NAA80

N-alpha-acetyltransferase 80, NatH catalytic subunit, the group of GCN5 related N-acetyltransferases|N-alpha-acetyltransferase subunits

Basic information

Region (hg38): 3:50296401-50299416

Previous symbols: [ "NAT6" ]

Links

ENSG00000243477 ∙ NCBI:24142 ∙ OMIM:607073 ∙ HGNC:30252 ∙ Uniprot:Q93015 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Auroneurodental syndrome	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic; Cardiovascular; Craniofacial; Dental; Neurologic	34805998

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAA80 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA80 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			20	2		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	21	2	0

Variants in NAA80

This is a list of pathogenic ClinVar variants found in the NAA80 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-50296623-A-C		not specified	Uncertain significance (Nov 21, 2022)
3-50296635-G-A		not specified	Likely benign (Aug 08, 2023)
3-50296685-C-T		not specified	Uncertain significance (Feb 23, 2023)
3-50296731-G-C		not specified	Uncertain significance (Feb 10, 2023)
3-50296769-G-A		not specified	Uncertain significance (Mar 19, 2024)
3-50296808-C-T		not specified	Likely benign (Feb 09, 2022)
3-50296844-G-C		not specified	Uncertain significance (Aug 17, 2021)
3-50296856-C-T		not specified	Uncertain significance (Jan 19, 2024)
3-50296916-T-C		not specified	Uncertain significance (Apr 07, 2022)
3-50296917-A-T		not specified	Uncertain significance (Jul 12, 2022)
3-50296956-G-A		not specified	Uncertain significance (Aug 01, 2022)
3-50296994-A-G		not specified	Uncertain significance (May 01, 2024)
3-50297003-C-T		not specified	Uncertain significance (Jul 26, 2022)
3-50297049-C-T		not specified	Uncertain significance (Dec 07, 2021)
3-50297105-A-G		not specified	Uncertain significance (Dec 22, 2023)
3-50297121-C-T		not specified	Uncertain significance (Oct 12, 2021)
3-50297133-G-C		not specified	Uncertain significance (May 04, 2022)
3-50297133-G-T		not specified	Uncertain significance (May 30, 2023)
3-50297141-A-G		See cases • Auroneurodental syndrome	Pathogenic/Likely pathogenic (Aug 06, 2024)
3-50297210-C-T		not specified	Uncertain significance (Dec 09, 2023)
3-50297258-G-A		not specified	Uncertain significance (Nov 21, 2023)
3-50297264-C-T		not specified	Uncertain significance (Dec 21, 2023)
3-50297276-T-A		not specified	Uncertain significance (Feb 05, 2024)
3-50297313-C-G		not specified	Uncertain significance (Jun 22, 2024)
3-50297348-G-A		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA80	protein_coding	protein_coding	ENST00000354862	2	3020

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.169	0.777	124795	0	18	124813	0.0000721

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.563	155	176	0.880	0.0000103	1924
Missense in Polyphen		52	66.061	0.78715		744
Synonymous	0.719	64	71.7	0.892	0.00000339	733
Loss of Function	1.58	2	6.29	0.318	3.51e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000218	0.000216
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000101	0.0000971
Middle Eastern	0.000113	0.000111
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: N-alpha-acetyltransferase that specifically mediates the acetylation of the acidic amino terminus of processed forms of beta- and gamma-actin (ACTB and ACTG, respectively) (PubMed:30028079, PubMed:29581253). N-terminal acetylation of processed beta- and gamma-actin regulates actin filament depolymerization and elongation (PubMed:29581253). In vivo, preferentially displays N-terminal acetyltransferase activity towards acid N-terminal sequences starting with Asp-Asp-Asp and Glu-Glu-Glu (PubMed:30028079, PubMed:29581253). In vitro, shows high activity towards Met-Asp-Glu-Leu and Met-Asp-Asp-Asp (PubMed:10644992, PubMed:29581307). May act as a tumor suppressor (PubMed:10644992). {ECO:0000269|PubMed:10644992, ECO:0000269|PubMed:29581253, ECO:0000269|PubMed:29581307, ECO:0000269|PubMed:30028079}.

Recessive Scores

• pRec: 0.0776

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.49

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.145
• ghis: 0.499

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Naa80

Gene ontology

• Biological process: protein acetylation;regulation of actin polymerization or depolymerization;N-terminal peptidyl-aspartic acid acetylation;N-terminal peptidyl-glutamic acid acetylation;actin modification
• Cellular component: cytoplasm;cytosol
• Molecular function: peptide alpha-N-acetyltransferase activity;N-acetyltransferase activity;acetyl-CoA binding