NAA16

Summary

NAA16 (N-alpha-acetyltransferase 16, NatA auxiliary subunit, HGNC:26164) is a protein-coding gene on chromosome 13q14.11, encoding N-alpha-acetyltransferase 16, NatA auxiliary subunit (Q6N069). Auxillary subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity.

Enables ribosome binding activity. Involved in N-terminal protein amino acid acetylation; negative regulation of apoptotic process; and protein stabilization. Located in cytosol. Part of NatA complex.

Source: NCBI Gene 79612 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 127 total
• Druggable target: yes
• MANE Select transcript: NM_024561

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26164
Approved symbol	NAA16
Name	N-alpha-acetyltransferase 16, NatA auxiliary subunit
Location	13q14.11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22054, MGC40612, PRO2435
Ensembl gene	ENSG00000172766
Ensembl biotype	protein_coding
OMIM	619497
Entrez	79612

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 8 protein_coding_CDS_not_defined, 3 protein_coding, 1 nonsense_mediated_decay

ENST00000379406, ENST00000403412, ENST00000463114, ENST00000464857, ENST00000469708, ENST00000476980, ENST00000477452, ENST00000483215, ENST00000495148, ENST00000497143, ENST00000497727, ENST00000931430

RefSeq mRNA: 3 — MANE Select: NM_024561 NM_001110798, NM_018527, NM_024561

CCDS: CCDS45044, CCDS9379

Canonical transcript exons

ENST00000379406 — 20 exons

Exon	Start	End
ENSE00001287560	41336650	41336756
ENSE00001559903	41311267	41311582
ENSE00001779271	41358304	41358473
ENSE00003477104	41358810	41358962
ENSE00003480167	41355144	41355216
ENSE00003487465	41323056	41323190
ENSE00003506885	41331274	41331369
ENSE00003507156	41362031	41362159
ENSE00003510305	41374742	41374839
ENSE00003513264	41375405	41377030
ENSE00003519412	41316846	41316930
ENSE00003537013	41367439	41367652
ENSE00003575368	41325698	41325851
ENSE00003583901	41369090	41369283
ENSE00003605982	41372732	41372830
ENSE00003619284	41320667	41320824
ENSE00003621795	41373637	41373780
ENSE00003636453	41318806	41318910
ENSE00003640880	41372203	41372311
ENSE00003663916	41328724	41328843

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 95.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.5799 / max 142.0891, expressed in 1761 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
134837	11.3017	1740
134838	1.2714	634
134840	0.0068	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	95.73	gold quality
sural nerve	UBERON:0015488	95.66	gold quality
sperm	CL:0000019	93.72	gold quality
male germ cell	CL:0000015	91.87	gold quality
superficial temporal artery	UBERON:0001614	91.81	gold quality
calcaneal tendon	UBERON:0003701	91.44	gold quality
germinal epithelium of ovary	UBERON:0001304	91.29	gold quality
adrenal tissue	UBERON:0018303	91.24	gold quality
cardia of stomach	UBERON:0001162	91.17	gold quality
ventricular zone	UBERON:0003053	91.08	gold quality
mucosa of urinary bladder	UBERON:0001259	90.40	gold quality
pancreas	UBERON:0001264	90.35	gold quality
bone marrow	UBERON:0002371	90.25	gold quality
pylorus	UBERON:0001166	90.15	gold quality
corpus callosum	UBERON:0002336	90.12	gold quality
cerebellar hemisphere	UBERON:0002245	89.89	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.80	gold quality
trabecular bone tissue	UBERON:0002483	89.80	gold quality
cerebellar cortex	UBERON:0002129	89.77	gold quality
cerebellum	UBERON:0002037	89.60	gold quality
embryo	UBERON:0000922	89.56	gold quality
skin of hip	UBERON:0001554	89.55	gold quality
visceral pleura	UBERON:0002401	89.25	gold quality
thymus	UBERON:0002370	89.23	gold quality
cervix squamous epithelium	UBERON:0006922	89.12	silver quality
bone marrow cell	CL:0002092	88.87	gold quality
uterine cervix	UBERON:0000002	88.66	gold quality
endocervix	UBERON:0000458	88.62	gold quality
right hemisphere of cerebellum	UBERON:0014890	88.57	gold quality
oviduct epithelium	UBERON:0004804	88.52	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.35
E-MTAB-6379	no	1141.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

34 targeting NAA16, 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-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-3941	99.86	70.54	2735
HSA-MIR-4320	99.75	65.80	793
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-4672	99.50	71.58	2893
HSA-MIR-7849-3P	99.47	68.17	1224
HSA-MIR-582-5P	99.47	70.79	2635
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-410-3P	99.27	69.98	2457
HSA-MIR-520G-3P	98.91	67.38	1914
HSA-MIR-520H	98.91	67.38	1914

Literature-anchored findings (GeneRIF, showing 1)

• hNaa16p (NARG1L) interacts with hNaa10p (hArd1) making a distinct ribosome associated human NatA N-terminal acetyltransferase complex. hNAA16 is expressed in a variety of human cell lines and specific knockdown of hNAA16 induces cell death. (PMID:19480662)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Naa16	ENSMUSG00000022020
rattus_norvegicus	Naa16	ENSRNOG00000045863
drosophila_melanogaster	Naa15-16	FBGN0031020
caenorhabditis_elegans		WBGENE00021754

Paralogs (2): NAA25 (ENSG00000111300), NAA15 (ENSG00000164134)

Protein

Protein identifiers

N-alpha-acetyltransferase 16, NatA auxiliary subunit — Q6N069 (reviewed: Q6N069)

Alternative names: NMDA receptor-regulated 1-like protein

All UniProt accessions (2): Q6N069, A4FU51

UniProt curated annotations — full annotation on UniProt →

Function. Auxillary subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity.

Subunit / interactions. Component of the N-terminal acetyltransferase A (NatA) complex composed of NAA10 and NAA16.

Isoforms (5)

UniProt ID	Names	Canonical?
Q6N069-1	1	yes
Q6N069-2	2, Long
Q6N069-3	3
Q6N069-4	4, Short
Q6N069-5	5

RefSeq proteins (3): NP_001104268, NP_060997, NP_078837* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR013105	TPR_2	Repeat
IPR019734	TPR_rpt	Repeat
IPR021183	NatA_aux_su	Family

Pfam: PF07719, PF12569

UniProt features (19 total): splice variant 8, repeat 7, chain 1, sequence variant 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6N069-F1	89.49	0.79

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 163 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_PROTEIN_MATURATION, GOBP_PROTEIN_STABILIZATION, GOBP_REGULATION_OF_PROTEIN_STABILITY, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, MODULE_332, chr13q14, MULLIGHAN_MLL_SIGNATURE_2_DN, NUYTTEN_EZH2_TARGETS_DN, GOCC_TRANSFERASE_COMPLEX, GOCC_TRANSCRIPTION_REGULATOR_COMPLEX, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_N_TERMINAL_PROTEIN_ACETYLTRANSFERASE_COMPLEX, VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP

GO Biological Process (5): positive regulation of DNA-templated transcription (GO:0045893), protein stabilization (GO:0050821), protein maturation (GO:0051604), N-terminal protein amino acid acetylation (GO:0006474), negative regulation of apoptotic process (GO:0043066)

GO Molecular Function (4): acetyltransferase activator activity (GO:0010698), ribosome binding (GO:0043022), protein binding (GO:0005515), acetyltransferase activity (GO:0016407)

GO Cellular Component (6): nucleus (GO:0005634), transcription regulator complex (GO:0005667), cytoplasm (GO:0005737), cytosol (GO:0005829), NatA complex (GO:0031415), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
regulation of protein stability	1
gene expression	1
protein metabolic process	1
protein acetylation	1
N-terminal protein amino acid modification	1
protein maturation	1
apoptotic process	1
regulation of apoptotic process	1
negative regulation of programmed cell death	1
enzyme activator activity	1
acetyltransferase activity	1
ribonucleoprotein complex binding	1
binding	1
acyltransferase activity, transferring groups other than amino-acyl groups	1
intracellular membrane-bounded organelle	1
protein-containing complex	1
intracellular anatomical structure	1
cytoplasm	1
N-terminal protein acetyltransferase complex	1
extracellular vesicle	1

Protein interactions and networks

STRING

1050 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NAA16	NAA10	P41227	899
NAA16	NAA11	Q9BSU3	870
NAA16	HYPK	Q9NX55	724
NAA16	NAA50	Q9GZZ1	717
NAA16	NAA20	P61599	646
NAA16	NAA30	Q147X3	645
NAA16	NAA25	Q14CX7	604
NAA16	NAA35	Q5VZE5	589
NAA16	NAA40	Q86UY6	585
NAA16	NAA60	Q9H7X0	543
NAA16	VWA8	A3KMH1	476
NAA16	TCEA1	P23193	437
NAA16	SIRT1	Q96EB6	406
NAA16	MTRF1	O75570	392
NAA16	PROSER1	Q86XN7	376

IntAct

32 interactions, top by confidence:

A	B	Type	Score
NAA15	NAA10	psi-mi:“MI:0914”(association)	0.840
NAA10	NAA16	psi-mi:“MI:0914”(association)	0.710
NAA10	NAA16	psi-mi:“MI:0915”(physical association)	0.710
HYPK	NAA10	psi-mi:“MI:0914”(association)	0.640
NAA50	NAA16	psi-mi:“MI:0915”(physical association)	0.620
NAA11	NAA16	psi-mi:“MI:0915”(physical association)	0.560
NAA10	OFD1	psi-mi:“MI:0914”(association)	0.480
NAA16	HNRNPU	psi-mi:“MI:0915”(physical association)	0.400
NAA16	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
Naa10	NAA10	psi-mi:“MI:0915”(physical association)	0.400
Naa10	MYO9A	psi-mi:“MI:0914”(association)	0.350
Naa11		psi-mi:“MI:0914”(association)	0.350
Naa50	WDR46	psi-mi:“MI:0914”(association)	0.350
RIPK4	VWA8	psi-mi:“MI:0914”(association)	0.350
MRPS11	HNRNPR	psi-mi:“MI:0914”(association)	0.350
TSGA10IP	NAA10	psi-mi:“MI:0914”(association)	0.350
HYPK	APOA1	psi-mi:“MI:0914”(association)	0.350
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
FGFR1	NDUFA4	psi-mi:“MI:0914”(association)	0.350
ALPK2	C2CD4B	psi-mi:“MI:0914”(association)	0.350
NAA11	DVL2	psi-mi:“MI:0914”(association)	0.350
NAA15	ARRB1	psi-mi:“MI:0914”(association)	0.350
TSGA10IP	BRCA2	psi-mi:“MI:0914”(association)	0.350
HYPK	RPSA2	psi-mi:“MI:0914”(association)	0.350
NAA50	VSIG8	psi-mi:“MI:0914”(association)	0.350
NAA10	SUPT5H	psi-mi:“MI:0914”(association)	0.350

BioGRID (53): NAA16 (Affinity Capture-MS), NAA16 (Co-fractionation), NAA16 (Co-fractionation), NAA16 (Co-fractionation), NAA16 (Co-fractionation), NAA16 (Co-fractionation), NAA16 (Affinity Capture-MS), NAA16 (Two-hybrid), NAA16 (Affinity Capture-MS), NAA16 (Affinity Capture-MS), NAA16 (Affinity Capture-MS), NAA16 (Affinity Capture-MS), NAA16 (Affinity Capture-MS), NAA16 (Affinity Capture-MS), NAA16 (Affinity Capture-MS)

ESM2 similar proteins: A0JN39, A8WGF4, B5DGH9, D2SW95, O00232, O60763, O95782, P17426, P23514, P41541, P53618, P91926, P93768, Q05AY2, Q0JNK5, Q1LUA8, Q29N38, Q2KJ25, Q3B8M3, Q3UGF1, Q4R4I8, Q53PC7, Q5R4J9, Q5R664, Q5R922, Q5RBI3, Q5VQ78, Q5XI83, Q5ZIA5, Q5ZLA5, Q66HV4, Q6DRI1, Q6H8D5, Q6H8D6, Q6N069, Q6NWV3, Q6P7L9, Q7QG73, Q80UM3, Q8BWQ6

Diamond homologs: O74985, P12945, Q5R4J9, Q6N069, Q80UM3, Q8VZM1, Q9BXJ9, Q9DBB4, Q9Y7X2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	111
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3778 predictions. Top by Δscore:

Variant	Effect	Δscore
13:41311578:TCTTG:T	donor_gain	1.0000
13:41311583:G:GG	donor_gain	1.0000
13:41311584:T:A	donor_loss	1.0000
13:41316841:TACA:T	acceptor_loss	1.0000
13:41316843:CA:C	acceptor_loss	1.0000
13:41316844:A:AG	acceptor_gain	1.0000
13:41316844:A:AT	acceptor_loss	1.0000
13:41316845:G:GG	acceptor_gain	1.0000
13:41316845:G:T	acceptor_loss	1.0000
13:41316845:GA:G	acceptor_gain	1.0000
13:41316845:GAA:G	acceptor_gain	1.0000
13:41316845:GAAAT:G	acceptor_gain	1.0000
13:41316926:TGGAG:T	donor_loss	1.0000
13:41316928:G:GT	donor_gain	1.0000
13:41316928:G:T	donor_gain	1.0000
13:41316930:GGTAT:G	donor_loss	1.0000
13:41316931:G:GA	donor_loss	1.0000
13:41320818:TTACC:T	donor_gain	1.0000
13:41320821:CCGA:C	donor_gain	1.0000
13:41320822:CGAG:C	donor_loss	1.0000
13:41320823:GA:G	donor_gain	1.0000
13:41320824:AG:A	donor_loss	1.0000
13:41320825:G:GG	donor_gain	1.0000
13:41320825:GT:G	donor_loss	1.0000
13:41320826:TAAGT:T	donor_loss	1.0000
13:41320827:AA:A	donor_loss	1.0000
13:41320828:AGTA:A	donor_loss	1.0000
13:41323050:TTTTA:T	acceptor_loss	1.0000
13:41323051:TTTA:T	acceptor_loss	1.0000
13:41323053:TA:T	acceptor_loss	1.0000

AlphaMissense

5774 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:41316876:G:C	G29R	1.000
13:41316877:G:A	G29D	1.000
13:41318815:C:A	A50D	1.000
13:41318818:T:A	M51K	1.000
13:41318823:G:A	G53R	1.000
13:41318823:G:C	G53R	1.000
13:41318824:G:A	G53E	1.000
13:41318827:T:C	L54S	1.000
13:41318872:T:A	V69D	1.000
13:41318880:G:A	G72R	1.000
13:41318880:G:C	G72R	1.000
13:41318881:G:A	G72E	1.000
13:41318884:T:C	L73P	1.000
13:41320668:T:G	C82W	1.000
13:41320669:T:A	W83R	1.000
13:41320669:T:C	W83R	1.000
13:41320672:C:G	H84D	1.000
13:41320674:T:A	H84Q	1.000
13:41320674:T:G	H84Q	1.000
13:41320676:T:A	V85E	1.000
13:41320681:G:A	G87R	1.000
13:41320681:G:C	G87R	1.000
13:41320682:G:A	G87E	1.000
13:41320682:G:T	G87V	1.000
13:41320685:T:C	L88P	1.000
13:41320693:C:A	R91S	1.000
13:41320694:G:C	R91P	1.000
13:41320717:G:C	A99P	1.000
13:41320718:C:A	A99D	1.000
13:41320738:G:C	A106P	1.000

dbSNP variants (sampled 300 via entrez): RS1000027487 (13:41349193 A>G), RS1000059218 (13:41326428 A>C,G), RS1000075493 (13:41345268 C>A), RS1000104628 (13:41332891 A>G), RS1000136118 (13:41345860 C>A), RS1000299452 (13:41310368 G>A), RS1000326246 (13:41363500 G>A), RS1000515592 (13:41311812 A>C,G,T), RS1000628385 (13:41351023 G>A,C), RS1000691879 (13:41352498 T>C), RS1000706337 (13:41311482 G>C), RS1000709896 (13:41338779 A>G), RS1000711302 (13:41334218 A>G), RS1000735134 (13:41376289 GA>G,GAA,GAAAAAAAAAAA), RS1000774902 (13:41344785 A>G)

Disease associations

OMIM: gene MIM:619497 | 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
GCST006628_20	Systolic blood pressure	3.000000e-13
GCST90013442_21	Keratoconus	6.000000e-35

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3430873 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	increases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
2,3,5-(triglutathion-S-yl)hydroquinone	increases ADP-ribosylation	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Vorinostat	decreases expression	1
Amiodarone	increases expression	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Mercuric Chloride	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Ribonucleotides	affects binding	1
Thimerosal	decreases expression	1
Valproic Acid	increases expression	1
Aflatoxin B1	increases methylation	1
Asbestos, Serpentine	increases methylation	1
Asbestos, Crocidolite	affects expression	1
Acrylamide	increases 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_SZ73	HAP1 NAA16 (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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