NAA50

protein-coding

N-alpha-acetyltransferase 50, NatE catalytic subunit, the group of N-alpha-acetyltransferase subunits|GCN5 related N-acetyltransferases

Gene summary

Enables histone H4 acetyltransferase activity and protein-N-terminal amino-acid acetyltransferase activity. Involved in N-terminal protein amino acid acetylation; establishment of mitotic sister chromatid cohesion; and mitotic sister chromatid cohesion, centromeric. Located in cytosol and nucleolus. Part of NatA complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

MAK3
NAT13

MANE transcript

NM_025146.4

Inheritance

—

ClinVar variants

U:11B:1

Top phenotype

NAA50-related disorder

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr3:113,716,458-113,746,300

External References & Databases

Ensembl (ENSG00000121579)

Transcript & Mutation Effects

hg38 • Region Span ~29.8 kb

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GenCC 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 NAA50 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 9

NAA50-related disorderTotal: 2

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025146.4. 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					1 clinvar	1
missense			9 clinvar			9
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	11	0	1	12

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025146.4	RefSeq	NP_079422.1	5	MANE Select
ENST00000240922.8	Ensembl	ENSP00000240922.2	5	MANE Select
NM_001308445.2	RefSeq	NP_001295374.1	5	Standard
ENST00000477813.5	Ensembl	ENSP00000417110.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metapathway biotransformation Phase I and II

Biological Process

N-terminal protein amino acid acetylation
mitotic sister chromatid cohesion
histone acetylation
establishment of mitotic sister chromatid cohesion
histone H4 acetylation

Molecular Function

peptide alpha-N-acetyltransferase activity
protein binding
N-acetyltransferase activity
H4 histone acetyltransferase activity
peptidyl-lysine acetyltransferase activity

Cellular Component

nucleus
cytoplasm
cytosol
NatA complex
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000240922
Coding exons: 5
Length: 29841
Individuals with no LoFs: 125601
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125603
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.78	40	86.6	0.462	0.00000418	1121
Missense (PolyPhen)		11	29.211	0.37657		390
Synonymous	-0.0466	33	32.7	1.01	0.00000173	294
Loss of Function	2.42	1	8.71	0.115	4.52e-7	113

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: N-alpha-acetyltransferase that acetylates the N-terminus of proteins that retain their initiating methionine (PubMed:19744929, PubMed:22311970, PubMed:21900231, PubMed:27484799). Has a broad substrate specificity: able to acetylate the initiator methionine of most peptides, except for those with a proline in second position (PubMed:27484799). Also displays N-epsilon-acetyltransferase activity by mediating acetylation of the side chain of specific lysines on proteins (PubMed:19744929). Autoacetylates in vivo (PubMed:19744929). The relevance of N-epsilon-acetyltransferase activity is however unclear: able to acetylate H4 in vitro, but this result has not been confirmed in vivo (PubMed:19744929). Component of a N-alpha- acetyltransferase complex containing NAA10 and NAA15, but NAA50 does not influence the acetyltransferase activity of NAA10: this multiprotein complex probably constitutes the major contributor for N-terminal acetylation at the ribosome exit tunnel, with NAA10 acetylating all amino termini that are devoid of methionine and NAA50 acetylating other peptides (PubMed:16507339, PubMed:27484799). Required for sister chromatid cohesion during mitosis by promoting binding of CDCA5/sororin to cohesin: may act by counteracting the function of NAA10 (PubMed:17502424, PubMed:27422821). {ECO:0000269|PubMed:16507339, ECO:0000269|PubMed:17502424, ECO:0000269|PubMed:19744929, ECO:0000269|PubMed:21900231, ECO:0000269|PubMed:22311970, ECO:0000269|PubMed:27422821, ECO:0000269|PubMed:27484799}.;

Recessive Scores

pRec: 0.173

Intolerance Scores

RVIS EVS: -0.03
RVIS percentile EVS: 51.04

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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