NAA10

N-alpha-acetyltransferase 10, NatA catalytic subunit, the group of GCN5 related N-acetyltransferases|N-alpha-acetyltransferase subunits

Basic information

Region (hg38): X:153929225-153935080

Previous symbols: [ "ARD1", "ARD1A" ]

Links

ENSG00000102030NCBI:8260OMIM:300013HGNC:18704Uniprot:P41227AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Ogden syndrome (Strong), mode of inheritance: XL
  • microphthalmia, syndromic 1 (Limited), mode of inheritance: XL
  • microphthalmia, Lenz type (Supportive), mode of inheritance: XL
  • Ogden syndrome (Supportive), mode of inheritance: XL
  • Ogden syndrome (Strong), mode of inheritance: XL
  • Ogden syndrome (Definitive), mode of inheritance: XL
  • microphthalmia, syndromic 1 (Definitive), mode of inheritance: XL
  • microphthalmia, syndromic 1 (Limited), mode of inheritance: Unknown
  • NAA10-related syndrome (Definitive), mode of inheritance: XL
  • NAA10-related syndrome (Definitive), mode of inheritance: XL
  • NAA10-related syndrome (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Ogden syndromeXLCardiovascularThough the overall phenotype may be recognizable, reported individuals have died due to sequelae of arrhythmias, and surveillance and awareness may allow early diagnosis and treatment, which may reduce morbidity and mortalityCardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic; Renal11426460; 21700266; 24431331; 25099252; 26522270; 31127942

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAA10 gene.

  • not_provided (133 variants)
  • Ogden_syndrome (42 variants)
  • NAA10-related_disorder (12 variants)
  • Microphthalmia,_syndromic_1 (11 variants)
  • Inborn_genetic_diseases (11 variants)
  • Intellectual_disability (6 variants)
  • not_specified (5 variants)
  • Neurodevelopmental_disorder (2 variants)
  • Xq28_related_immunodeficiency (2 variants)
  • See_cases (1 variants)
  • Kleine-Levin_syndrome (1 variants)
  • Intellectual_disability,_severe (1 variants)
  • Intellectual_disability,_autosomal_dominant (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA10 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003491.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
24
clinvar
7
clinvar
31
missense
10
clinvar
26
clinvar
51
clinvar
5
clinvar
92
nonsense
0
start loss
0
frameshift
1
clinvar
1
clinvar
1
clinvar
3
splice donor/acceptor (+/-2bp)
2
clinvar
1
clinvar
3
Total 13 28 52 29 7

Highest pathogenic variant AF is 0.00000182175

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
NAA10protein_codingprotein_codingENST00000464845 85982
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7620.237125714111257160.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.41331010.3260.000008321555
Missense in Polyphen222.8560.087503354
Synonymous-0.3084542.41.060.00000372431
Loss of Function2.4919.090.1106.30e-7164

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00007300.0000730
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalytic subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity (PubMed:15496142, PubMed:19826488, PubMed:19420222, PubMed:20145209, PubMed:27708256, PubMed:25489052). Acetylates amino termini that are devoid of initiator methionine (PubMed:19420222). 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 (PubMed:12464182). Represses MYLK kinase activity by acetylation, and thus represses tumor cell migration (PubMed:19826488). Acetylates, and stabilizes TSC2, thereby repressing mTOR activity and suppressing cancer development (PubMed:20145209). Acetylates HSPA1A and HSPA1B at 'Lys-77' which enhances its chaperone activity and leads to preferential binding to co-chaperone HOPX (PubMed:27708256). Acts as a negative regulator of sister chromatid cohesion during mitosis (PubMed:27422821). {ECO:0000269|PubMed:12464182, ECO:0000269|PubMed:15496142, ECO:0000269|PubMed:19420222, ECO:0000269|PubMed:19826488, ECO:0000269|PubMed:20145209, ECO:0000269|PubMed:25489052, ECO:0000269|PubMed:27422821, ECO:0000269|PubMed:27708256}.;
Disease
DISEASE: 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. {ECO:0000269|PubMed:21700266, ECO:0000269|PubMed:25489052, ECO:0000269|PubMed:26522270}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: 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. {ECO:0000269|PubMed:24431331}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
Leukotriene metabolism;Hypoxic and oxygen homeostasis regulation of HIF-1-alpha (Consensus)

Recessive Scores

pRec
0.281

Intolerance Scores

loftool
0.309
rvis_EVS
-0.03
rvis_percentile_EVS
51.04

Haploinsufficiency Scores

pHI
0.575
hipred
Y
hipred_score
0.682
ghis
0.508

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.824

Mouse Genome Informatics

Gene name
Naa10
Phenotype

Zebrafish Information Network

Gene name
naa10
Affected structure
ventral mandibular arch
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
DNA packaging;protein acetylation;N-terminal protein amino acid acetylation;internal protein amino acid acetylation;N-terminal peptidyl-serine acetylation;N-terminal peptidyl-glutamic acid acetylation;negative regulation of maintenance of mitotic sister chromatid cohesion, centromeric
Cellular component
nucleus;nucleolus;cytoplasm;cytosol;membrane;NatA complex
Molecular function
peptide alpha-N-acetyltransferase activity;protein binding;N-acetyltransferase activity;acetyltransferase activity;ribosome binding;peptide-serine-N-acetyltransferase activity;peptide-glutamate-N-acetyltransferase activity