NAT9

Summary

NAT9 (N-acetyltransferase 9, HGNC:23133) is a protein-coding gene on chromosome 17q25.2, encoding Alpha/beta-tubulin-N-acetyltransferase 9 (Q9BTE0). N-acetyltransferase that mediates the acetylation of the N-terminal residues of alpha- and beta-tubulin.

Predicted to enable tubulin N-terminal-methionine acetyltransferase activity. Part of protein-containing complex.

Source: NCBI Gene 26151 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_015654

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23133
Approved symbol	NAT9
Name	N-acetyltransferase 9
Location	17q25.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP564C103
Ensembl gene	ENSG00000109065
Ensembl biotype	protein_coding
OMIM	620913
Entrez	26151

Gene structure

Transcript identifiers

Ensembl transcripts: 66 — 50 protein_coding, 10 retained_intron, 5 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000357814, ENST00000577428, ENST00000578798, ENST00000578822, ENST00000578862, ENST00000578947, ENST00000579218, ENST00000579837, ENST00000580216, ENST00000580301, ENST00000580632, ENST00000581136, ENST00000581451, ENST00000581466, ENST00000581762, ENST00000582118, ENST00000582168, ENST00000582359, ENST00000582524, ENST00000582870, ENST00000582993, ENST00000583476, ENST00000583689, ENST00000583757, ENST00000583834, ENST00000583989, ENST00000584022, ENST00000584409, ENST00000585240, ENST00000906714, ENST00000906715, ENST00000906716, ENST00000906717, ENST00000906718, ENST00000906719, ENST00000906720, ENST00000906721, ENST00000906722, ENST00000933013, ENST00000933014, ENST00000933015, ENST00000933016, ENST00000933017, ENST00000933018, ENST00000933019, ENST00000933020, ENST00000933021, ENST00000933022, ENST00000933023, ENST00000933024, ENST00000933025, ENST00000933026, ENST00000933027, ENST00000933028, ENST00000956106, ENST00000956107, ENST00000956108, ENST00000956109, ENST00000956110, ENST00000956111, ENST00000956112, ENST00000956113, ENST00000956114, ENST00000956115, ENST00000956116, ENST00000956117

RefSeq mRNA: 13 — MANE Select: NM_015654 NM_001305077, NM_001305078, NM_001305079, NM_001305080, NM_001305081, NM_001305082, NM_001305083, NM_001305084, NM_001305085, NM_001305086, NM_001305087, NM_001305088, NM_015654

CCDS: CCDS11706, CCDS77101, CCDS77102, CCDS77103, CCDS77104, CCDS82199, CCDS82200

Canonical transcript exons

ENST00000357814 — 7 exons

Exon	Start	End
ENSE00000744086	74771960	74772054
ENSE00000744087	74772218	74772277
ENSE00002705586	74776267	74776345
ENSE00002732383	74770529	74771858
ENSE00003461372	74772896	74773039
ENSE00003533791	74773576	74773688
ENSE00003561342	74775622	74775707

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 96.04.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.0010 / max 65.7214, expressed in 1760 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
168001	7.9954	1742
168000	1.0055	709

Top tissues by expression

292 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
adenohypophysis	UBERON:0002196	96.04	gold quality
right adrenal gland	UBERON:0001233	95.93	gold quality
left adrenal gland cortex	UBERON:0035825	95.68	gold quality
left adrenal gland	UBERON:0001234	95.66	gold quality
right adrenal gland cortex	UBERON:0035827	95.48	gold quality
adrenal cortex	UBERON:0001235	95.10	gold quality
pituitary gland	UBERON:0000007	94.81	gold quality
right ovary	UBERON:0002118	94.75	gold quality
left ovary	UBERON:0002119	94.68	gold quality
adrenal gland	UBERON:0002369	94.57	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.56	gold quality
right lobe of thyroid gland	UBERON:0001119	94.13	gold quality
left lobe of thyroid gland	UBERON:0001120	94.05	gold quality
cerebellar hemisphere	UBERON:0002245	93.63	gold quality
cerebellar cortex	UBERON:0002129	93.43	gold quality
endocervix	UBERON:0000458	93.08	gold quality
apex of heart	UBERON:0002098	92.93	gold quality
lower esophagus mucosa	UBERON:0035834	92.91	gold quality
left uterine tube	UBERON:0001303	92.86	gold quality
thyroid gland	UBERON:0002046	92.78	gold quality
body of uterus	UBERON:0009853	92.76	gold quality
tibial nerve	UBERON:0001323	92.68	gold quality
ascending aorta	UBERON:0001496	92.67	gold quality
thoracic aorta	UBERON:0001515	92.54	gold quality
ectocervix	UBERON:0012249	92.51	gold quality
stromal cell of endometrium	CL:0002255	92.47	gold quality
right frontal lobe	UBERON:0002810	92.26	gold quality
body of stomach	UBERON:0001161	92.25	gold quality
metanephros cortex	UBERON:0010533	92.24	gold quality
right lobe of liver	UBERON:0001114	92.07	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting NAT9, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-33A-3P	99.70	70.27	3362
HSA-MIR-6512-3P	99.65	66.07	1468
HSA-MIR-6720-5P	99.65	66.22	1459
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-6132	99.60	65.83	1554
HSA-MIR-6836-5P	99.60	65.62	1538
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-3176	99.25	64.35	954
HSA-MIR-3922-3P	99.25	64.96	1136
HSA-MIR-7974	99.24	65.48	1137
HSA-MIR-6744-3P	99.22	64.41	972
HSA-MIR-4757-5P	99.12	64.51	981
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-1286	99.09	66.23	1046
HSA-MIR-4716-5P	98.82	68.57	1168
HSA-MIR-4751	98.80	64.95	525
HSA-MIR-7977	98.65	66.18	2590
HSA-MIR-1914-5P	97.83	66.21	807
HSA-MIR-3928-3P	97.61	66.53	1096
HSA-MIR-665	97.60	65.64	1781
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-1224-3P	97.24	65.92	851
HSA-MIR-4776-5P	97.14	66.63	405

Literature-anchored findings (GeneRIF, showing 3)

• Results suggest that hNATL may play an important role in the development of embryo brain and may also be important for function of adult brain and gonad (PMID:16944568)
• no evidence was found for association of SNPs mapping to the NAT9, SLC9A3R1 and RAPTOR loci with susceptibility to psoriatic arthritis (PMID:19139211)
• N-Acetyltransferase 9 ameliorates Abeta42-mediated neurodegeneration in the Drosophila eye. (PMID:37507384)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	nat9	ENSDARG00000071425
mus_musculus	Nat9	ENSMUSG00000015542
rattus_norvegicus	Nat9	ENSRNOG00000003264
drosophila_melanogaster	Mnat9	FBGN0039859
caenorhabditis_elegans		WBGENE00022055

Protein

Protein identifiers

Alpha/beta-tubulin-N-acetyltransferase 9 — Q9BTE0 (reviewed: Q9BTE0)

Alternative names: Embryo brain-specific protein

All UniProt accessions (13): Q9BTE0, J3KRQ7, J3KSE9, J3KT72, J3QL33, J3QLF4, J3QQJ2, J3QQP3, J3QQR6, J3QRC3, J3QRL7, J3QS35, J3QSG9

UniProt curated annotations — full annotation on UniProt →

Function. N-acetyltransferase that mediates the acetylation of the N-terminal residues of alpha- and beta-tubulin.

Similarity. Belongs to the acetyltransferase family. GNAT subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BTE0-1	1	yes
Q9BTE0-2	2

RefSeq proteins (13): NP_001292006, NP_001292007, NP_001292008, NP_001292009, NP_001292010, NP_001292011, NP_001292012, NP_001292013, NP_001292014, NP_001292015, NP_001292016, NP_001292017, NP_056469* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000182	GNAT_dom	Domain
IPR016181	Acyl_CoA_acyltransferase	Homologous_superfamily
IPR039135	NAT9-like	Family

Pfam: PF13302

Catalyzed reactions (Rhea), 1 shown:

• N-terminal L-methionyl-[tubulin] + acetyl-CoA = N-terminal N(alpha)-acetyl-L-methionyl-[tubulin] + CoA + H(+) (RHEA:69607)

UniProt features (5 total): chain 1, domain 1, splice variant 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BTE0-F1	92.36	0.78

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 145 (showing top): GOBP_CHROMOSOME_ORGANIZATION, RRAGTTGT_UNKNOWN, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, CAGCTG_AP4_Q5, TTGCWCAAY_CEBPB_02, GOBP_MITOTIC_SPINDLE_ASSEMBLY, GOBP_ORGANELLE_FISSION, MYOD_01, GOBP_REGULATION_OF_SPINDLE_ORGANIZATION, BILD_E2F3_ONCOGENIC_SIGNATURE, GOBP_REGULATION_OF_CELL_CYCLE

GO Biological Process (0):

GO Molecular Function (6): tubulin N-terminal-methionine acetyltransferase activity (GO:0120519), protein binding (GO:0005515), N-acetyltransferase activity (GO:0008080), transferase activity (GO:0016740), acyltransferase activity (GO:0016746), acyltransferase activity, transferring groups other than amino-acyl groups (GO:0016747)

GO Cellular Component (1): protein-containing complex (GO:0032991)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein-N-terminal amino-acid acetyltransferase activity	1
binding	1
acetyltransferase activity	1
catalytic activity	1
transferase activity	1
acyltransferase activity	1
cellular_component	1

Protein interactions and networks

STRING

608 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NAT9	CARD14	Q9BXL6	807
NAT9	NHERF1	O14745	769
NAT9	ESCO1	Q5FWF5	746
NAT9	ESCO2	Q56NI9	744
NAT9	RPTOR	Q8N122	707
NAT9	CD300LB	A8K4G0	636
NAT9	CD300A	Q9UGN4	618
NAT9	SVOPL	Q8N434	614
NAT9	SLC22A4	Q9H015	576
NAT9	COQ9	O75208	573
NAT9	LRGUK	Q96M69	561
NAT9	EMP1	P54849	549
NAT9	RAD51AP1	Q96B01	542
NAT9	NAT14	Q8WUY8	532
NAT9	ZNF205	O95201	518

IntAct

20 interactions, top by confidence:

A	B	Type	Score
NAT9	EEF1E1	psi-mi:“MI:0915”(physical association)	0.670
EEF1E1	NAT9	psi-mi:“MI:0915”(physical association)	0.670
NUDT18	NAT9	psi-mi:“MI:0915”(physical association)	0.490
NAT9	NAT9	psi-mi:“MI:0915”(physical association)	0.370
GSK3B	NAT9	psi-mi:“MI:0915”(physical association)	0.370
NAT9	MAPK6	psi-mi:“MI:0915”(physical association)	0.370
NAT9	CHEK1	psi-mi:“MI:0914”(association)	0.350
NAT9	POTEF	psi-mi:“MI:0914”(association)	0.350
ANKRD55	H2AC11	psi-mi:“MI:0914”(association)	0.350
FLII	STRN	psi-mi:“MI:0914”(association)	0.350
NAT9	CRMP1	psi-mi:“MI:0915”(physical association)	0.000
NAT9	ERG28	psi-mi:“MI:0915”(physical association)	0.000
NAT9	CEP126	psi-mi:“MI:0915”(physical association)	0.000
ENO2	NAT9	psi-mi:“MI:0915”(physical association)	0.000
NAT9		psi-mi:“MI:0915”(physical association)	0.000
NAT9	LUC7L2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (24): NAT9 (Two-hybrid), NAT9 (Two-hybrid), EEF1E1 (Two-hybrid), CHEK1 (Affinity Capture-MS), MPP6 (Affinity Capture-MS), FLII (Affinity Capture-MS), NAT9 (Affinity Capture-RNA), LUC7L2 (Two-hybrid), C14orf1 (Two-hybrid), KIAA1377 (Two-hybrid), NAT9 (Two-hybrid), CRMP1 (Two-hybrid), NAT9 (Proximity Label-MS), FLII (Affinity Capture-MS), CHEK1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D6NER6, A5DSR2, A7SLC8, B0BML1, C4V922, C8YTM5, E9P8D2, O05501, O74234, P30418, P38074, P46328, P54441, P54562, Q09927, Q10170, Q29LW1, Q3THK7, Q3UG98, Q54J08, Q54MJ7, Q55EJ3, Q59DX8, Q59LF2, Q5WL79, Q61FA3, Q6BJF4, Q6C7G2, Q6PR33, Q7KWM5, Q86II5, Q87NZ6, Q8ESU9, Q8S8E7, Q8VYX1, Q944H0, Q9BKR0, Q9BTE0, Q9C6B9, Q9FR44

Diamond homologs: A7SLC8, P05332, Q3UG98, Q61FA3, Q86II5, Q8S8E7, Q9BKR0, Q9BTE0, Q9USR6, Q9V9V9, O31633, O31648, O31995, O34569, P0A948, P0A949, P0A950, P49855, P94482, P96579, Q7VG78, Q9I2H6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

37 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1601 predictions. Top by Δscore:

Variant	Effect	Δscore
17:74771954:CCTTA:C	donor_loss	1.0000
17:74771955:CTTA:C	donor_loss	1.0000
17:74771956:TTAC:T	donor_loss	1.0000
17:74771957:TA:T	donor_loss	1.0000
17:74771958:A:C	donor_loss	1.0000
17:74771959:C:CG	donor_loss	1.0000
17:74771959:CCTG:C	donor_gain	1.0000
17:74772057:C:CT	acceptor_gain	1.0000
17:74772059:C:CT	acceptor_gain	1.0000
17:74772060:A:T	acceptor_gain	1.0000
17:74772891:CAAA:C	donor_loss	1.0000
17:74772893:AACC:A	donor_loss	1.0000
17:74772894:A:C	donor_loss	1.0000
17:74773020:C:CT	acceptor_gain	1.0000
17:74773021:A:T	acceptor_gain	1.0000
17:74773023:C:CT	acceptor_gain	1.0000
17:74773036:CACT:C	acceptor_gain	1.0000
17:74773038:CT:C	acceptor_gain	1.0000
17:74773039:TC:T	acceptor_loss	1.0000
17:74773040:C:CC	acceptor_gain	1.0000
17:74773569:T:A	donor_gain	1.0000
17:74773574:A:AC	donor_gain	1.0000
17:74773575:C:CT	donor_gain	1.0000
17:74773575:CT:C	donor_gain	1.0000
17:74773575:CTGT:C	donor_gain	1.0000
17:74773587:T:TA	donor_gain	1.0000
17:74773612:ACT:A	donor_gain	1.0000
17:74773613:CTC:C	donor_gain	1.0000
17:74773615:C:CA	donor_gain	1.0000
17:74773682:GTACC:G	acceptor_loss	1.0000

AlphaMissense

1361 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:74772948:G:C	F94L	0.983
17:74772948:G:T	F94L	0.983
17:74772950:A:G	F94L	0.983
17:74773029:G:C	F67L	0.981
17:74773029:G:T	F67L	0.981
17:74773031:A:G	F67L	0.981
17:74771838:A:C	F170L	0.978
17:74771838:A:T	F170L	0.978
17:74771840:A:G	F170L	0.978
17:74771993:G:C	S152R	0.974
17:74771993:G:T	S152R	0.974
17:74771995:T:G	S152R	0.974
17:74771981:G:C	F156L	0.970
17:74771981:G:T	F156L	0.970
17:74771983:A:G	F156L	0.970
17:74771966:A:C	F161L	0.967
17:74771966:A:T	F161L	0.967
17:74771968:A:G	F161L	0.967
17:74773671:A:G	M32T	0.948
17:74773675:A:G	W31R	0.948
17:74773675:A:T	W31R	0.948
17:74773592:C:A	W58C	0.946
17:74773592:C:G	W58C	0.946
17:74772903:C:A	M109I	0.945
17:74772903:C:G	M109I	0.945
17:74772903:C:T	M109I	0.945
17:74773673:C:A	W31C	0.944
17:74773673:C:G	W31C	0.944
17:74772954:G:C	N92K	0.938
17:74772954:G:T	N92K	0.938

dbSNP variants (sampled 300 via entrez): RS1000175461 (17:74775486 G>A), RS1000883352 (17:74777604 C>G,T), RS1001063711 (17:74770852 T>C), RS1001480797 (17:74773345 T>A), RS1001636969 (17:74775010 C>A), RS1001969064 (17:74776195 G>A,C), RS1002399286 (17:74776389 C>T), RS1002430702 (17:74770521 C>G,T), RS1002641266 (17:74773344 C>T), RS1003068853 (17:74773575 C>T), RS1003402503 (17:74775222 C>G), RS1004375669 (17:74776114 A>C), RS1004641327 (17:74773928 C>A,G,T), RS1004777168 (17:74774247 G>C), RS1004834325 (17:74775862 A>C)

Disease associations

OMIM: gene MIM:620913 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST000368_4	Fibrinogen	8.000000e-11
GCST90002404_176	Red cell distribution width	3.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	2
bisphenol F	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects expression	1
afimoxifene	decreases expression	1
sodium arsenite	increases abundance, increases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
K 7174	increases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
jinfukang	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Cadmium	increases abundance, increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Doxorubicin	increases expression	1
Gasoline	increases abundance, increases expression, affects cotreatment	1
Indomethacin	affects cotreatment, decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Quercetin	increases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1
Cadmium Chloride	increases abundance, increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_SZ99	HAP1 NAT9 (-) 1	Cancer cell line	Male
CVCL_TA00	HAP1 NAT9 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.