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

ENSG00000102030 ∙ NCBI:8260 ∙ OMIM:300013 ∙ HGNC:18704 ∙ Uniprot:P41227 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Ogden syndrome (Definitive), mode of inheritance: XLR
• 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

Clinical Genomic Database

Source: CGD

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 ClinVar and linked to the NAA10 gene.

• Ogden syndrome (6 variants)
• not provided (3 variants)
• Microphthalmia, syndromic 1;Ogden syndrome (1 variants)
• NAA10-related disorder (1 variants)
• Intellectual disability (1 variants)
• Inborn genetic diseases (1 variants)
• See cases (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				16	7	23
missense	5	17	34	2		58
nonsense						0
start loss						0
frameshift	1					1
inframe indel			3			3
splice donor/acceptor (+/-2bp)	1					1
splice region			2	8		10
non coding		2	2	14	20	38
Total	7	19	39	32	27

Variants in NAA10

This is a list of pathogenic ClinVar variants found in the NAA10 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-153929940-G-A			Benign (Jun 19, 2018)
X-153929944-T-C		Microphthalmia, syndromic 1	Likely pathogenic (Jan 14, 2019)
X-153929947-T-C		Microphthalmia, syndromic 1	Conflicting classifications of pathogenicity (Jan 02, 2024)
X-153929948-T-C		Microphthalmia, syndromic 1	Pathogenic/Likely pathogenic (Jan 11, 2022)
X-153930002-G-A			Benign (Mar 16, 2023)
X-153930036-T-C			Uncertain significance (Nov 01, 2019)
X-153930043-TCTCGCTGAC-T			Uncertain significance (Feb 09, 2024)
X-153930056-G-A			Likely benign (Sep 27, 2022)
X-153930068-G-A			Likely benign (Jun 07, 2023)
X-153930070-T-C			Uncertain significance (Jul 06, 2020)
X-153930076-C-G			Uncertain significance (Sep 27, 2022)
X-153930078-C-G			Uncertain significance (Sep 01, 2022)
X-153930079-C-T		not specified	Uncertain significance (Dec 17, 2014)
X-153930079-CACT-C			Uncertain significance (Jun 15, 2017)
X-153930081-C-T			Uncertain significance (Nov 13, 2023)
X-153930097-G-A			Benign (Oct 14, 2023)
X-153930103-TCTC-T		NAA10-related disorder	Uncertain significance (Jan 19, 2023)
X-153930109-C-T		Inborn genetic diseases	Uncertain significance (Oct 04, 2022)
X-153930112-G-A		Intellectual disability, autosomal dominant	Likely benign (Jul 11, 2016)
X-153930112-G-T			Uncertain significance (May 10, 2024)
X-153930118-C-G			Conflicting classifications of pathogenicity (Dec 20, 2023)
X-153930131-C-T			Conflicting classifications of pathogenicity (Jan 07, 2023)
X-153930132-G-A			Uncertain significance (May 15, 2023)
X-153930158-C-T			Benign (Aug 09, 2022)
X-153930161-G-T		Ogden syndrome	Uncertain significance (Aug 03, 2019)

GnomAD

Source: gnomAD

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: 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

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