NAT16

Summary

NAT16 (N-acetyltransferase 16 (putative), HGNC:22030) is a protein-coding gene on chromosome 7q22.1, encoding Probable N-acetyltransferase 16 (Q8N8M0). Probable N-acetyltransferase.

Predicted to enable acyltransferase activity, transferring groups other than amino-acyl groups.

Source: NCBI Gene 375607 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 75 total
• MANE Select transcript: NM_198571

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22030
Approved symbol	NAT16
Name	N-acetyltransferase 16 (putative)
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ39237
Ensembl gene	ENSG00000167011
Ensembl biotype	protein_coding
OMIM	615783
Entrez	375607

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000300303, ENST00000443096, ENST00000444446, ENST00000455377

RefSeq mRNA: 3 — MANE Select: NM_198571 NM_001369694, NM_001369695, NM_198571

CCDS: CCDS5713

Canonical transcript exons

ENST00000300303 — 4 exons

Exon	Start	End
ENSE00001108752	101174496	101174811
ENSE00001108756	101173296	101173520
ENSE00001245316	101180042	101180293
ENSE00001245325	101170496	101172651

Expression profiles

Bgee: expression breadth broad, 66 present calls, max score 81.81.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0731 / max 10.2580, expressed in 28 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85309	0.0491	18
85308	0.0240	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	81.81	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	75.25	gold quality
buccal mucosa cell	CL:0002336	73.63	silver quality
biceps brachii	UBERON:0001507	72.71	silver quality
ganglionic eminence	UBERON:0004023	71.75	gold quality
tendon of biceps brachii	UBERON:0008188	71.69	silver quality
islet of Langerhans	UBERON:0000006	70.54	gold quality
nucleus accumbens	UBERON:0001882	69.03	gold quality
deltoid	UBERON:0001476	68.42	silver quality
esophagus squamous epithelium	UBERON:0006920	68.28	gold quality
lateral globus pallidus	UBERON:0002476	67.90	gold quality
trabecular bone tissue	UBERON:0002483	67.51	gold quality
oocyte	CL:0000023	66.20	gold quality
heart right ventricle	UBERON:0002080	65.82	gold quality
hypothalamus	UBERON:0001898	65.01	gold quality
nasal cavity epithelium	UBERON:0005384	64.94	gold quality
pituitary gland	UBERON:0000007	64.66	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	64.65	silver quality
epithelium of nasopharynx	UBERON:0001951	64.39	gold quality
substantia nigra pars reticulata	UBERON:0001966	64.38	silver quality
substantia nigra pars compacta	UBERON:0001965	64.23	silver quality
adenohypophysis	UBERON:0002196	64.02	gold quality
anterior cingulate cortex	UBERON:0009835	64.02	gold quality
cartilage tissue	UBERON:0002418	63.46	gold quality
gingiva	UBERON:0001828	62.76	gold quality
skin of hip	UBERON:0001554	62.73	gold quality
gingival epithelium	UBERON:0001949	62.53	gold quality
sperm	CL:0000019	62.19	gold quality
parotid gland	UBERON:0001831	61.75	gold quality
decidua	UBERON:0002450	61.73	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-137537	yes	6.44
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting NAT16, 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-7110-3P	100.00	73.18	2486
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-7845-5P	99.88	64.88	771
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-6817-3P	99.79	68.35	2126
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-1275	99.47	67.90	2749
HSA-MIR-520A-5P	99.35	66.72	1632
HSA-MIR-525-5P	99.35	66.85	1615
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-5701	98.97	69.54	1502

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
danio_rerio	nat16l	ENSDARG00000076402
danio_rerio	nat16	ENSDARG00000086222

Protein

Protein identifiers

Probable N-acetyltransferase 16 — Q8N8M0 (reviewed: Q8N8M0)

All UniProt accessions (2): Q8N8M0, C9JB11

UniProt curated annotations — full annotation on UniProt →

Function. Probable N-acetyltransferase. Shows only trace activity toward L-His and no N-acetyltransferase activity toward other amino acids. The physiological substrate of this enzyme is unknown.

Miscellaneous. NAT16 is the ortholog of the ectothermic vertebrates enzyme HISAT (AC I3J7Q8) responsible for the synthesis of N-acetyl-histidine (NAH). NAT16 protein, unlike fish HISAT, has only trace enzyme activity for NAH synthesis.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N8M0-1	1	yes
Q8N8M0-2	2

RefSeq proteins (3): NP_001356623, NP_001356624, NP_940973* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000182	GNAT_dom	Domain
IPR016181	Acyl_CoA_acyltransferase	Homologous_superfamily
IPR056483	Hisat_C	Domain

Pfam: PF00583, PF24066

Enzyme classification (BRENDA):

• EC 2.3.1.33 — histidine N-acetyltransferase (BRENDA: 4 organisms, 6 substrates, 15 inhibitors, 2 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ACETYLCOENZYME A	0.027	1
L-HISTIDINE	0.45	1

UniProt features (7 total): splice variant 2, chain 1, domain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
9EMT	X-RAY DIFFRACTION	1.4
9EN3	X-RAY DIFFRACTION	1.4
9EMP	X-RAY DIFFRACTION	1.45
9EMD	X-RAY DIFFRACTION	1.6
9EMO	X-RAY DIFFRACTION	1.9

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N8M0-F1	88.07	0.84

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GOMF_ACYLTRANSFERASE_ACTIVITY, KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES, KUMAR_AUTOPHAGY_NETWORK, CBX7_TARGET_GENES, NFKBIA_TARGET_GENES, MIR4723_5P, MIR6870_5P, MIR7111_5P, MIR5698, MIR5701, MIR939_5P, GSE14000_TRANSLATED_RNA_VS_MRNA_16H_LPS_DC_DN, chr7q22, GOMF_ACYLTRANSFERASE_ACTIVITY_TRANSFERRING_GROUPS_OTHER_THAN_AMINO_ACYL_GROUPS

GO Biological Process (0):

GO Molecular Function (3): acyltransferase activity, transferring groups other than amino-acyl groups (GO:0016747), transferase activity (GO:0016740), acyltransferase activity (GO:0016746)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
acyltransferase activity	1
catalytic activity	1
transferase activity	1

Protein interactions and networks

STRING

104 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NAT16	CARNMT1	Q8N4J0	542
NAT16	TRAPPC14	Q8WVR3	445
NAT16	CARNS1	A5YM72	419
NAT16	NAT10	Q9H0A0	417
NAT16	ZAN	Q9Y493	406
NAT16	NAA40	Q86UY6	392
NAT16	HBQ1	P09105	369
NAT16	AP1S1	P61966	348
NAT16	PLS1	Q14651	310
NAT16	AIG1	Q9NVV5	309
NAT16	SLC6A5	Q9Y345	274
NAT16	SF3B2	Q13435	263
NAT16	RBM3	P98179	226
NAT16	MIF4GD	A9UHW6	210
NAT16	PITX3	O75364	204
NAT16	NXNL1	Q96CM4	204

IntAct

5 interactions, top by confidence:

A	B	Type	Score
TIGD3	CTPS1	psi-mi:“MI:0914”(association)	0.530
NAT16	CCT6A	psi-mi:“MI:0914”(association)	0.350
NAT16	HSPA8	psi-mi:“MI:0914”(association)	0.350

BioGRID (13): METTL2B (Affinity Capture-MS), RBM12 (Affinity Capture-MS), NAT16 (Affinity Capture-MS), STUB1 (Affinity Capture-MS), CCT6A (Affinity Capture-MS), GNB2 (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), METTL2B (Affinity Capture-MS), FUT1 (Affinity Capture-MS), NAT16 (Affinity Capture-MS), RBM12 (Affinity Capture-MS), NAT16 (Affinity Capture-Western), NAT16 (Affinity Capture-Western)

ESM2 similar proteins: A0A1B3PEJ0, A2X4M8, A2X8W3, A2XFU4, A2XFU5, A2YQ58, A8IF44, A8JBB2, G4NEA9, O24594, P17289, P45623, Q0D3F2, Q0DM48, Q0DSH9, Q0DY59, Q10KF5, Q10MI9, Q10RZ1, Q4ADV8, Q53JI9, Q5GA22, Q5NAI7, Q5VQG4, Q5W6G0, Q5Z678, Q6ATB2, Q6K7B8, Q6L534, Q6Z690, Q6Z955, Q750J3, Q75AT3, Q75IS2, Q7XK12, Q8H8N3, Q8LH82, Q8N8M0, Q94GM9, Q9AV88

Diamond homologs: I3J7Q8, Q0P4Y1, Q8N8M0, U3U715

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	72
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

796 predictions. Top by Δscore:

Variant	Effect	Δscore
7:101173290:TCTCA:T	donor_loss	1.0000
7:101173291:CTCAC:C	donor_loss	1.0000
7:101173292:TCA:T	donor_loss	1.0000
7:101173293:CACCT:C	donor_loss	1.0000
7:101173294:A:T	donor_loss	1.0000
7:101173295:C:CG	donor_loss	1.0000
7:101173517:CGAT:C	acceptor_gain	1.0000
7:101173520:TCTG:T	acceptor_loss	1.0000
7:101173521:CTGCG:C	acceptor_loss	1.0000
7:101174522:C:CT	donor_gain	1.0000
7:101174614:T:TA	donor_gain	1.0000
7:101174807:TGACC:T	acceptor_gain	1.0000
7:101174808:GACC:G	acceptor_gain	1.0000
7:101174809:ACC:A	acceptor_gain	1.0000
7:101174809:ACCC:A	acceptor_loss	1.0000
7:101174810:CC:C	acceptor_gain	1.0000
7:101174810:CCC:C	acceptor_gain	1.0000
7:101174811:CC:C	acceptor_gain	1.0000
7:101174812:C:CC	acceptor_gain	1.0000
7:101174812:C:CG	acceptor_loss	1.0000
7:101174813:T:C	acceptor_loss	1.0000
7:101173295:CCTG:C	donor_gain	0.9900
7:101173521:C:CC	acceptor_gain	0.9900
7:101173522:T:A	acceptor_loss	0.9900
7:101174494:A:AC	donor_gain	0.9900
7:101174495:C:CC	donor_gain	0.9900
7:101174495:CCACG:C	donor_gain	0.9900
7:101174502:T:TA	donor_gain	0.9900
7:101174523:C:CT	donor_gain	0.9900
7:101174812:C:T	acceptor_gain	0.9900

AlphaMissense

2319 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:101172453:A:G	W246R	0.999
7:101172453:A:T	W246R	0.999
7:101173460:G:T	R125S	0.998
7:101173466:C:G	G123R	0.998
7:101173466:C:T	G123R	0.998
7:101172451:C:A	W246C	0.997
7:101172451:C:G	W246C	0.997
7:101173466:C:A	G123W	0.996
7:101174573:A:G	Y79H	0.996
7:101172452:C:A	W246L	0.995
7:101173462:A:G	L124P	0.995
7:101173465:C:T	G123E	0.995
7:101172187:G:C	F334L	0.994
7:101172187:G:T	F334L	0.994
7:101172189:A:G	F334L	0.994
7:101172456:C:G	D245H	0.994
7:101173351:C:G	R161P	0.994
7:101173516:G:T	A106E	0.994
7:101174575:T:A	D78V	0.994
7:101172455:T:A	D245V	0.993
7:101174515:G:T	A98D	0.993
7:101173426:G:T	A136D	0.992
7:101173508:A:G	S109P	0.992
7:101174549:A:G	W87R	0.992
7:101174549:A:T	W87R	0.992
7:101174558:A:C	Y84D	0.992
7:101174569:A:G	L80P	0.992
7:101174576:C:G	D78H	0.992
7:101173442:G:T	R131S	0.991
7:101173459:C:G	R125P	0.991

dbSNP variants (sampled 300 via entrez): RS1000275390 (7:101174055 C>T), RS1000853888 (7:101173895 T>C), RS1000978974 (7:101179537 A>G), RS1001031284 (7:101179845 G>A,C,T), RS1001162583 (7:101177969 A>G,T), RS1001327930 (7:101175028 C>T), RS1001367180 (7:101180887 A>G), RS1001391057 (7:101174123 A>T), RS1001487809 (7:101178177 T>C), RS1001587451 (7:101174889 T>A), RS1001964212 (7:101182196 G>C), RS1002013828 (7:101171210 G>A,T), RS1002092360 (7:101176897 ATTTTTATTTTT>A), RS1002236685 (7:101171680 C>G,T), RS1002269211 (7:101171393 CT>C)

Disease associations

OMIM: gene MIM:615783 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST012020_393	Serum metabolite levels	9.000000e-14
GCST012020_394	Serum metabolite levels	1.000000e-16
GCST012020_395	Serum metabolite levels	3.000000e-57

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, decreases expression	2
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	2
lasiocarpine	decreases expression	1
methyleugenol	decreases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
terbufos	increases methylation	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
abrine	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Troglitazone	decreases expression	1
Fonofos	increases methylation	1
Niclosamide	increases expression	1
Parathion	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_E2D6	HAP1 NAT16 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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