioredoxin domain containing

Gene summary

Predicted to enable nucleoside diphosphate kinase activity. Predicted to be involved in CTP biosynthetic process; GTP biosynthetic process; and UTP biosynthetic process. Predicted to be located in dynein axonemal particle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

TXNDC6

MANE transcript

NM_001349018.2

Inheritance

—

ClinVar variants

U:24B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr3:138,261,437-138,329,886

External References & Databases

Ensembl (ENSG00000181322)

Transcript & Mutation Effects

hg38 • Region Span ~68.4 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 NME9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001349018.2. 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						0
missense			24 clinvar	4 clinvar		28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	24	4	0	28

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001349018.2	RefSeq	NP_001335947.1	11	MANE Select
ENST00000333911.9	Ensembl	ENSP00000335444.3	11	MANE Select
NM_001349020.2	RefSeq	NP_001335949.1	9	Standard
NM_001349021.2	RefSeq	NP_001335950.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

nucleoside diphosphate phosphorylation
GTP biosynthetic process
UTP biosynthetic process
CTP biosynthetic process
cell redox homeostasis

Molecular Function

nucleoside diphosphate kinase activity

Cellular Component

cytoplasm
cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000383180
Coding exons: 9
Length: 68450
Individuals with no LoFs: 125688
Homozygous LoFs: 0
Heterozygous LoFs: 60
Defined: 125748
p: 0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.961	116	149	0.779	0.00000780	1741
Missense (PolyPhen)		34	51.848	0.65576		648
Synonymous	-1.40	69	55.7	1.24	0.00000312	484
Loss of Function	0.631	14	16.8	0.834	9.68e-7	180

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00024	0.00020	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00033	0.00030	rare
South Asian	0.00029	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be a regulator of microtubule physiology.;

Recessive Scores

pRec: 0.0965

Intolerance Scores

RVIS EVS: 0.37
RVIS percentile EVS: 75.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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