NAA50

N-alpha-acetyltransferase 50, NatE catalytic subunit, the group of N-alpha-acetyltransferase subunits|GCN5 related N-acetyltransferases

Basic information

Region (hg38): 3:113716458-113746300

Previous symbols: [ "MAK3", "NAT13" ]

Links

ENSG00000121579 ∙ NCBI:80218 ∙ OMIM:610834 ∙ HGNC:29533 ∙ Uniprot:Q9GZZ1 ∙ 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 NAA50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA50 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					1	1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	6	0	1

Variants in NAA50

This is a list of pathogenic ClinVar variants found in the NAA50 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-113721800-G-A		not specified	Uncertain significance (Mar 06, 2023)
3-113721801-G-A		not specified	Uncertain significance (Feb 28, 2023)
3-113721812-T-A		not specified	Uncertain significance (Aug 29, 2024)
3-113722971-T-C		NAA50-related disorder	Benign (Nov 07, 2019)
3-113723423-T-C		not specified	Uncertain significance (Dec 03, 2021)
3-113723456-T-C		NAA50-related disorder	Benign (Nov 26, 2019)
3-113723475-C-G		not specified	Uncertain significance (Dec 27, 2023)
3-113723532-T-C		not specified	Uncertain significance (Mar 01, 2023)
3-113723951-T-C		NAA50-related disorder	Benign (Jul 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA50	protein_coding	protein_coding	ENST00000240922	5	29841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.735	0.263	125601	0	2	125603	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.78	40	86.6	0.462	0.00000418	1121
Missense in Polyphen		11	29.211	0.37657		390
Synonymous	-0.0466	33	32.7	1.01	0.00000173	294
Loss of Function	2.42	1	8.71	0.115	4.52e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000884	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: N-alpha-acetyltransferase that acetylates the N-terminus of proteins that retain their initiating methionine (PubMed:19744929, PubMed:22311970, PubMed:21900231, PubMed:27484799). Has a broad substrate specificity: able to acetylate the initiator methionine of most peptides, except for those with a proline in second position (PubMed:27484799). Also displays N-epsilon-acetyltransferase activity by mediating acetylation of the side chain of specific lysines on proteins (PubMed:19744929). Autoacetylates in vivo (PubMed:19744929). The relevance of N-epsilon-acetyltransferase activity is however unclear: able to acetylate H4 in vitro, but this result has not been confirmed in vivo (PubMed:19744929). Component of a N-alpha- acetyltransferase complex containing NAA10 and NAA15, but NAA50 does not influence the acetyltransferase activity of NAA10: this multiprotein complex probably constitutes the major contributor for N-terminal acetylation at the ribosome exit tunnel, with NAA10 acetylating all amino termini that are devoid of methionine and NAA50 acetylating other peptides (PubMed:16507339, PubMed:27484799). Required for sister chromatid cohesion during mitosis by promoting binding of CDCA5/sororin to cohesin: may act by counteracting the function of NAA10 (PubMed:17502424, PubMed:27422821). {ECO:0000269|PubMed:16507339, ECO:0000269|PubMed:17502424, ECO:0000269|PubMed:19744929, ECO:0000269|PubMed:21900231, ECO:0000269|PubMed:22311970, ECO:0000269|PubMed:27422821, ECO:0000269|PubMed:27484799}.
• Pathway: Metapathway biotransformation Phase I and II (Consensus)

Recessive Scores

• pRec: 0.173

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.806
• hipred: Y
• hipred_score: 0.783
• ghis: 0.674

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naa50

Gene ontology

• Biological process: N-terminal protein amino acid acetylation;mitotic sister chromatid cohesion;histone acetylation;establishment of mitotic sister chromatid cohesion;histone H4 acetylation;mitotic sister chromatid cohesion, centromeric
• Cellular component: nucleus;cytoplasm;cytosol;NatA complex;extracellular exosome
• Molecular function: peptide alpha-N-acetyltransferase activity;protein binding;N-acetyltransferase activity;H4 histone acetyltransferase activity;peptidyl-lysine acetyltransferase activity