Table 1:
Description of NAT1 haplotypes *4, *10 and *11A-C. The current NAT nomenclature is aligned to the consensus Human Genome Variation Society (HGVS) nomenclature used by public electronic databases to localize SNPs in the human genome1–3.
| Homo sapiens chromosome 8 GRCh38.p12 primary assembly4, GeneID: 95, HGNC:76456, official gene symbol: NAT1 (arylamine N-acetyltransferase 1)6 | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Description of nucleotide change (Current NAT nomenclature)7 | −344C>T | −40A>T | 445G>A | 459G>A | 640T>G | Δ9 between 1065–1090 | 1088T>A | 1095C>A | |
| Description of nucleotide change (HGVS nomenclature)8 | c.−344C>T | c.−40A>T | c.445G>A | c.459G>A | c.640T>G | c.*192_c.*217del AATAATAAT | c.*215T>A | c.*222C>A | |
| Reference (Allele)3 | NAT1*4 (AJ307007.1) | C | A | G | G | T | No deletion | T | C |
| Variant 1 | NAT1*10 | C | A | G | G | T | No deletion | A | A |
| Variant 2 | NAT1*11A | T | T | A | A | G | Deletion | T | A |
| Variant 3 | NAT1*11B | T | T | A | A | G | Deletion | T | C |
| Variant 4 | NAT1*11C | T | T | G | A | G | Deletion | T | A |
| Location in Gene | Intron 8, upstream of exon 9 (coding) | Intron 8, upstream of exon 9 (coding) | Exon 9 (coding) | Exon 9 (coding) | Exon 9 (coding) | 3’-untranslated region (polyA-1) | 3’-untranslated region (polyA-1) | 3’-untranslated region | |
| Description of amino acid change (Current NAT nomenclature)7 | N/A | N/A | V149I | T153T | S214A | N/A | N/A | N/A | |
| Description of amino acid change (HGVS nomenclature)8 | N/A | N/A | p.Val149Ile | p.Thr153= | p.Ser214Ala | N/A | N/A | N/A | |
| Reference (SNP)9 | rs4986988 | rs4986989 | rs4987076 | rs4986990 | rs4986783 | rs367921464 | rs1057126 | rs15561 | |
| Reference (Genomic)10 | NC_000008.11 | g.18221704C>T | g.18222008A>T | g.18222492G>A | g.18222506G>A | g.18222687T>G | g.18223127_18223135delAATAATAAA | g.18223135A>T | g.18223142A>C |
| Reference (Gene)11 | NG_012245.2 | g.56243C>T | g.56547A>T | g.57031G>A | g.57045G>A | g.57226T>G | g.57666_57674delAATAATAAA | g.57674A>T | g.57681A>C |
| Reference (Transcript)12 | NM_000662.7 (Exons 4,8,9) | c.−6–338C>T | c.−6–34A>T | c.445G>A | c.459G>A | c.640T>G | c.*207_*215delAATAATAAA | c.*215A>T | c.*222A>C |
| Reference (Protein)13 | NP_000653.3 | N/A | N/A | p.Val149Ile | p.Thr153= | p.Ser214Ala | N/A | N/A | N/A |
| Minor Allele Frequency/Minor Allele Count (1000 Genomes)14 | T=0.0168/84 | T=0.0168/84 | A=0.0170/85 | A=0.0170/85 | G=0.0170/85 | −=0.0170/85 | A=0.4006/2006 | A=0.4373/2190 | |
Harmonization of allele nomenclature was recently proposed for all human genes relevant to pharmacogenomics research and clinical practice, and designations should follow the consensus HGVS nomenclature [62].
All websites/databases were accessed on May 14, 2018.
Note that all sequences derived from the Human Genome Reference Consortium (see footnotes 9–12 below) correspond to NAT1 gene variant NAT1*10, instead of the most common functional NAT1 allele found in global populations, designated as NAT1*4 (Nucleotide ID: AJ307007.1) and considered as the reference allele for human NAT1 (see NAT website, http://nat.mbg.duth.gr/background_2013.html).
Genome Reference Consortium Human Build 38 patch release 12 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.38/#/st).
NCBI Gene Database page for human NAT1 gene (https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=9).
HUGO Gene Nomenclature Committee (HGNC) page for human NAT1 gene (https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:7645).
NAT database page for human NAT1 alleles (http://nat.mbg.duth.gr/).
Sequence variant nomenclature according to current recommendations of the Human Genome Variation Society (HGVS) (http://varnomen.hgvs.org/).
Reference SNP (rs) numbers available from the NCBI dbSNP Database (https://www.ncbi.nlm.nih.gov/snp/?term=).
Homo sapiens chromosome 8 NCBI reference sequence NC_000008.11 (GRCh38.p12) (https://www.ncbi.nlm.nih.gov/nuccore/NC_000008.11).
Homo sapiens NAT1 NCBI RefSeqGene NG_012245.2 (https://www.ncbi.nlm.nih.gov/nuccore/NG_012245.2).
Homo sapiens NAT1 major transcript comprising non-coding exons 4 and 8, together with coding exon 9 [8, 43, 44] (NCBI RefSeq NM_000662.7, https://www.ncbi.nlm.nih.gov/nuccore/NM_000662.7).
Homo sapiens NAT1 protein, allozyme NAT1_4 expressed from reference allele NAT1*4 (NCBI RefSeq NP_000653.3 (https://www.ncbi.nlm.nih.gov/protein/NP_000653.3).
Reported by the NCBI dbSNP Database in the context of allele frequencies determined by the 1000 Genomes project.