NAA40

N-alpha-acetyltransferase 40, NatD catalytic subunit, the group of GCN5 related N-acetyltransferases|N-alpha-acetyltransferase subunits

Basic information

Region (hg38): 11:63938959-63957319

Previous symbols: [ "NAT11" ]

Links

ENSG00000110583 ∙ NCBI:79829 ∙ OMIM:619999 ∙ HGNC:25845 ∙ Uniprot:Q86UY6 ∙ 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 NAA40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA40 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 NAA40

This is a list of pathogenic ClinVar variants found in the NAA40 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-63945927-G-C		not specified	Uncertain significance (Apr 23, 2024)
11-63952263-C-G		not specified	Uncertain significance (Mar 29, 2022)
11-63952332-A-G		not specified	Uncertain significance (Feb 07, 2025)
11-63952439-G-A		not specified	Uncertain significance (Feb 06, 2024)
11-63952472-C-T		not specified	Uncertain significance (Oct 09, 2024)
11-63952499-G-C		not specified	Uncertain significance (Feb 25, 2025)
11-63952522-C-T		not specified	Uncertain significance (Jun 07, 2024)
11-63952758-A-G		not specified	Uncertain significance (Jun 02, 2023)
11-63952775-A-G		not specified	Uncertain significance (Jun 10, 2022)
11-63952784-C-T		not specified	Uncertain significance (Oct 06, 2024)
11-63952787-C-T		not specified	Uncertain significance (Aug 20, 2024)
11-63952829-A-G		not specified	Uncertain significance (Nov 17, 2023)
11-63954030-T-C		not specified	Uncertain significance (Dec 06, 2023)
11-63954345-A-G		not specified	Uncertain significance (Jan 23, 2024)
11-63954391-G-C		not specified	Uncertain significance (Oct 25, 2023)
11-63954447-G-A		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA40	protein_coding	protein_coding	ENST00000377793	8	18370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.79e-9	0.313	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	102	144	0.709	0.00000853	1579
Missense in Polyphen		19	32.135	0.59126		393
Synonymous	-0.230	54	51.9	1.04	0.00000308	409
Loss of Function	0.690	14	17.1	0.820	0.00000104	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000314	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: N-alpha-acetyltransferase that specifically mediates the acetylation of the N-terminal residues of histones H4 and H2A (PubMed:21935442, PubMed:25619998). In contrast to other N-alpha- acetyltransferase, has a very specific selectivity for histones H4 and H2A N-terminus and specifically recognizes the 'Ser-Gly-Arg- Gly sequence' (PubMed:21935442, PubMed:25619998). Acts as a negative regulator of apoptosis (PubMed:26666750). May play a role in hepatic lipid metabolism (By similarity). {ECO:0000250|UniProtKB:Q8VE10, ECO:0000269|PubMed:21935442, ECO:0000269|PubMed:25619998, ECO:0000269|PubMed:26666750}.
• Pathway: Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.355
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.343
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naa40
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype

Gene ontology

• Biological process: N-terminal protein amino acid acetylation;lipid metabolic process;histone H4 acetylation;histone H2A acetylation;regulation of chromatin silencing at rDNA
• Cellular component: nucleus;cytoplasm
• Molecular function: H4 histone acetyltransferase activity;H2A histone acetyltransferase activity;peptide-serine-N-acetyltransferase activity