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
Phenotypes
GenCC
Source:
- 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:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Ogden syndrome | XL | Cardiovascular | Though 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 mortality | Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic; Renal | 11426460; 21700266; 24431331; 25099252; 26522270; 31127942 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 24 | 31 | ||||
| missense | 10 | 26 | 51 | 92 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 3 | |||||
| Total | 13 | 28 | 52 | 29 | 7 |
Highest pathogenic variant AF is 0.00000182175
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NAA10 | protein_coding | protein_coding | ENST00000464845 | 8 | 5982 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.762 | 0.237 | 125714 | 1 | 1 | 125716 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.41 | 33 | 101 | 0.326 | 0.00000832 | 1555 |
| Missense in Polyphen | 2 | 22.856 | 0.087503 | 354 | ||
| Synonymous | -0.308 | 45 | 42.4 | 1.06 | 0.00000372 | 431 |
| Loss of Function | 2.49 | 1 | 9.09 | 0.110 | 6.30e-7 | 164 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000730 | 0.0000730 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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