NAT10

protein-coding

N-acetyltransferase 10, the group of SSU processome|GCN5 related N-acetyltransferases

Gene summary

The protein encoded by this gene is an RNA cytidine acetyltransferase involved in histone acetylation, tRNA acetylation, the biosynthesis of 18S rRNA, and the enhancement of nuclear architecture and chromatin organization. [provided by RefSeq, Oct 2016]

MANE transcript

NM_024662.3

Inheritance

—

ClinVar variants

U:138B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr11:34,105,617-34,147,670

External References & Databases

Ensembl (ENSG00000135372)

Transcript & Mutation Effects

hg38 • Region Span ~42.1 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 NAT10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 119

not providedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024662.3. 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			7 clinvar	1 clinvar	4 clinvar	12
missense			122 clinvar	2 clinvar	2 clinvar	126
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	138	3	6	147

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024662.3	RefSeq	NP_078938.3	28	MANE Select
ENST00000257829.8	Ensembl	ENSP00000257829.3	28	MANE Select
NM_001144030.2	RefSeq	NP_001137502.2	26	Standard
ENST00000527971.5	Ensembl	ENSP00000437324.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ribosome biogenesis in eukaryotes - Homo sapiens (human)
Metapathway biotransformation Phase I and II

Biological Process

rRNA modification
negative regulation of telomere maintenance via telomerase
tRNA acetylation
rRNA acetylation involved in maturation of SSU-rRNA

Molecular Function

RNA binding
protein binding
ATP binding
N-acetyltransferase activity
DNA polymerase binding

Cellular Component

nuclear chromosome, telomeric region
nucleus
nucleoplasm
telomerase holoenzyme complex
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000257829
Coding exons: 28
Length: 42069
Individuals with no LoFs: 125548
Homozygous LoFs: 0
Heterozygous LoFs: 200
Defined: 125748
p: 0.000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.17	505	585	0.864	0.0000330	6665
Missense (PolyPhen)		122	159.12	0.76673		1811
Synonymous	2.10	186	226	0.823	0.0000125	2036
Loss of Function	2.12	43	60.9	0.706	0.00000329	679

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00068	0.00068	rare
Latino/Admixed American	0.00049	0.00049	rare
Ashkenazi Jewish	0.0035	0.0034	notable
East Asian	0.00071	0.00065	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00072	0.00071	rare
South Asian	0.0011	0.0011	notable
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: RNA cytidine acetyltransferase with specificity toward both 18S rRNA and tRNAs (PubMed:25411247, PubMed:25653167). Catalyzes the formation of N(4)-acetylcytidine (ac4C) at position 1842 in 18S rRNA (PubMed:25411247). May also catalyze the formation of ac4C at position 1337 in 18S rRNA (By similarity). Required for early nucleolar cleavages of precursor rRNA at sites A0, A1 and A2 during 18S rRNA synthesis (PubMed:25411247, PubMed:25653167). Catalyzes the formation of ac4C in serine and leucine tRNAs (By similarity). Requires the tRNA-binding adapter protein THUMBD1 for full tRNA acetyltransferase activity but not for 18S rRNA acetylation (PubMed:25653167). Can acetylate both histones and microtubules (PubMed:14592445, PubMed:17631499, PubMed:19303003). Histone acetylation may regulate transcription and mitotic chromosome de-condensation (PubMed:17631499). Activates telomerase activity by stimulating the transcription of TERT, and may also regulate telomerase function by affecting the balance of telomerase subunit assembly, disassembly, and localization (PubMed:14592445, PubMed:18082603). Acetylates alpha- tubulin, which may affect microtubule stability and cell division (PubMed:19303003). {ECO:0000250|UniProtKB:P53914, ECO:0000255|HAMAP-Rule:MF_03211, ECO:0000269|PubMed:14592445, ECO:0000269|PubMed:17631499, ECO:0000269|PubMed:18082603, ECO:0000269|PubMed:19303003, ECO:0000269|PubMed:25411247, ECO:0000269|PubMed:25653167}.;

Recessive Scores

pRec: 0.136

Intolerance Scores

RVIS EVS: -0.55
RVIS percentile EVS: 20.02

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.934

Gene Damage Prediction

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