NAA60

Summary

NAA60 (N-alpha-acetyltransferase 60, NatF catalytic subunit, HGNC:25875) is a protein-coding gene on chromosome 16p13.3, encoding N-alpha-acetyltransferase 60 (Q9H7X0). N-alpha-acetyltransferase that specifically mediates the acetylation of N-terminal residues of the transmembrane proteins, with a strong preference for N-termini facing the cytosol.

This gene encodes an enzyme that localizes to the Golgi apparatus, where it transfers an acetyl group to the N-terminus of free proteins. This enzyme acts on histones, and its activity is important for chromatin assembly and chromosome integrity. Alternative splicing and the use of alternative promoters results in multiple transcript variants. The upstream promoter is located in a differentially methylated region (DMR) and undergoes imprinting; transcript variants originating from this position are expressed from the maternal allele.

Source: NCBI Gene 79903 — RefSeq curated summary.

At a glance

• Gene–disease (curated): basal ganglia calcification, idiopathic, 9, autosomal recessive (Strong, GenCC)
• GWAS associations: 5
• Clinical variants (ClinVar): 49 total — 6 pathogenic
• Phenotypes (HPO): 85
• Druggable target: yes
• MANE Select transcript: NM_001083601

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25875
Approved symbol	NAA60
Name	N-alpha-acetyltransferase 60, NatF catalytic subunit
Location	16p13.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ14154, HAT4, NatF, hNaa60
Ensembl gene	ENSG00000122390
Ensembl biotype	protein_coding
OMIM	614246
Entrez	79903

Gene structure

Transcript identifiers

Ensembl transcripts: 42 — 25 protein_coding, 8 retained_intron, 7 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000360862, ENST00000407558, ENST00000414063, ENST00000421765, ENST00000424546, ENST00000570372, ENST00000570551, ENST00000570819, ENST00000571107, ENST00000571696, ENST00000571798, ENST00000572131, ENST00000572169, ENST00000572584, ENST00000572739, ENST00000572757, ENST00000572942, ENST00000573201, ENST00000573345, ENST00000573580, ENST00000573593, ENST00000573617, ENST00000574256, ENST00000574328, ENST00000574380, ENST00000574762, ENST00000574950, ENST00000575042, ENST00000575076, ENST00000575733, ENST00000575754, ENST00000575936, ENST00000576787, ENST00000576819, ENST00000576916, ENST00000577013, ENST00000615865, ENST00000648681, ENST00000649205, ENST00000649360, ENST00000864505, ENST00000932110

RefSeq mRNA: 9 — MANE Select: NM_001083601 NM_001083600, NM_001083601, NM_001317093, NM_001317094, NM_001317095, NM_001317096, NM_001317097, NM_001317098, NM_024845

CCDS: CCDS45396, CCDS81937, CCDS81938, CCDS81939, CCDS81940, CCDS81941

Canonical transcript exons

ENST00000407558 — 8 exons

Exon	Start	End
ENSE00002648422	3443680	3443837
ENSE00002656365	3485467	3486953
ENSE00003461333	3484699	3485061
ENSE00003503367	3483363	3483597
ENSE00003533124	3482502	3482598
ENSE00003538620	3476222	3476337
ENSE00003599277	3448471	3448540
ENSE00003654850	3479471	3479600

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 98.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 54.6317 / max 222.3631, expressed in 1823 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
152425	20.4603	1804
152426	13.3766	1803
152427	13.2892	1802
152424	6.9165	1694
207710	0.4554	237
152428	0.1336	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	98.42	gold quality
endothelial cell	CL:0000115	97.04	gold quality
ileal mucosa	UBERON:0000331	96.56	gold quality
cervix squamous epithelium	UBERON:0006922	96.21	gold quality
parotid gland	UBERON:0001831	95.64	gold quality
body of stomach	UBERON:0001161	95.11	gold quality
mucosa of transverse colon	UBERON:0004991	94.51	gold quality
metanephric glomerulus	UBERON:0004736	94.50	gold quality
apex of heart	UBERON:0002098	94.49	gold quality
renal medulla	UBERON:0000362	94.42	gold quality
duodenum	UBERON:0002114	94.40	gold quality
renal glomerulus	UBERON:0000074	94.34	gold quality
stromal cell of endometrium	CL:0002255	94.27	gold quality
adult mammalian kidney	UBERON:0000082	94.26	gold quality
stomach	UBERON:0000945	94.20	gold quality
kidney epithelium	UBERON:0004819	94.20	gold quality
cortex of kidney	UBERON:0001225	94.18	gold quality
olfactory bulb	UBERON:0002264	94.15	gold quality
metanephros cortex	UBERON:0010533	94.01	gold quality
metanephros	UBERON:0000081	93.95	gold quality
colonic mucosa	UBERON:0000317	93.94	gold quality
cardia of stomach	UBERON:0001162	93.92	gold quality
adenohypophysis	UBERON:0002196	93.90	gold quality
blood	UBERON:0000178	93.83	gold quality
pituitary gland	UBERON:0000007	93.80	gold quality
granulocyte	CL:0000094	93.57	gold quality
nephron tubule	UBERON:0001231	93.56	gold quality
right lobe of liver	UBERON:0001114	93.54	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.52	gold quality
kidney	UBERON:0002113	93.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-70580	no	162.86
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

93 targeting NAA60, 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-4692	100.00	67.32	2066
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-103A-3P	99.98	69.14	1595
HSA-MIR-107	99.98	69.14	1595
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-11181-3P	99.75	66.38	2205
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-149-3P	99.72	68.22	3963

Literature-anchored findings (GeneRIF, showing 10)

• Naa60 is an N-terminal acetyltransferase defined as NatF. Human and Drosophila melanogaster Naa60 acetylate Met-Lys- and other Met-starting N-termini. In Drosophila cells, NAA60 knockdown induced chromosomal segregation defects. (PMID:21750686)
• HAT4 is an important player in the organization and function of the genome and may contribute to the diversity and complexity of higher eukaryotic organisms [HAT4] (PMID:21981917)
• Naa60 is necessary for maintenance of the Golgi ribbon through its Nt-acetylation of substrate protein(s) that is/are involved in Golgi ribbon structural and/or functional organization. (PMID:25732826)
• Knockdown of the N-terminal acetyltransferase Naa60 compromises Golgi ribbon integrity. (PMID:26164078)
• Results from a study on gene expression variability markers in early-stage human embryos shows that NAA60 (NAT15) is a putative expression variability marker for the 3-day, 8-cell embryo stage. (PMID:26288249)
• The first crystal structure of the N-terminal acetyltransferase Naa60 reveals two elongated loops important for substrate-specific binding not found in other NAT structures. (PMID:27320834)
• The hNaa60 protein contains an amphipathic helix following its GNAT domain that may contribute to Golgi localization of hNaa60, and the beta7-beta8 hairpin adopted different conformations in the hNaa60(1-242) and hNaa60(1-199) crystal structures. (PMID:27550639)
• analysis of the mode of cytosolic Naa60 anchoring to the Golgi apparatus, most likely occurring post-translationally and specifically facilitating post-translational N-terminal acetylation of many transmembrane proteins (PMID:28196861)
• NAA60 (HAT4): the newly discovered bi-functional Golgi member of the acetyltransferase family. (PMID:36539894)
• Biallelic NAA60 variants with impaired n-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications. (PMID:38480682)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	naa60	ENSDARG00000061185
mus_musculus	Naa60	ENSMUSG00000005982
rattus_norvegicus	Naa60	ENSRNOG00000007280
drosophila_melanogaster	Naa60	FBGN0036039
caenorhabditis_elegans	F30F8.10	WBGENE00009277

Protein

Protein identifiers

N-alpha-acetyltransferase 60 — Q9H7X0 (reviewed: Q9H7X0)

Alternative names: Histone acetyltransferase type B protein 4, N-acetyltransferase 15, N-alpha-acetyltransferase F

All UniProt accessions (13): A0A384NYU5, Q9H7X0, I3L153, I3L1B9, I3L1T4, I3L1X5, I3L205, I3L2B4, I3L2K7, I3L2M6, I3L4Q3, I3L4Q5, I3L4T5

UniProt curated annotations — full annotation on UniProt →

Function. N-alpha-acetyltransferase that specifically mediates the acetylation of N-terminal residues of the transmembrane proteins, with a strong preference for N-termini facing the cytosol. Displays N-terminal acetyltransferase activity towards a range of N-terminal sequences including those starting with Met-Lys, Met-Val, Met-Ala and Met-Met. Required for normal chromosomal segregation during anaphase. May also show histone acetyltransferase activity; such results are however unclear in vivo and would require additional experimental evidences.

Subunit / interactions. Monomer and homodimer; monomer in presence of substrate and homodimer in its absence.

Subcellular location. Golgi apparatus membrane.

Post-translational modifications. Acetylated: autoacetylation is required for optimal acetyltransferase activity.

Disease relevance. Basal ganglia calcification, idiopathic, 9, autosomal recessive (IBGC9) [MIM:620786] A form of basal ganglia calcification, a genetically heterogeneous condition characterized by symmetric calcification in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms, including parkinsonism, dystonia, tremor, ataxia, dementia, psychosis, seizures, and chronic headache. Serum levels of calcium, phosphate, alkaline phosphatase and parathyroid hormone are normal. The neuropathological hallmark of the disease is vascular and pericapillary calcification, mainly of calcium phosphate, in the affected brain areas. The disease is caused by variants affecting the gene represented in this entry.

Induction. Isoform 2: Imprinted. Promoter methylation of the paternal allele may restrict expression to the maternal allele in placenta and leukocytes. Isoform 1: Biallelically expressed.

Miscellaneous. In placenta and leukocytes, expressed from the maternal allele, due to imprinting of the paternal allele. Produced by alternative splicing. Produced by alternative splicing. Produced by alternative splicing.

Similarity. Belongs to the acetyltransferase family. NAA60 subfamily.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9H7X0-1	1	yes
Q9H7X0-2	2
Q9H7X0-3	3
Q9H7X0-4	4
Q9H7X0-5	5

RefSeq proteins (9): NP_001077069, NP_001077070, NP_001304022, NP_001304023, NP_001304024, NP_001304025, NP_001304026, NP_001304027, NP_079121 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000182	GNAT_dom	Domain
IPR016181	Acyl_CoA_acyltransferase	Homologous_superfamily
IPR045141	NAA60-like	Family

Pfam: PF00583

Enzyme classification (BRENDA):

• EC 2.3.1.259 — N-terminal methionine Nalpha-acetyltransferase NatF (BRENDA: 2 organisms, 24 substrates, 4 inhibitors, 10 Km, 10 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ACETYL-COA	0.0018–0.0606	10

Catalyzed reactions (Rhea), 2 shown:

• L-lysyl-[protein] + acetyl-CoA = N(6)-acetyl-L-lysyl-[protein] + CoA + H(+) (RHEA:45948)
• N-terminal L-methionyl-[transmembrane protein] + acetyl-CoA = N-terminal N(alpha)-acetyl-L-methionyl-[transmembrane protein] + CoA + H(+) (RHEA:50604)

UniProt features (84 total): mutagenesis site 30, helix 11, binding site 7, strand 7, modified residue 5, sequence variant 5, splice variant 4, sequence conflict 3, turn 3, topological domain 2, active site 2, chain 1, site 1, intramembrane region 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
5HGZ	X-RAY DIFFRACTION	1.38
5ICV	X-RAY DIFFRACTION	1.53
5HH0	X-RAY DIFFRACTION	1.6
5HH1	X-RAY DIFFRACTION	1.8
5ICW	X-RAY DIFFRACTION	1.95

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H7X0-F1	88.53	0.73

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 34 (required to position thioacetyl group); 97; 138

Ligand- & substrate-binding residues (7): 101–103; 109–114; 143; 150–153; 165; 38; 99

Post-translational modifications (5): 79, 105, 109, 121, 156

Mutagenesis-validated functional residues (30):

Position	Phenotype
19	does not affect localization to the golgi apparatus; when associated with s-30; s-132; s-207 and s-222.
30	does not affect localization to the golgi apparatus; when associated with s-19; s-132; s-207 and s-222.
34	abolished acetyltransferase activity.
35	reduced acetyltransferase activity.
36	reduced acetyltransferase activity.
37	only slightly affects acetyltransferase activity.
38	strongly reduced acetyltransferase activity.
79	slightly reduced acetyltransferase activity.
79	increased acetyltransferase activity.
79	decreased acetyltransferase activity; when associated with r-105, r-109, r-121 and r-156.
80	slightly increased acetyltransferase activity.
81	slightly increased acetyltransferase activity.
83	slightly increased acetyltransferase activity.
84	slightly altered acetyltransferase activity.
97	abolished acetyltransferase activity.
105	decreased acetyltransferase activity; when associated with r-79, r-109, r-121 and r-156.
109	decreased acetyltransferase activity; when associated with r-79, r-105, r-121 and r-156.
111	abolishes acetyltransferase activity.
121	decreased acetyltransferase activity; when associated with r-79, r-105, r-109 and r-156.
132	does not affect localization to the golgi apparatus; when associated with s-19; s-30; s-207 and s-222.
138	abolished acetyltransferase activity.
140	decreased acetyltransferase activity.
143	strongly reduced acetyltransferase activity.
156	decreased histone acetyltransferase activity; when associated with r-79, r-105, r-109 and r-121.
164	slightly altered acetyltransferase activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 276 (showing top): GOBP_N_TERMINAL_PROTEIN_AMINO_ACID_ACETYLATION, GOBP_PROTEIN_MATURATION, GOBP_PROTEIN_ACETYLATION, GOBP_PROTEIN_DNA_COMPLEX_ORGANIZATION, DBP_Q6, CREBP1_01, GOBP_PROTEIN_ACYLATION, GOBP_CHROMATIN_REMODELING, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, AGCTCCT_MIR28, GOBP_N_TERMINAL_PROTEIN_AMINO_ACID_MODIFICATION, RFX1_01, GOBP_CELL_CYCLE_PROCESS, SCGGAAGY_ELK1_02, MGGAAGTG_GABP_B

GO Biological Process (6): nucleosome assembly (GO:0006334), N-terminal protein amino acid acetylation (GO:0006474), chromosome segregation (GO:0007059), cell population proliferation (GO:0008283), N-terminal peptidyl-methionine acetylation (GO:0017196), chromatin organization (GO:0006325)

GO Molecular Function (10): histone acetyltransferase activity (GO:0004402), protein-N-terminal amino-acid acetyltransferase activity (GO:0004596), histone H4 acetyltransferase activity (GO:0010485), protein homodimerization activity (GO:0042803), protein N-terminal-methionine acetyltransferase activity (GO:0120518), protein binding (GO:0005515), transferase activity (GO:0016740), acyltransferase activity (GO:0016746), acyltransferase activity, transferring groups other than amino-acyl groups (GO:0016747), protein-lysine-acetyltransferase activity (GO:0061733)

GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein N-acetyltransferase activity	2
chromatin organization	1
nucleosome organization	1
protein-DNA complex assembly	1
protein acetylation	1
N-terminal protein amino acid modification	1
protein maturation	1
cell cycle process	1
cellular process	1
N-terminal protein amino acid acetylation	1
peptidyl-methionine modification	1
cellular component organization	1
protein-lysine-acetyltransferase activity	1
histone modifying activity	1
histone acetyltransferase activity	1
identical protein binding	1
protein dimerization activity	1
protein-N-terminal amino-acid acetyltransferase activity	1
binding	1
catalytic activity	1
transferase activity	1
acyltransferase activity	1
Golgi apparatus	1
bounding membrane of organelle	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

954 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NAA60	NAA10	P41227	903
NAA60	NAA50	Q9GZZ1	876
NAA60	NAA40	Q86UY6	871
NAA60	NAA80	Q93015	824
NAA60	NAA20	P61599	794
NAA60	NAA15	Q9BXJ9	766
NAA60	NAA30	Q147X3	760
NAA60	ZNF597	Q96LX8	723
NAA60	HYPK	Q9NX55	682
NAA60	NAA35	Q5VZE5	650
NAA60	NAA25	Q14CX7	622
NAA60	GLYATL1	Q969I3	621
NAA60	NAA11	Q9BSU3	611
NAA60	NAA16	Q6N069	543
NAA60	KAT2A	Q92830	517

IntAct

17 interactions, top by confidence:

A	B	Type	Score
MEOX2	NAA60	psi-mi:“MI:0915”(physical association)	0.560
NAA60	CASP6	psi-mi:“MI:0915”(physical association)	0.560
NAA60	LAMP2	psi-mi:“MI:0915”(physical association)	0.560
NAA60	SH3GLB1	psi-mi:“MI:0915”(physical association)	0.560
PRPF40A	NAA60	psi-mi:“MI:0915”(physical association)	0.560
PLEKHN1	NAA60	psi-mi:“MI:0915”(physical association)	0.400
NAA60	MEOX2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): NAA60 (Affinity Capture-RNA), NAA60 (Two-hybrid), NAA60 (Affinity Capture-RNA)

ESM2 similar proteins: A0JMU5, A1A4L5, A1CBC9, A1DE13, A2QX45, A2RAF3, A3KPA3, A6H8I2, A7UL74, A8E5V7, C5IAW9, D6WMX4, E0W1I1, F8VPZ3, I3J7Q8, O22977, O44997, P53355, P54789, Q008S8, Q02723, Q0CW42, Q0P564, Q17QK9, Q1DKI1, Q2TBM9, Q2U6C4, Q38898, Q3MHC1, Q3TL26, Q3U213, Q4U3Y2, Q4WVE3, Q5R4A6, Q5R6Y2, Q5SNQ7, Q5U2T7, Q6DCB7, Q6NRS1, Q7T2Z5

Diamond homologs: A3KPA3, A8E5V7, Q17QK9, Q3MHC1, Q4JBG0, Q95SX8, Q9DBU2, Q9H7X0, A1R8Y2, A9WNI5, C0ZP17, C1ATC6, C3PIU4, C6WPR7, D0L3V5, D2S4P5, D6Y4C5, E0CYC6, O05517, O34376, O74311, O80438, P36416, Q03503, Q0IHH1, Q0S740, Q147X3, Q3UX61, Q4V8K3, Q54MP9, Q58925, Q5Z297, Q66KL0, Q6DBY2, Q8CES0, Q95RC0, Q976C3, Q980R9, Q9BSU3, Q9FKI4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	6
Likely pathogenic	0
Uncertain significance	26
Likely benign	4
Benign	2

Top pathogenic / likely-pathogenic (6)

Variant ID	HGVS	Classification
3076205	NM_001083601.3(NAA60):c.323_329del (p.Arg108fs)	Pathogenic
3076206	NM_001083601.3(NAA60):c.338-1G>C	Pathogenic
3076207	NM_001083601.3(NAA60):c.391C>T (p.His131Tyr)	Pathogenic
3076208	NM_001083601.3(NAA60):c.130C>T (p.Arg44Cys)	Pathogenic
3076209	NM_001083601.3(NAA60):c.50T>G (p.Leu17Arg)	Pathogenic
3076210	NM_001083601.3(NAA60):c.428A>C (p.Asn143Thr)	Pathogenic

SpliceAI

1851 predictions. Top by Δscore:

Variant	Effect	Δscore
16:3448537:GAGA:G	donor_gain	1.0000
16:3448539:GA:G	donor_gain	1.0000
16:3476217:CACA:C	acceptor_loss	1.0000
16:3476219:CA:C	acceptor_loss	1.0000
16:3476220:A:AT	acceptor_loss	1.0000
16:3476221:GGT:G	acceptor_gain	1.0000
16:3476333:ATCGA:A	donor_gain	1.0000
16:3476334:TCGA:T	donor_gain	1.0000
16:3476336:GA:G	donor_gain	1.0000
16:3476337:AGT:A	donor_loss	1.0000
16:3476338:G:GA	donor_loss	1.0000
16:3476338:G:GG	donor_gain	1.0000
16:3476339:T:A	donor_loss	1.0000
16:3482498:CTAG:C	acceptor_loss	1.0000
16:3482499:TA:T	acceptor_loss	1.0000
16:3482500:A:AG	acceptor_gain	1.0000
16:3482500:AG:A	acceptor_gain	1.0000
16:3482500:AGG:A	acceptor_loss	1.0000
16:3482500:AGGAT:A	acceptor_gain	1.0000
16:3482501:G:GT	acceptor_gain	1.0000
16:3482501:GG:G	acceptor_gain	1.0000
16:3482501:GGAT:G	acceptor_gain	1.0000
16:3482501:GGATG:G	acceptor_gain	1.0000
16:3482585:G:GT	donor_gain	1.0000
16:3482593:GCA:G	donor_gain	1.0000
16:3482598:GGT:G	donor_loss	1.0000
16:3482599:G:GG	donor_gain	1.0000
16:3482599:GTAA:G	donor_loss	1.0000
16:3482600:T:G	donor_loss	1.0000
16:3448541:G:GG	donor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000001155 (16:3474158 A>G), RS1000007986 (16:3448237 G>T), RS1000055627 (16:3443745 A>C), RS1000111807 (16:3444239 G>T), RS1000181126 (16:3472965 C>T), RS1000188309 (16:3458350 C>A,T), RS1000201595 (16:3470347 A>G), RS1000277784 (16:3482738 C>T), RS1000306129 (16:3458512 G>A,C), RS1000443449 (16:3483087 C>G), RS1000488448 (16:3454527 TAAAAA>T,TAAAA,TAAAAAA), RS1000526613 (16:3473789 C>A,T), RS1000539152 (16:3467025 G>A,T), RS1000545509 (16:3441834 G>A,C), RS1000694746 (16:3467189 G>A)

Disease associations

OMIM: gene MIM:614246 | disease phenotypes: MIM:620786

GenCC curated gene-disease

Disease	Classification	Inheritance
basal ganglia calcification, idiopathic, 9, autosomal recessive	Strong	Autosomal recessive

Mondo (1): basal ganglia calcification, idiopathic, 9, autosomal recessive (MONDO:0968977)

Orphanet (0):

HPO phenotypes

85 total (30 of 85 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000007	Autosomal recessive inheritance
HP:0000012	Urinary urgency
HP:0000020	Urinary incontinence
HP:0000218	High palate
HP:0000252	Microcephaly
HP:0000256	Macrocephaly
HP:0000298	Mask-like facies
HP:0000369	Low-set ears
HP:0000486	Strabismus
HP:0000519	Developmental cataract
HP:0000520	Proptosis
HP:0000709	Psychosis
HP:0000716	Depression
HP:0000726	Dementia
HP:0000733	Motor stereotypy
HP:0000739	Anxiety
HP:0000751	Personality changes
HP:0000802	Impotence
HP:0000822	Hypertension
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001252	Hypotonia
HP:0001256	Mild intellectual disability
HP:0001260	Dysarthria
HP:0001263	Global developmental delay
HP:0001266	Choreoathetosis
HP:0001268	Mental deterioration
HP:0001270	Motor delay
HP:0001288	Gait disturbance

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST002198_6	Tuberculosis	3.000000e-06
GCST003073_16	Cerebral amyloid deposition (PET imaging)	6.000000e-07
GCST003073_7	Cerebral amyloid deposition (PET imaging)	5.000000e-07
GCST90002381_636	Eosinophil count	1.000000e-10
GCST90002382_428	Eosinophil percentage of white cells	3.000000e-11

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007707	cerebral amyloid deposition measurement
EFO:0004842	eosinophil count
EFO:0007991	eosinophil percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4630856 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
bisphenol S	decreases methylation	1
Temozolomide	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Cadmium	decreases expression, increases abundance	1
Doxorubicin	decreases expression	1
Gallic Acid	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Urethane	increases expression	1
Valproic Acid	affects expression	1
Vitamin E	decreases expression	1
Cyclosporine	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4618913	Binding	Binding affinity to Naa60 in human A549 cell lysates assessed as thermal stabilization of protein at 50 uM after 30 mins followed by heating at 40 to 64 degC for 3 mins by immunoblot-based CESTA	Characterization of Specific N-α-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library. — ACS Med Chem Lett

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1Y5	Abcam HeLa NAA60 KO	Cancer cell line	Female
CVCL_SZ82	HAP1 NAA60 (-) 1	Cancer cell line	Male
CVCL_SZ83	HAP1 NAA60 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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