NAT9

protein-coding

N-acetyltransferase 9 (putative), the group of GCN5 related N-acetyltransferases

Gene summary

Predicted to enable tubulin N-terminal-methionine acetyltransferase activity. Predicted to be involved in regulation of mitotic spindle assembly. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015654.5

Inheritance

—

ClinVar variants

U:34

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr17:74,770,529-74,776,367

External References & Databases

Ensembl (ENSG00000109065)

Transcript & Mutation Effects

hg38 • Region Span ~5.8 kb

Loading mutation effect viewer...

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 NAT9 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 30

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015654.5. 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			32 clinvar			32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	34	0	0	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 197 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015654.5	RefSeq	NP_056469.2	6	MANE Select
ENST00000357814.8	Ensembl	ENSP00000350467.3	6	MANE Select
NM_001305077.2	RefSeq	NP_001292006.1	6	Standard
NM_001305078.2	RefSeq	NP_001292007.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metapathway biotransformation Phase I and II

Molecular Function

protein binding
transferase activity, transferring acyl groups other than amino-acyl groups

Cellular Component

protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357814
Coding exons: 6
Length: 5821
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125748
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0971	117	120	0.975	0.00000689	1353
Missense (PolyPhen)		34	42.763	0.79508		516
Synonymous	-0.608	58	52.4	1.11	0.00000362	385
Loss of Function	1.03	7	10.6	0.658	4.54e-7	121

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00043	0.00044	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.114

Intolerance Scores

LoFtool: 0.738
RVIS EVS: 0.44
RVIS percentile EVS: 77.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.901

Gene Damage Prediction

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