NAA30

protein-coding

N-alpha-acetyltransferase 30, NatC catalytic subunit, the group of GCN5 related N-acetyltransferases|N-alpha-acetyltransferase subunits

Gene summary

Enables protein-N-terminal amino-acid acetyltransferase activity. Involved in protein stabilization. Located in cytosol and nucleus. Part of NatC complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf35
NAT12

MANE transcript

NM_001011713.3

Inheritance

ClinVar variants

P:1U:39B:1

Top phenotype

Lethal multiystemic syndrome

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr14:57,390,544-57,415,906

External References & Databases

Ensembl (ENSG00000139977)

Transcript & Mutation Effects

hg38 • Region Span ~25.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NAA30 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 38

not providedTotal: 1

Lethal multiystemic syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001011713.3. 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		1 clinvar	39 clinvar	1 clinvar		41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	39	1	0	41

Highest pathogenic variant AF is 0.0000013743532

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001011713.3	RefSeq	NP_001011713.2	4	MANE Select
ENST00000556492.6	Ensembl	ENSP00000452521.1	4	MANE Select
ENST00000298406.6	Ensembl	ENSP00000298406.6	4	Standard
ENST00000554703.1	Ensembl	ENSP00000451255.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metapathway biotransformation Phase I and II
Vesicle-mediated transport
Membrane Trafficking
Retrograde transport at the Trans-Golgi-Network
Intra-Golgi and retrograde Golgi-to-ER traffic

Biological Process

N-terminal peptidyl-methionine acetylation

Molecular Function

peptide alpha-N-acetyltransferase activity
protein binding

Cellular Component

nucleus
cytoplasm
cytosol
polysome
NatC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000556492
Coding exons: 4
Length: 25374
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125693
p: 0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.61	142	207	0.685	0.00000990	2306
Missense (PolyPhen)		9	45.412	0.19819		539
Synonymous	-0.587	96	89.0	1.08	0.00000454	749
Loss of Function	3.35	0	13.1	0.00	6.31e-7	164

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
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)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalytic subunit of the N-terminal acetyltransferase C (NatC) complex. Catalyzes acetylation of the N-terminal methionine residues of peptides beginning with Met-Leu-Ala and Met-Leu-Gly. Necessary for the lysosomal localization and function of ARL8B sugeesting that ARL8B is a NatC substrate. {ECO:0000269|PubMed:19398576}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.159
RVIS EVS: -0.16
RVIS percentile EVS: 41.64

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
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