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.

not_specified (25 variants)

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. These statistics are base on transcript: NM_000024771.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			25 clinvar			25
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	0	0

Loading clinvar variants...

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