NAT1

N-acetyltransferase 1, the group of Arylamine N-acetyltransferases

Basic information

Region (hg38): 8:18170476-18223689

Previous symbols: [ "AAC1" ]

Links

ENSG00000171428 ∙ NCBI:9 ∙ OMIM:108345 ∙ HGNC:7645 ∙ Uniprot:P18440 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Acetylation, NAT1-related	AD	Pharmacogenomic	Medication dosage/selection may be affected related to multiple agents, including isoniazid, hydralazine, phenytoin, procainamide, and some sulfa drugs	Biochemical	17909564; 21878835

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAT1 gene.

• Inborn genetic diseases (7 variants)
• not specified (2 variants)
• - (2 variants)
• not provided (1 variants)
• NAT1*17 ALLELE (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAT1 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						0
missense			7	1	2	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	2

Variants in NAT1

This is a list of pathogenic ClinVar variants found in the NAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-18222164-C-G		not specified	Uncertain significance (Mar 06, 2023)
8-18222237-C-T		not specified	Benign (Dec 17, 2015)
8-18222362-G-T			Likely benign (Jun 23, 2018)
8-18222427-G-A		not specified	Uncertain significance (Aug 02, 2023)
8-18222433-A-T		not specified	Uncertain significance (Dec 07, 2021)
8-18222492-G-A		NAT1*17 ALLELE • not specified	Benign (Mar 28, 2016)
8-18222551-G-T		not specified	Uncertain significance (Oct 26, 2021)
8-18222552-T-A		not specified	Uncertain significance (Aug 08, 2023)
8-18222582-G-A		not specified	Uncertain significance (Jan 09, 2024)
8-18222636-C-G		not specified	Uncertain significance (Feb 08, 2023)
8-18222855-A-G		not specified	Uncertain significance (Dec 08, 2023)
8-18222857-A-G		not specified	Uncertain significance (Feb 17, 2022)
8-18223135-A-A		-	no classification for the single variant (-)
8-18223142-A-A		-	no classification for the single variant (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAT1	protein_coding	protein_coding	ENST00000545197	3	53213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.93e-14	0.00218	125105	3	634	125742	0.00254

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.499	196	177	1.11	0.00000854	2313
Missense in Polyphen		46	41.821	1.0999		564
Synonymous	-1.14	78	66.2	1.18	0.00000315	662
Loss of Function	-1.33	18	12.9	1.40	6.97e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00469	0.00469
Ashkenazi Jewish	0.00251	0.00248
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00374	0.00372
Middle Eastern	0.0000544	0.0000544
South Asian	0.000755	0.000719
Other	0.00577	0.00572

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the detoxification of a plethora of hydrazine and arylamine drugs. Catalyzes the N- or O-acetylation of various arylamine and heterocyclic amine substrates and is able to bioactivate several known carcinogens.
• Pathway: Drug metabolism - other enzymes - Homo sapiens (human);Caffeine metabolism - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Busulfan Pathway, Pharmacodynamics;Arylamine metabolism;Metapathway biotransformation Phase I and II;Acetylation;Phase II - Conjugation of compounds;Biological oxidations;Metabolism (Consensus)

Recessive Scores

• pRec: 0.0920

Intolerance Scores

• loftool: 0.996
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.44

Haploinsufficiency Scores

• pHI: 0.0842
• hipred: N
• hipred_score: 0.112
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nat3
• Phenotype: normal phenotype

Gene ontology

• Biological process: xenobiotic metabolic process
• Cellular component: cytosol
• Molecular function: arylamine N-acetyltransferase activity