NAA15

N-alpha-acetyltransferase 15, NatA auxiliary subunit, the group of N-alpha-acetyltransferase subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 4:139301445-139420033

Previous symbols: [ "NARG1" ]

Links

ENSG00000164134 ∙ NCBI:80155 ∙ OMIM:608000 ∙ HGNC:30782 ∙ Uniprot:Q9BXJ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal dominant 50 (Definitive), mode of inheritance: AD
• intellectual disability, autosomal dominant 50 (Strong), mode of inheritance: AD
• intellectual disability, autosomal dominant 50 (Strong), mode of inheritance: AD
• syndromic intellectual disability (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal dominant 50, with behavioral abnormalities	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	28191889; 31127942

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAA15 gene.

• not provided (200 variants)
• Intellectual disability, autosomal dominant 50 (59 variants)
• Inborn genetic diseases (30 variants)
• See cases (6 variants)
• Neurodevelopmental disorder (5 variants)
• NAA15-related condition (3 variants)
• not specified (2 variants)
• Global developmental delay (1 variants)
• Developmental disorder (1 variants)
• Neurodevelopmental delay (1 variants)
• Autism spectrum disorder (1 variants)
• NAA15-related disorder (1 variants)
• NAA15-related syndrome (1 variants)
• Autism (1 variants)
• intellectual developmental disorder-50 with behavioral abnormalities (MRD50) (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA15 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			1	27	7	35
missense		7	93	2	1	103
nonsense	21	6	1			28
start loss						0
frameshift	18	13	1			32
inframe indel			5			5
splice donor/acceptor (+/-2bp)	7	12	3			22
splice region	1		5	10		16
non coding			2	13	28	43
Total	46	38	106	42	36

Highest pathogenic variant AF is 0.00000659

Variants in NAA15

This is a list of pathogenic ClinVar variants found in the NAA15 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-139301797-C-T			Uncertain significance (Dec 01, 2023)
4-139301802-A-G			Uncertain significance (May 24, 2021)
4-139301805-G-T			Pathogenic (Jul 30, 2022)
4-139301823-C-G			Likely pathogenic (Jan 16, 2020)
4-139301831-GGT-G			Likely pathogenic (Jun 17, 2021)
4-139301847-C-T			Benign (Dec 27, 2023)
4-139331311-G-C		Intellectual disability, autosomal dominant 50	Uncertain significance (Jul 16, 2021)
4-139334157-C-G			Benign (Jan 10, 2024)
4-139334164-G-A			Likely benign (Aug 25, 2022)
4-139334172-A-C		Focal-onset seizure;Autism;Intellectual disability • Intellectual disability, autosomal dominant 50	Likely pathogenic (Apr 20, 2020)
4-139334191-A-G			Likely benign (Jan 08, 2024)
4-139334194-G-A			Likely benign (Dec 16, 2023)
4-139334204-G-T			Pathogenic (Nov 14, 2023)
4-139334217-G-A			Uncertain significance (May 11, 2023)
4-139334222-C-T			Pathogenic (Aug 17, 2018)
4-139334224-A-G			Likely benign (Apr 09, 2023)
4-139334253-A-G		Intellectual disability, autosomal dominant 50 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Feb 14, 2024)
4-139334257-A-AGG		Intellectual disability, autosomal dominant 50	Likely pathogenic (Jul 26, 2022)
4-139334265-G-A			Likely benign (Jun 21, 2022)
4-139334274-T-A			Benign (Jan 14, 2024)
4-139334493-GA-G			Benign (Nov 12, 2018)
4-139336837-TTTGAAAA-T			Likely benign (Sep 27, 2022)
4-139336851-C-A		Intellectual disability, autosomal dominant 50	Uncertain significance (Oct 25, 2021)
4-139336869-TA-T		Intellectual disability, autosomal dominant 50	Pathogenic (Jul 07, 2021)
4-139336874-T-C			Likely benign (Dec 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA15	protein_coding	protein_coding	ENST00000296543	20	118579

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00422	124766	0	13	124779	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.81	202	422	0.478	0.0000201	5720
Missense in Polyphen		51	164.36	0.3103		2209
Synonymous	0.686	136	147	0.928	0.00000713	1460
Loss of Function	5.41	7	47.0	0.149	0.00000220	686

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000631	0.0000631
Ashkenazi Jewish	0.000101	0.0000993
East Asian	0.0000564	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000618
Middle Eastern	0.0000564	0.0000556
South Asian	0.0000365	0.0000327
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Auxillary subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity. The NAT activity may be important for vascular, hematopoietic and neuronal growth and development. Required to control retinal neovascularization in adult ocular endothelial cells. In complex with XRCC6 and XRCC5 (Ku80), up-regulates transcription from the osteocalcin promoter. {ECO:0000269|PubMed:11687548, ECO:0000269|PubMed:12145306, ECO:0000269|PubMed:15496142}.
• Disease: DISEASE: Mental retardation, autosomal dominant 50 (MRD50) [MIM:617787]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:28191889}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.198

Intolerance Scores

• loftool: 0.438
• rvis_EVS: -0.89
• rvis_percentile_EVS: 10.3

Haploinsufficiency Scores

• pHI: 0.990
• hipred: Y
• hipred_score: 0.783
• ghis: 0.713

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Naa15

Gene ontology

• Biological process: angiogenesis;N-terminal protein amino acid acetylation;N-terminal peptidyl-methionine acetylation;cell differentiation;negative regulation of apoptotic process;positive regulation of transcription, DNA-templated;protein stabilization
• Cellular component: nucleus;transcription factor complex;cytoplasm;cytosol;membrane;NatA complex
• Molecular function: RNA binding;peptide alpha-N-acetyltransferase activity;protein binding;acetyltransferase activity;ribosome binding