NAA16

N-alpha-acetyltransferase 16, NatA auxiliary subunit, the group of N-alpha-acetyltransferase subunits|Tetratricopeptide repeat domain containing|Armadillo like helical domain containing

Basic information

Region (hg38): 13:41311267-41377030

Previous symbols: [ "NARG1L" ]

Links

ENSG00000172766 ∙ NCBI:79612 ∙ OMIM:619497 ∙ HGNC:26164 ∙ Uniprot:Q6N069 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAA16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA16 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						0
missense			68	1		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	68	1	0

Variants in NAA16

This is a list of pathogenic ClinVar variants found in the NAA16 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-41316900-C-G		not specified	Uncertain significance (Aug 30, 2022)
13-41318807-G-T		not specified	Uncertain significance (Jun 02, 2024)
13-41318817-A-G		not specified	Uncertain significance (Apr 23, 2024)
13-41318832-C-G		not specified	Uncertain significance (Feb 26, 2025)
13-41318842-T-C		not specified	Uncertain significance (Dec 08, 2023)
13-41318847-A-G		not specified	Uncertain significance (Jun 22, 2024)
13-41318857-A-C		not specified	Uncertain significance (Apr 08, 2024)
13-41318870-T-G		not specified	Uncertain significance (Nov 10, 2024)
13-41318875-G-A		not specified	Uncertain significance (Oct 26, 2022)
13-41318875-G-C		not specified	Uncertain significance (Dec 21, 2024)
13-41320693-C-A		not specified	Uncertain significance (Jan 23, 2023)
13-41320697-C-G		not specified	Uncertain significance (Dec 10, 2024)
13-41320720-A-G		not specified	Uncertain significance (Oct 28, 2024)
13-41320750-G-A		not specified	Uncertain significance (Aug 16, 2022)
13-41320756-G-T		not specified	Uncertain significance (Mar 14, 2025)
13-41323107-A-G		not specified	Uncertain significance (Aug 30, 2022)
13-41325698-G-T		not specified	Uncertain significance (Apr 23, 2024)
13-41325699-T-C		not specified	Uncertain significance (Mar 01, 2023)
13-41325760-G-A		not specified	Uncertain significance (Jul 30, 2024)
13-41325779-C-G		not specified	Uncertain significance (Jan 04, 2024)
13-41325807-A-T		not specified	Uncertain significance (Jan 08, 2025)
13-41325821-T-C		not specified	Uncertain significance (Nov 15, 2021)
13-41328732-C-A		not specified	Uncertain significance (Apr 26, 2023)
13-41331301-A-G		not specified	Uncertain significance (Jul 07, 2022)
13-41331312-A-G		not specified	Uncertain significance (Feb 15, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA16	protein_coding	protein_coding	ENST00000379406	20	65826

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-18	0.488	125621	0	125	125746	0.000497

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0715	427	431	0.990	0.0000210	5735
Missense in Polyphen		113	144.41	0.78248		1881
Synonymous	-1.88	176	147	1.20	0.00000712	1456
Loss of Function	1.80	35	48.6	0.721	0.00000244	662

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00108
Ashkenazi Jewish	0.000201	0.000198
East Asian	0.000632	0.000598
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000526	0.000510
Middle Eastern	0.000632	0.000598
South Asian	0.000745	0.000686
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Auxillary subunit of the N-terminal acetyltransferase A (NatA) complex which displays alpha (N-terminal) acetyltransferase activity.

Recessive Scores

• pRec: 0.134

Intolerance Scores

• loftool: 0.969
• rvis_EVS: -0.78
• rvis_percentile_EVS: 13.05

Haploinsufficiency Scores

• pHI: 0.787
• hipred: N
• hipred_score: 0.322
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naa16

Gene ontology

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