NAT9

N-acetyltransferase 9 (putative), the group of GCN5 related N-acetyltransferases

Basic information

Region (hg38): 17:74770529-74776367

Links

ENSG00000109065 ∙ NCBI:26151 ∙ ∙ HGNC:23133 ∙ Uniprot:Q9BTE0 ∙ 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 NAT9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAT9 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in NAT9

This is a list of pathogenic ClinVar variants found in the NAT9 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-74771737-G-A		not specified	Uncertain significance (Apr 08, 2022)
17-74771765-C-T		not specified	Uncertain significance (Jun 13, 2024)
17-74771801-C-T		not specified	Uncertain significance (Oct 16, 2023)
17-74771854-G-C		not specified	Uncertain significance (Jul 22, 2024)
17-74771855-C-T		not specified	Uncertain significance (Jul 22, 2024)
17-74771988-C-G		not specified	Uncertain significance (Feb 28, 2024)
17-74771998-G-A		not specified	Uncertain significance (Apr 20, 2024)
17-74772001-C-T		not specified	Uncertain significance (Jan 24, 2023)
17-74772045-G-A		not specified	Uncertain significance (Feb 13, 2025)
17-74772228-C-A		not specified	Uncertain significance (Feb 04, 2025)
17-74772263-C-A		not specified	Uncertain significance (Jul 25, 2024)
17-74772274-G-C		not specified	Uncertain significance (Jun 13, 2024)
17-74773033-G-A		not specified	Uncertain significance (Jan 29, 2024)
17-74773033-G-T		not specified	Uncertain significance (Jun 07, 2024)
17-74773638-G-A		not specified	Uncertain significance (Feb 26, 2025)
17-74775634-T-A		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAT9	protein_coding	protein_coding	ENST00000357814	6	5821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000220	0.759	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0971	117	120	0.975	0.00000689	1353
Missense in Polyphen		34	42.763	0.79508		516
Synonymous	-0.608	58	52.4	1.11	0.00000362	385
Loss of Function	1.03	7	10.6	0.658	4.54e-7	121

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.000435	0.000435
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.738
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.57

Haploinsufficiency Scores

• pHI: 0.0437
• hipred: N
• hipred_score: 0.290
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.901

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nat9

Gene ontology

• Cellular component: protein-containing complex
• Molecular function: protein binding;transferase activity, transferring acyl groups other than amino-acyl groups