NAT10

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

Basic information

Region (hg38): 11:34105617-34147670

Links

ENSG00000135372 ∙ NCBI:55226 ∙ OMIM:609221 ∙ HGNC:29830 ∙ Uniprot:Q9H0A0 ∙ 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 NAT10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAT10 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				1	5	6
missense			46	1	2	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	46	2	7

Variants in NAT10

This is a list of pathogenic ClinVar variants found in the NAT10 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-34108232-C-T		not specified	Uncertain significance (Jun 17, 2024)
11-34108262-C-T		not specified	Uncertain significance (Mar 21, 2022)
11-34108314-G-A		not specified	Uncertain significance (Apr 26, 2023)
11-34108767-C-T		not specified	Uncertain significance (Apr 09, 2024)
11-34108810-T-C			Benign (Feb 20, 2018)
11-34112124-C-T			Likely benign (Feb 20, 2018)
11-34112138-T-C		not specified	Uncertain significance (Jul 25, 2023)
11-34112168-A-G		not specified	Uncertain significance (Dec 07, 2021)
11-34112187-G-T		not specified	Uncertain significance (Jul 25, 2023)
11-34112216-T-C		not specified	Uncertain significance (Dec 01, 2022)
11-34112220-G-A			Benign (Feb 20, 2018)
11-34113709-C-T			Benign (Dec 31, 2019)
11-34113737-A-G		Intellectual disability • not specified	Uncertain significance (Jan 26, 2022)
11-34113802-C-T			Benign (Dec 31, 2019)
11-34113809-T-G		not specified	Uncertain significance (Apr 08, 2024)
11-34113828-C-T		not specified	Uncertain significance (Jun 16, 2024)
11-34118231-G-A			Benign (Mar 30, 2018)
11-34118233-T-A		not specified	Uncertain significance (May 14, 2024)
11-34118265-A-G		not specified	Uncertain significance (Dec 26, 2023)
11-34118274-G-A		not specified	Uncertain significance (Sep 12, 2023)
11-34118293-C-T			Benign (Apr 16, 2018)
11-34118408-G-C		not specified	Uncertain significance (Jan 31, 2022)
11-34118415-C-G		not specified	Uncertain significance (Jul 05, 2023)
11-34118418-A-T		not specified	Uncertain significance (Jan 31, 2024)
11-34118443-G-C		not specified	Uncertain significance (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAT10	protein_coding	protein_coding	ENST00000257829	28	42069

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.12e-22	0.598	125548	0	200	125748	0.000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	505	585	0.864	0.0000330	6665
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00117	0.00117
Ashkenazi Jewish	0.00354	0.00338
East Asian	0.000707	0.000653
Finnish	0.000279	0.000277
European (Non-Finnish)	0.000717	0.000712
Middle Eastern	0.000707	0.000653
South Asian	0.00114	0.00114
Other	0.000662	0.000652

dbNSFP

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}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: -0.55
• rvis_percentile_EVS: 20.02

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.637
• ghis: 0.626

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.934

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nat10
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Gene ontology

• Biological process: rRNA modification;negative regulation of telomere maintenance via telomerase;tRNA acetylation;rRNA acetylation involved in maturation of SSU-rRNA
• Cellular component: nuclear chromosome, telomeric region;nucleus;nucleoplasm;telomerase holoenzyme complex;nucleolus;membrane;midbody
• Molecular function: RNA binding;protein binding;ATP binding;N-acetyltransferase activity;DNA polymerase binding;rRNA cytidine N-acetyltransferase activity