NAA10

gene
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Also known as DXS707TE2

Summary

NAA10 (N-alpha-acetyltransferase 10, NatA catalytic subunit, HGNC:18704) is a protein-coding gene on chromosome Xq28, encoding N-alpha-acetyltransferase 10 (P41227). Catalytic subunit of N-terminal acetyltransferase complexes which display alpha (N-terminal) acetyltransferase activity. It is a common-essential gene (DepMap: required in 92.8% of cancer cell lines).

N-alpha-acetylation is among the most common post-translational protein modifications in eukaryotic cells. This process involves the transfer of an acetyl group from acetyl-coenzyme A to the alpha-amino group on a nascent polypeptide and is essential for normal cell function. This gene encodes an N-terminal acetyltransferase that functions as the catalytic subunit of the major amino-terminal acetyltransferase A complex. Mutations in this gene are the cause of Ogden syndrome. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 8260 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): NAA10-related syndrome (Definitive, ClinGen) — +3 more curated relationships
  • GWAS associations: 1
  • Clinical variants (ClinVar): 231 total — 14 pathogenic, 14 likely-pathogenic
  • Phenotypes (HPO): 216
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 92.8% of screened cell lines (common-essential)
  • Dosage sensitivity (ClinGen): haploinsufficiency little evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_003491

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18704
Approved symbolNAA10
NameN-alpha-acetyltransferase 10, NatA catalytic subunit
LocationXq28
Locus typegene with protein product
StatusApproved
AliasesDXS707, TE2
Ensembl geneENSG00000102030
Ensembl biotypeprotein_coding
OMIM300013
Entrez8260

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 11 protein_coding, 9 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000370009, ENST00000370011, ENST00000370015, ENST00000393710, ENST00000393712, ENST00000432089, ENST00000460996, ENST00000464845, ENST00000466877, ENST00000467451, ENST00000477750, ENST00000477882, ENST00000478177, ENST00000484950, ENST00000488481, ENST00000700299, ENST00000854040, ENST00000930123, ENST00000930124, ENST00000930125, ENST00000930126

RefSeq mRNA: 3 — MANE Select: NM_003491 NM_001256119, NM_001256120, NM_003491

CCDS: CCDS14737, CCDS59179

Canonical transcript exons

ENST00000464845 — 8 exons

ExonStartEnd
ENSE00001870438153929225153930223
ENSE00001918122153934884153935037
ENSE00003486656153930763153930847
ENSE00003505156153932316153932431
ENSE00003574243153932539153932584
ENSE00003586877153934377153934475
ENSE00003623423153932071153932115
ENSE00003659133153933943153934001

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 97.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 78.0360 / max 369.0907, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
20092778.03601822
2009284.42101521

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489097.73gold quality
apex of heartUBERON:000209897.63gold quality
lower esophagus muscularis layerUBERON:003583397.40gold quality
lower esophagusUBERON:001347397.39gold quality
cerebellar hemisphereUBERON:000224597.37gold quality
esophagogastric junction muscularis propriaUBERON:003584197.33gold quality
gastrocnemiusUBERON:000138897.30gold quality
left coronary arteryUBERON:000162697.27gold quality
cerebellar cortexUBERON:000212997.27gold quality
hindlimb stylopod muscleUBERON:000425297.27gold quality
adenohypophysisUBERON:000219697.25gold quality
body of uterusUBERON:000985397.24gold quality
right frontal lobeUBERON:000281097.19gold quality
lower esophagus mucosaUBERON:003583497.11gold quality
muscle layer of sigmoid colonUBERON:003580597.03gold quality
ascending aortaUBERON:000149696.94gold quality
thoracic aortaUBERON:000151596.93gold quality
left adrenal gland cortexUBERON:003582596.88gold quality
metanephros cortexUBERON:001053396.86gold quality
stromal cell of endometriumCL:000225596.85gold quality
right coronary arteryUBERON:000162596.84gold quality
coronary arteryUBERON:000162196.83gold quality
left adrenal glandUBERON:000123496.81gold quality
muscle of legUBERON:000138396.79gold quality
granulocyteCL:000009496.78gold quality
left uterine tubeUBERON:000130396.78gold quality
aortaUBERON:000094796.74gold quality
popliteal arteryUBERON:000225096.73gold quality
tibial arteryUBERON:000761096.73gold quality
right adrenal glandUBERON:000123396.69gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.64
E-MTAB-6379no378.22

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): HIF1A

miRNA regulators (miRDB)

4 targeting NAA10, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-428499.3665.251293
HSA-MIR-6865-3P97.5464.67684
HSA-MIR-428697.2064.371587
HSA-MIR-6729-3P96.9166.79703

Functional genomics

ClinGen dosage: haploinsufficiency 1 (little evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 92.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

  • ARD1-mediated acetylation regulates and destabilizes HIF-1 alpha by directly binding to it. (PMID:12464182)
  • Human Naa15 (NATH) and Naa10 (ARD1) form a stable NatA complex which associates with ribosomes and performs co-translational N-terminal acetylation; Naa15 (NATH) and Naa10 (ARD1) are cleaved during apoptosis resulting in decreased acetyltransferase activity (PMID:15496142)
  • description of the human homologue of Nat1p, NATH (NAT human), as the binding partner of the hARD1 (human ARD1) protein (PMID:15496142)
  • hARD1 complexes with NATH in a ribosomal associated protein-N-acetyltransferase complex. (PMID:15496142)
  • Amino-terminal acetyltransferase ARD1 (hARD1) interacts with a novel motif, 658-HGVVEVD-664, in the cytoplasmic domain of beta-amyloid precursor protein. (PMID:15749829)
  • ARD1 is involved in cell proliferation and in regulating a series of cellular metabolic pathways that are regulated during hypoxia response. (PMID:15755738)
  • Data demonstrate that ARD1 has limited, if any, impact on the HIF-1alpha signaling pathway. (PMID:15994306)
  • levels of endogenous NATH and hARD1 proteins in thyroid papillary carcinoma patients; results suggest that NATH positively affects the level of hARD1 protein both in vivo and in cell cultures (PMID:16279846)
  • ARD1 specifically binds HIF-1 alpha, suggesting a putative, still unclear, connection between these proteins. (PMID:16288748)
  • A human ARD1 variant ortholog (235) has weak effects on hypoxia inducible factor (HIF)-1 alpha and VEGF mRNA stability compared to mouse ARD1 ortholog 225. (PMID:16376303)
  • Essential role in cell survival through protein N-alpha-acetylation. (PMID:16518407)
  • Structural characterization of native hARD1 using size exclusion chromatography, circular dichroism, & fluorescence spectroscopy shows the protein consists of compact globular region comprising 2 thirds of the protein & a flexible unstructured C terminus. (PMID:16823041)
  • These results indicate that ARD1(235) and ARD1(225) isoforms may have different activities and function in different subcellular compartments of mammalian cells. (PMID:17161380)
  • HIF-1alpha was found to inactivate the Wnt signaling by binding to hARD1 or beta-catenin, which may contribute to the hypoxia-induced growth arrest of tumor cells. (PMID:18593917)
  • ARD1A is implicated in cellular proliferation and carcinogenesis. (PMID:18794801)
  • This review focuses on the enzymatic and biological activities of human ARD1, the reduction of which negatively affects cell growth and may be a potential cancer drug target. (PMID:18991565)
  • accumulation of hARD1 protein may be related to carcinogenesis of various types of cancer. (PMID:19287988)
  • ARD1 is indeed a bona fide substrate of IKKbeta. (PMID:19716809)
  • hARD1 is a bona fide regulator of MLCK, and hARD1 plays a crucial role in the balance between tumor cell migration and stasis (PMID:19826488)
  • Results suggest that hARD1 might play an important role in breast cancer carcinogenesis. (PMID:19909012)
  • ARD1 functions as an inhibitor of the mTOR pathway and that dysregulation of the ARD1-TSC2-mTOR axis may contribute to cancer development (PMID:20145209)
  • Data indicate that the physical interaction between HYPK and NatA Naa10/15 seems to be of functional importance both for huntingtin aggregation and for N-terminal acetylation. (PMID:20154145)
  • Results show that hARD1 autoacetylation is critical for its activation and its ability to stimulate cancer cell proliferation and tumorigenesis. (PMID:20501853)
  • interaction between hNaa10p and DNMT1 was required for E-cadherin silencing through promoter CpG methylation, and E-cadherin repression contributed to the oncogenic effects of hNaa10p. (PMID:20592467)
  • These results indicate that ARD1A is a novel tumor-associated antigen and a potential prognostic factor for colon cancer. (PMID:20639454)
  • suggest that Naa10p functions as a tumor metastasis suppressor by disrupting the migratory complex, PIX-GIT- Paxillin, in cancer cells (PMID:21295525)
  • N(alpha)-acetyltransferase 10 may function as a post-translational actin N(alpha)-acetyltransferase. (PMID:21383206)
  • A reduction in acetylation by hNaa10p causes lethal X-linked disorder of infancy. (PMID:21700266)
  • Arrest-defective protein 1 homolog A (ARD1) in combination with SNCG/Hiwi/PRL-3 may lead to a poor outcome in patients with or without lymph node metastatic colon cancer. (PMID:22261620)
  • ARD1 functions as a unique AR regulator in prostate cancer cells. (PMID:22315407)
  • study revealed a novel mechanism controlling MCL1 expression, in which Naa10p and RelA/p65 synergistically interact with MCL1 promoter region and promote MCL1 transcription (PMID:22496479)
  • These data indicate that the interaction between ARD1 and RIP1 plays an important role in the DNA damage-induced NF-kappaB activation, and that the acetyltransferase activity of ARD1 and its localization in to the nucleus are involved in such stress response. (PMID:22580278)
  • Protein N-terminal acetyltransferases (NATs), including Naa10, act as N-terminal propionyltransferases. (PMID:23043182)
  • The expression level of NAA10 is inversely correlated with that of MMP-9 in breast cancer samples. (PMID:23550278)
  • Development of the first specific NAT-inhibitors, including inhibitors targeting Naa10. (PMID:23557624)
  • Naa10p suppresses 28S proteasome activity through interaction with PA28beta. (PMID:23624078)
  • Study describes a Saccharomyces cerevisiae model developed by introducing the human wild-type (wt) or mutant NatA complex into yeast lacking NatA (NatA-Delta). The wt human NatA complex phenotypically complemented the NatA-Delta strain, whereas only a partial rescue was observed for the Ogden mutant NatA complex suggesting that hNaa10 S37P is only partially functional in vivo. (PMID:24408909)
  • The study concludes that the NAA10 mutation is the cause of Lenz microphthalmia syndrome in a family, likely through the dysregulation of the retinoic acid signalling pathway. (PMID:24431331)
  • Naa10p inhibits the metastasis of breast cancer cells by targeting STAT5a. (PMID:24925029)
  • De novo missense mutations in the NAA10 gene cause severe non-syndromic developmental delay in males and females (PMID:25099252)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerionaa10ENSDARG00000071060
mus_musculusNaa10ENSMUSG00000031388
rattus_norvegicusNaa10ENSRNOG00000060063
drosophila_melanogastervncFBGN0263251
caenorhabditis_elegansWBGENE00000923

Paralogs (4): NAA50 (ENSG00000121579), NAA30 (ENSG00000139977), NAA11 (ENSG00000156269), NAA20 (ENSG00000173418)

Protein

Protein identifiers

N-alpha-acetyltransferase 10P41227 (reviewed: P41227)

Alternative names: N-terminal acetyltransferase complex ARD1 subunit homolog A, NatA catalytic subunit Naa10

All UniProt accessions (5): P41227, A8MWP7, C9JN83, C9JW55, F8W808

UniProt curated annotations — full annotation on UniProt →

Function. Catalytic subunit of N-terminal acetyltransferase complexes which display alpha (N-terminal) acetyltransferase activity. Acetylates amino termini that are devoid of initiator methionine. The alpha (N-terminal) acetyltransferase activity may be important for vascular, hematopoietic and neuronal growth and development. Without NAA15, displays epsilon (internal) acetyltransferase activity towards HIF1A, thereby promoting its degradation. Represses MYLK kinase activity by acetylation, and thus represses tumor cell migration. Acetylates, and stabilizes TSC2, thereby repressing mTOR activity and suppressing cancer development. Acetylates HSPA1A and HSPA1B at ‘Lys-77’ which enhances its chaperone activity and leads to preferential binding to co-chaperone HOPX. Acetylates HIST1H4A. Acts as a negative regulator of sister chromatid cohesion during mitosis.

Subunit / interactions. Component of the N-terminal acetyltransferase A complex (also called the NatA complex) composed of NAA10 and NAA15. Within the complex interacts with NAA15. Component of the N-terminal acetyltransferase A (NatA)/HYPK complex at least composed of NAA10, NAA15 and HYPK, which has N-terminal acetyltransferase activity. In complex with NAA15, interacts with HYPK. Component of the N-terminal acetyltransferase E (NatE) complex at least composed of NAA10, NAA15 and NAA50. Within the complex interacts with NAA15; the interaction is required for binding to NAAT50. Interacts with NAAT50. The interaction of the NatA complex with NAA50 reduces the acetylation activity of the NatA complex. Component of the N-terminal acetyltransferase E (NatE)/HYPK complex at least composed of NAA10, NAA15, NAA50 and HYPK. In complex with NAA15, interacts with HYPK; the interaction with HYPK reduces the capacity of the NatA complex to interact with NAA50. Interacts with HIF1A (via its ODD domain); the interaction increases HIF1A protein stability during normoxia, an down-regulates it when induced by hypoxia. Interacts with the ribosome. Binds to MYLK. Interacts with NAA16. Interacts (via its C-terminal domain) with TSC2, leading to its acetylation. Interacts with IKBKB. Interacts with HSPA1A and HSPA1B leading to its acetylation.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Ubiquitous.

Post-translational modifications. Cleaved by caspases during apoptosis. Phosphorylation by IKBKB/IKKB at Ser-209 promotes its proteasome-mediated degradation. Autoacetylated at Lys-136 which stimulates its catalytic activity.

Disease relevance. N-terminal acetyltransferase deficiency (NATD) [MIM:300855] An enzymatic deficiency resulting in postnatal growth failure with severe delays and dysmorphic features. It is clinically characterized by wrinkled forehead, prominent eyes, widely opened anterior and posterior fontanels, downsloping palpebral fissures, thickened lids, large ears, flared nares, hypoplastic alae, short columella, protruding upper lip, and microretrognathia. There are also delayed closing of fontanels and broad great toes. Skin is characterized by redundancy or laxity with minimal subcutaneous fat, cutaneous capillary malformations, and very fine hair and eyebrows. Death results from cardiogenic shock following arrhythmia. The disease is caused by variants affecting the gene represented in this entry. Microphthalmia, syndromic, 1 (MCOPS1) [MIM:309800] A rare syndrome defined by the canonical features of unilateral or bilateral microphthalmia or anophthalmia and defects in the skeletal and genitourinary systems. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. Anomalies of the digits, teeth, and ears are hallmarks of MCOPS1. Intellectual disability ranges from mild to severe, with self-mutilating behaviors and seizures in severely affected MCOPS1 individuals. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the acetyltransferase family. ARD1 subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
P41227-11yes
P41227-22

RefSeq proteins (3): NP_001243048, NP_001243049, NP_003482* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000182GNAT_domDomain
IPR016181Acyl_CoA_acyltransferaseHomologous_superfamily
IPR045047Ard1-likeFamily

Pfam: PF00583

Enzyme classification (BRENDA):

  • EC 2.3.1.255 — N-terminal amino-acid Nalpha-acetyltransferase NatA (BRENDA: 13 organisms, 96 substrates, 5 inhibitors, 24 Km, 23 kcat entries)
  • EC 2.3.1.258 — N-terminal methionine Nalpha-acetyltransferase NatE (BRENDA: 8 organisms, 79 substrates, 9 inhibitors, 25 Km, 15 kcat entries)
  • EC 2.3.1.48 — histone acetyltransferase (BRENDA: 41 organisms, 681 substrates, 1134 inhibitors, 140 Km, 96 kcat entries)

Substrate kinetics (BRENDA)

42 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
ACETYL-COA0.0002–0.04651
HISTONE H30.007–2.0923
SASEAGVRWGRPVGRRRRP0.3–1.8519
HISTONE H411
HISTONE H4 PEPTIDE0.0208–0.1977
MVNALE0.0153–0.14696
HISTONE0.075–1.46
ACETYL-COA0.196–0.67174
HISTONE H3 TAIL PEPTIDE0.044–0.1124
PICCOLONUA4 PEPTIDE0.135–0.3724
3-AZIDOPROPIONYL-COA0.0002–0.00863
4-PENTYNOYL-COA0.0009–0.08593
SPERMIDINE0.18–0.273
ACETYL-COA0.005–0.00692
N-TERMINAL-L-METHIONYL-L-LEUCYL-GLYCYL-L-PROLINE0.0962–0.83152

Catalyzed reactions (Rhea), 6 shown:

  • N-terminal glycyl-[protein] + acetyl-CoA = N-terminal N(alpha)-acetylglycyl-[protein] + CoA + H(+) (RHEA:50496)
  • N-terminal L-alanyl-[protein] + acetyl-CoA = N-terminal N(alpha)-acetyl-L-alanyl-[protein] + CoA + H(+) (RHEA:50500)
  • N-terminal L-seryl-[protein] + acetyl-CoA = N-terminal N(alpha)-acetyl-L-seryl-[protein] + CoA + H(+) (RHEA:50504)
  • N-terminal L-valyl-[protein] + acetyl-CoA = N-terminal N(alpha)-acetyl-L-valyl-[protein] + CoA + H(+) (RHEA:50508)
  • N-terminal L-cysteinyl-[protein] + acetyl-CoA = N-terminal N(alpha)-acetyl-L-cysteinyl-[protein] + CoA + H(+) (RHEA:50512)
  • N-terminal L-threonyl-[protein] + acetyl-CoA = N-terminal N(alpha)-acetyl-L-threonyl-[protein] + CoA + H(+) (RHEA:50516)

UniProt features (37 total): strand 9, modified residue 8, helix 8, sequence variant 3, splice variant 2, mutagenesis site 2, region of interest 2, chain 1, domain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

12 structures.

PDBMethodResolution (Å)
9FPZELECTRON MICROSCOPY2.69
6C9MX-RAY DIFFRACTION2.8
9F1BELECTRON MICROSCOPY3.01
6PPLELECTRON MICROSCOPY3.02
6C95X-RAY DIFFRACTION3.15
9F1DELECTRON MICROSCOPY3.26
9QQBELECTRON MICROSCOPY3.43
9F1CELECTRON MICROSCOPY3.78
9GJ6ELECTRON MICROSCOPY3.91
6PW9ELECTRON MICROSCOPY4.03
9GJ5ELECTRON MICROSCOPY4.61
9FQ0ELECTRON MICROSCOPY4.67

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P41227-F181.990.71

Functional residue map

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

Post-translational modifications (8): 209, 213, 216, 1, 136, 182, 186, 205

Mutagenesis-validated functional residues (2):

PositionPhenotype
136loss of its ability to acetylate hspa1a and hspa1b.
209abolishes phosphorylation by ikkb and reduces cell growth.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 571 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, PUJANA_CHEK2_PCC_NETWORK, GOBP_PROTEIN_MATURATION, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_SISTER_CHROMATID_COHESION, GOBP_REGULATION_OF_CELL_CYCLE, MORF_BUB3, GOBP_NEGATIVE_REGULATION_OF_CHROMOSOME_ORGANIZATION, GOBP_PROTEIN_FOLDING, MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP, WANG_TARGETS_OF_MLL_CBP_FUSION_DN

GO Biological Process (7): protein maturation (GO:0051604), positive regulation of protein refolding (GO:1904592), negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric (GO:2000719), protein acetylation (GO:0006473), N-terminal protein amino acid acetylation (GO:0006474), internal protein amino acid acetylation (GO:0006475), chromosome organization (GO:0051276)

GO Molecular Function (11): protein-N-terminal amino-acid acetyltransferase activity (GO:0004596), N-acetyltransferase activity (GO:0008080), protein-N-terminal-alanine acetyltransferase activity (GO:0008999), protein N-terminal-serine acetyltransferase activity (GO:1990189), protein-N-terminal-glutamate acetyltransferase activity (GO:1990190), protein binding (GO:0005515), acetyltransferase activity (GO:0016407), transferase activity (GO:0016740), acyltransferase activity (GO:0016746), acyltransferase activity, transferring groups other than amino-acyl groups (GO:0016747), ribosome binding (GO:0043022)

GO Cellular Component (6): nucleus (GO:0005634), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), NatA complex (GO:0031415)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein-N-terminal amino-acid acetyltransferase activity3
cellular anatomical structure3
protein acetylation2
gene expression1
protein metabolic process1
protein refolding1
regulation of protein refolding1
positive regulation of protein folding1
negative regulation of maintenance of mitotic sister chromatid cohesion1
maintenance of mitotic sister chromatid cohesion, centromeric1
regulation of maintenance of mitotic sister chromatid cohesion, centromeric1
protein acylation1
N-terminal protein amino acid modification1
protein maturation1
organelle organization1
protein N-acetyltransferase activity1
acetyltransferase activity1
binding1
acyltransferase activity, transferring groups other than amino-acyl groups1
catalytic activity1
transferase activity1
acyltransferase activity1
ribonucleoprotein complex binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular membraneless organelle1
intracellular anatomical structure1
cytoplasm1
N-terminal protein acetyltransferase complex1

Protein interactions and networks

STRING

2043 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
NAA10NAA15Q9BXJ9999
NAA10NAA50Q9GZZ1981
NAA10HYPKQ9NX55977
NAA10NAA60Q9H7X0903
NAA10NAA16Q6N069899
NAA10RENBPP51606865
NAA10NAA25Q14CX7823
NAA10NAA40Q86UY6810
NAA10ESCO1Q5FWF5794
NAA10ESCO2Q56NI9793
NAA10NAA80Q93015774
NAA10ICE2Q659A1763
NAA10AVPR2P30518748
NAA10NAA35Q5VZE5742
NAA10L1CAMP32004741

IntAct

279 interactions, top by confidence:

ABTypeScore
NAA15NAA10psi-mi:“MI:0914”(association)0.840
NAA10NAA15psi-mi:“MI:0915”(physical association)0.840
NAA10NAA15psi-mi:“MI:0403”(colocalization)0.840
CALCOCO2NAA10psi-mi:“MI:0915”(physical association)0.780
KIFAP3NAA10psi-mi:“MI:0915”(physical association)0.780
NAA10CALCOCO2psi-mi:“MI:0915”(physical association)0.780
NAA10KIFAP3psi-mi:“MI:0915”(physical association)0.780
PDE4DIPNAA10psi-mi:“MI:0915”(physical association)0.740
NAA10PDE4DIPpsi-mi:“MI:0915”(physical association)0.740
ZBTB14NAA10psi-mi:“MI:0915”(physical association)0.720
NAA10ZBTB14psi-mi:“MI:0915”(physical association)0.720
NAA10CREBRFpsi-mi:“MI:0915”(physical association)0.670
NAA10CDCA5psi-mi:“MI:0915”(physical association)0.670
NAA10SNX33psi-mi:“MI:0915”(physical association)0.670
NAA10HIF1Apsi-mi:“MI:0915”(physical association)0.670
NAA10DDIT4Lpsi-mi:“MI:0915”(physical association)0.600
NAA10NOXA1psi-mi:“MI:0915”(physical association)0.600
DDIT4LNAA10psi-mi:“MI:0915”(physical association)0.600

BioGRID (257): NAA10 (Two-hybrid), NAA10 (Two-hybrid), PDE4DIP (Two-hybrid), CALCOCO2 (Two-hybrid), RBCK1 (Two-hybrid), EHMT2 (Two-hybrid), KIFAP3 (Two-hybrid), BCOR (Two-hybrid), CEP44 (Two-hybrid), FIP1L1 (Two-hybrid), RAB3IP (Two-hybrid), SSX2IP (Two-hybrid), KRTAP10-7 (Two-hybrid), KRTAP10-5 (Two-hybrid), KRTAP10-3 (Two-hybrid)

ESM2 similar proteins: A0A2R8QFQ6, A4IFE4, A9X1D0, B0VX69, B5FW36, C1FXW2, D1LYT2, D3Z7P3, G3MWR8, G3V6U9, O13016, O46411, O88508, O94925, O95544, P13264, P18031, P18507, P20417, P21548, P22723, P35790, P35821, P41227, P47870, P58058, Q01134, Q0VAM2, Q14722, Q1LZ53, Q2KI14, Q3ULA2, Q3UX61, Q4V8K3, Q4W5Z4, Q5RC04, Q5SRY7, Q5ZML9, Q6ZPR4, Q7RTP6

Diamond homologs: O61219, O74457, P07347, P36416, P41227, P61599, P61600, Q03503, Q05885, Q06504, Q2KI14, Q2PFM2, Q3UX61, Q4JBG0, Q4V8K3, Q58925, Q58ED9, Q6P632, Q7ZXR3, Q8SSN5, Q976C3, Q980R9, Q9BSU3, Q9FKI4, Q9QY36, Q9UTI3, A1ADU8, O74311, O80438, P63420, P63421, P63422, P63423, P63424, P76539, Q0IHH1, Q0T275, Q0TF35, Q147X3, Q1R8T7

SIGNOR signaling

1 interactions.

AEffectBMechanism
NAA10“form complex”NatAbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic14
Likely pathogenic14
Uncertain significance65
Likely benign44
Benign27

Top pathogenic / likely-pathogenic (28)

Variant IDHGVSClassification
102423NM_003491.4(NAA10):c.471+2T>APathogenic
1028122NM_003491.4(NAA10):c.472-2A>CPathogenic
139643NM_003491.4(NAA10):c.319G>T (p.Val107Phe)Pathogenic
208664NM_003491.4(NAA10):c.247C>T (p.Arg83Cys)Pathogenic
218104NM_003491.4(NAA10):c.128A>C (p.Tyr43Ser)Pathogenic
236258NM_003491.4(NAA10):c.384T>A (p.Phe128Leu)Pathogenic
280237NM_003491.4(NAA10):c.384T>G (p.Phe128Leu)Pathogenic
29927NM_003491.4(NAA10):c.109T>C (p.Ser37Pro)Pathogenic
3340772NM_003491.4(NAA10):c.226G>A (p.Ala76Thr)Pathogenic
3766065NM_003491.4(NAA10):c.50G>A (p.Cys17Tyr)Pathogenic
520542NM_003491.4(NAA10):c.332T>G (p.Val111Gly)Pathogenic
561061NM_003491.4(NAA10):c.494_495del (p.Lys165fs)Pathogenic
640994NC_000023.10:g.(?153137587)(153363142_?)dupPathogenic
973227NM_003491.4(NAA10):c.257T>G (p.Leu86Arg)Pathogenic
1211059NM_003491.4(NAA10):c.236G>A (p.Arg79His)Likely pathogenic
1299213NM_003491.4(NAA10):c.376C>G (p.Leu126Val)Likely pathogenic
1300802NM_003491.4(NAA10):c.49T>G (p.Cys17Gly)Likely pathogenic
1327568NM_003491.4(NAA10):c.469G>A (p.Glu157Lys)Likely pathogenic
1705306NM_003491.4(NAA10):c.128A>G (p.Tyr43Cys)Likely pathogenic
3376962NM_003491.4(NAA10):c.387-1G>ALikely pathogenic
372842NM_003491.4(NAA10):c.339G>T (p.Lys113Asn)Likely pathogenic
375388NM_003491.4(NAA10):c.215T>C (p.Ile72Thr)Likely pathogenic
431708NM_003491.4(NAA10):c.361C>G (p.Leu121Val)Likely pathogenic
432646NM_003491.4(NAA10):c.92A>G (p.Tyr31Cys)Likely pathogenic
4681857NM_003491.4(NAA10):c.445C>G (p.Arg149Gly)Likely pathogenic
617463NM_003491.4(NAA10):c.*43A>GLikely pathogenic
637034NM_003491.4(NAA10):c.115C>A (p.Pro39Thr)Likely pathogenic
804121NM_003491.4(NAA10):c.377T>G (p.Leu126Arg)Likely pathogenic

SpliceAI

1122 predictions. Top by Δscore:

VariantEffectΔscore
X:153930231:C:CTacceptor_gain1.0000
X:153930239:C:CTacceptor_gain1.0000
X:153930240:A:Tacceptor_gain1.0000
X:153930757:GCTTA:Gdonor_loss1.0000
X:153930759:TTACC:Tdonor_loss1.0000
X:153930760:TA:Tdonor_loss1.0000
X:153930761:A:ACdonor_gain1.0000
X:153930761:ACCTC:Adonor_loss1.0000
X:153930762:C:Adonor_loss1.0000
X:153930762:C:CCdonor_gain1.0000
X:153930762:CCT:Cdonor_gain1.0000
X:153930843:TGATC:Tacceptor_gain1.0000
X:153930846:TC:Tacceptor_gain1.0000
X:153930847:CC:Cacceptor_gain1.0000
X:153930848:C:CAacceptor_loss1.0000
X:153930848:C:CCacceptor_gain1.0000
X:153930849:T:Gacceptor_loss1.0000
X:153932116:C:CCacceptor_gain1.0000
X:153932297:C:Adonor_gain1.0000
X:153932311:T:TAdonor_gain1.0000
X:153932317:T:TAdonor_gain1.0000
X:153932320:T:Adonor_gain1.0000
X:153932341:A:ACdonor_gain1.0000
X:153932427:ACAGC:Aacceptor_gain1.0000
X:153932428:CAGC:Cacceptor_gain1.0000
X:153932428:CAGCC:Cacceptor_gain1.0000
X:153932429:AGC:Aacceptor_gain1.0000
X:153932430:GC:Gacceptor_gain1.0000
X:153932431:CC:Cacceptor_gain1.0000
X:153932432:C:Aacceptor_loss1.0000

AlphaMissense

1561 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:153930782:A:GL151P1.000
X:153930788:C:GR149P1.000
X:153930793:C:AM147I1.000
X:153930793:C:GM147I1.000
X:153930793:C:TM147I1.000
X:153930794:A:CM147R1.000
X:153930794:A:GM147T1.000
X:153930794:A:TM147K1.000
X:153930798:C:GA146P1.000
X:153930801:A:CY145D1.000
X:153930803:G:AA144V1.000
X:153930803:G:TA144D1.000
X:153930804:C:GA144P1.000
X:153930804:C:TA144T1.000
X:153930806:T:AD143V1.000
X:153930807:C:GD143H1.000
X:153930808:C:AE142D1.000
X:153930808:C:GE142D1.000
X:153930809:T:AE142V1.000
X:153930810:C:TE142K1.000
X:153930813:C:AG141W1.000
X:153930814:A:CD140E1.000
X:153930814:A:TD140E1.000
X:153930815:T:AD140V1.000
X:153930815:T:GD140A1.000
X:153930816:C:AD140Y1.000
X:153930816:C:GD140H1.000
X:153930818:G:TA139E1.000
X:153930819:C:GA139P1.000
X:153930821:T:CY138C1.000

dbSNP variants (sampled 300 via entrez): RS1000986627 (X:153936747 C>T), RS1001424554 (X:153932816 C>A), RS1002425512 (X:153934657 G>C), RS1003101587 (X:153931010 G>A), RS10046980 (X:153934130 C>A,T), RS1004954870 (X:153932494 C>A,T), RS1005415418 (X:153932876 T>C,G), RS1005542383 (X:153929540 G>C,T), RS1006071227 (X:153929124 C>T), RS1007349241 (X:153936399 G>C), RS1007463744 (X:153935989 C>T), RS1008183008 (X:153931519 A>G), RS1008483395 (X:153931833 C>T), RS1009346 (X:153931231 G>C), RS1009347 (X:153931408 C>T)

Disease associations

OMIM: gene MIM:300013 | disease phenotypes: MIM:309800, MIM:300855, MIM:148840, MIM:300100, MIM:156200, MIM:300673

GenCC curated gene-disease

DiseaseClassificationInheritance
Ogden syndromeDefinitiveX-linked
NAA10-related syndromeDefinitiveX-linked
microphthalmia, syndromic 1ModerateX-linked
microphthalmia, Lenz typeSupportiveX-linked

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
NAA10-related syndromeDefinitiveXL

Mondo (10): microphthalmia, syndromic 1 (MONDO:0010671), Ogden syndrome (MONDO:0010457), Kleine-Levin syndrome (MONDO:0007863), intellectual disability (MONDO:0001071), NAA10-related syndrome (MONDO:0100124), adrenoleukodystrophy (MONDO:0018544), intellectual disability, autosomal dominant (MONDO:0100172), severe neonatal-onset encephalopathy with microcephaly (MONDO:0010397), neurodevelopmental disorder (MONDO:0700092), microphthalmia, Lenz type (MONDO:0018924)

Orphanet (7): Microphthalmia, Lenz type (Orphanet:568), Microphthalmia-ankyloblepharon-intellectual disability syndrome (Orphanet:85275), Ogden syndrome (Orphanet:276432), Kleine-Levin syndrome (Orphanet:33543), X-linked adrenoleukodystrophy (Orphanet:43), MECP2-related severe neonatal encephalopathy (Orphanet:209370), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

216 total (30 of 216 shown, HPO-id order):

HPOTerm
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000034Hydrocele testis
HP:0000047Hypospadias
HP:0000072Hydroureter
HP:0000089Renal hypoplasia
HP:0000105Enlarged kidney
HP:0000113Polycystic kidney dysplasia
HP:0000126Hydronephrosis
HP:0000164Abnormality of the dentition
HP:0000189Narrow palate
HP:0000202Orofacial cleft
HP:0000204Cleft upper lip
HP:0000215Thick upper lip vermilion
HP:0000218High palate
HP:0000219Thin upper lip vermilion
HP:0000233Thin vermilion border
HP:0000252Microcephaly
HP:0000260Wide anterior fontanel
HP:0000270Delayed cranial suture closure
HP:0000280Coarse facial features
HP:0000286Epicanthus
HP:0000290Abnormal forehead morphology
HP:0000308Microretrognathia
HP:0000316Hypertelorism
HP:0000322Short philtrum
HP:0000337Broad forehead
HP:0000341Narrow forehead
HP:0000343Long philtrum
HP:0000347Micrognathia

GWAS associations

1 associations (top):

StudyTraitp-value
GCST003155_27Systemic lupus erythematosus2.000000e-15

MeSH disease descriptors (7)

DescriptorNameTree numbers
D000326AdrenoleukodystrophyC10.228.140.163.100.084; C10.228.140.163.100.362.250; C10.228.140.695.625.250; C10.314.400.250; C10.597.606.360.455.124; C16.320.322.500.124; C16.320.400.525.124; C16.320.565.189.084; C16.320.565.189.362.250; C16.320.565.663.100; C18.452.132.100.084; C18.452.132.100.362.250; C18.452.648.189.084; C18.452.648.189.362.250; C18.452.648.663.100; C19.053.500.270
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D017593Kleine-Levin SyndromeC10.886.425.800.200.500; F03.870.400.800.200.500
D065886Neurodevelopmental DisordersF03.625
C566878Encephalopathy, Neonatal Severe, Due To Mecp2 Mutations (supp.)
C537464Microphthalmia, syndromic 1 (supp.)
C536107N acetyltransferase deficiency (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4630819 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.09Kd817.3nMCHEMBL5653589
6.09ED50817.3nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148814: Binding affinity to human NAA10 incubated for 45 mins by Kinobead based pull down assaykd0.8173uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression4
bisphenol Aaffects expression, decreases expression3
sodium arseniteaffects cotreatment, decreases expression, increases abundance3
Tretinoinaffects cotreatment, decreases expression, increases expression3
Air Pollutantsaffects cotreatment, increases abundance, increases oxidation, affects expression2
Ozoneaffects cotreatment, increases oxidation, increases abundance, affects expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
FR900359decreases phosphorylation1
moringinaffects cotreatment, increases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases oxidation, increases abundance1
decabromobiphenyl etherincreases expression1
arseniteaffects binding, increases reaction1
cobaltous chloridedecreases expression1
tanshinoneincreases expression1
nickel chloridedecreases expression1
coumarinaffects phosphorylation1
methacrylaldehydeaffects cotreatment, increases oxidation, increases abundance1
di-n-butylphosphoric acidaffects expression1
2-palmitoylglycerolincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100increases expression1
hexabrominated diphenyl ether 153decreases expression1
bisphenol Sincreases methylation1
bisphenol AFincreases expression1
Temozolomideincreases expression1
Sunitinibdecreases expression1
Acroleinaffects cotreatment, increases oxidation, increases abundance1
Arsenicdecreases expression, increases abundance1
Vehicle Emissionsincreases abundance, decreases expression1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4618912BindingBinding affinity to Naa10 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 CESTACharacterization of Specific N-α-Acetyltransferase 50 (Naa50) Inhibitors Identified Using a DNA Encoded Library. — ACS Med Chem Lett

Cellosaurus cell lines

1 cell lines: 1 telomerase immortalized cell line

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

CellosaurusNameCategorySex
CVCL_C0QIS37P-hTERTTelomerase immortalized cell lineMale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT02337023Not specifiedCOMPLETEDBrain Scintigraphy in Normal Versus Kleine-Levin Syndrome Subjects
NCT03754348Not specifiedCOMPLETEDMicroglial Activation in Narcolepsy Type 1 and Kleine-Levin Syndrome: Positron Emission Tomography (PET) Study in [18F] DPA-714
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)