NME9

Chr 3

NME/NM23 family member 9

Also known as: NM23-H9, NXL2, TXL-2, TXL2, TXNDC6

NCBI Gene: 347736 ENSG00000181322 UniProt: Q86XW9 OMIM: 618584

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]

OMIM Research

OMIM ResearchGenerating clinical summary…

GOFmechanismLOEUF 1.30

Clinical Summary— NME9

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

41 VUS of 65 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.30LOEUF

pLI 0.000

Z-score 0.63

OE 0.83 (0.55–1.30)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.96Z-score

OE missense 0.78 (0.67–0.91)

116 obs / 149.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.83 (0.55–1.30)

0≤0.351.4

Missense OE?0.78 (0.67–0.91)

0≤0.61.4

Synonymous OE?1.24

0≤1.21.6

LoF obs/exp: 14 / 16.8Missense obs/exp: 116 / 149.0Syn Z: -1.40

This gene — mechanism propensity

0.6065th %ile

GOF

0.6638th %ile

LOF

0.2968th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

65 submitted variants in ClinVar

ClinVar

Classification Summary

VUS41

Likely Benign4

Benign1

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	41	0	41
Likely Benign	4	0	4
Benign	0	1	1
Total	45	1	46

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

20 pathogenic / likely-pathogenic (of 27) ClinVar copy-number / structural variants overlap NME9 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →