NAA16
protein-codingN-alpha-acetyltransferase 16, NatA auxiliary subunit, the group of N-alpha-acetyltransferase subunits|Tetratricopeptide repeat domain containing|Armadillo like helical domain containing
Gene summary
Enables ribosome binding activity. Involved in protein maturation. Located in cytosol. Part of NatA complex. [provided by Alliance of Genome Resources, Jun 2026]
- NARG1L
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~65.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NAA16 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024561.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 115 | 1 | 116 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 121 | 1 | 0 | 122 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_078837.3 | 20 | MANE Select | |
| Ensembl | ENSP00000368716.3 | 20 | MANE Select | |
| RefSeq | NP_001104268.1 | 11 | Standard | |
| RefSeq | NP_060997.2 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
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
Molecular Function
- peptide alpha-N-acetyltransferase activity
- protein binding
- acetyltransferase activity
- ribosome binding
Cellular Component
- nucleus
- transcription factor complex
- cytoplasm
- cytosol
- NatA complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000379406
- Coding exons
- 20
- Length
- 65826
- Individuals with no LoFs
- 125621
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 125
- Defined
- 125746
- p
- 0.000497
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0715 | 427 | 431 | 0.990 | 0.0000210 | 5735 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00044 | 0.00043 | rare |
| Latino/Admixed American | 0.00065 | 0.00061 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00063 | 0.00060 | rare |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.00053 | 0.00051 | rare |
| South Asian | 0.00075 | 0.00069 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |