NAA15

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

Basic information

Region (hg38): 4:139301446-139420033

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 (374 variants)
Intellectual_disability,_autosomal_dominant_50 (106 variants)
Inborn_genetic_diseases (71 variants)
NAA15-related_disorder (32 variants)
not_specified (8 variants)
Intellectual_disability (6 variants)
See_cases (6 variants)
Neurodevelopmental_disorder (5 variants)
Incidental_Discovery (1 variants)
Syndromic_intellectual_disability (1 variants)
Autism_spectrum_disorder (1 variants)
NAA15-related_syndrome (1 variants)
Global_developmental_delay (1 variants)
Neurodevelopmental_delay (1 variants)
Autism (1 variants)
intellectual_developmental_disorder-50_with_behavioral_abnormalities_(MRD50) (1 variants)
Developmental_disorder (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. These statistics are base on transcript: NM_000057175.5. 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			4 clinvar	54 clinvar	8 clinvar	66
missense	4 clinvar	14 clinvar	222 clinvar	13 clinvar		253
nonsense	30 clinvar	15 clinvar	4 clinvar			49
start loss						0
frameshift	29 clinvar	21 clinvar	3 clinvar			53
splice donor/acceptor (+/-2bp)	13 clinvar	17 clinvar	5 clinvar			35
Total	76	67	238	67	8

Highest pathogenic variant AF is 0.0000083671

Loading clinvar variants...

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
Phenotype

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