NAA60

N-alpha-acetyltransferase 60, NatF catalytic subunit, the group of GCN5 related N-acetyltransferases|N-alpha-acetyltransferase subunits

Basic information

Region (hg38): 16:3443649-3486953

Previous symbols: [ "NAT15" ]

Links

ENSG00000122390 ∙ NCBI:79903 ∙ OMIM:614246 ∙ HGNC:25875 ∙ Uniprot:Q9H7X0 ∙ 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
Basal ganglia calcification, idiopathic, 9, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	38480682

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAA60 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA60 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		2
missense			10	1	1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	1

Variants in NAA60

This is a list of pathogenic ClinVar variants found in the NAA60 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3476241-T-C		not specified	Uncertain significance (Apr 17, 2023)
16-3476259-G-A		not specified	Uncertain significance (Aug 10, 2021)
16-3476277-T-G		Basal ganglia calcification, idiopathic, 9, autosomal recessive	Pathogenic (Apr 16, 2024)
16-3476336-G-A		not specified	Uncertain significance (Apr 13, 2022)
16-3479490-C-T		Basal ganglia calcification, idiopathic, 9, autosomal recessive	Pathogenic (Apr 16, 2024)
16-3479541-G-A		not specified	Uncertain significance (Aug 25, 2021)
16-3482528-C-T			Likely benign (Mar 01, 2020)
16-3482581-TCAGGAAG-T		Basal ganglia calcification, idiopathic, 9, autosomal recessive	Pathogenic (Apr 16, 2024)
16-3483362-G-C		Basal ganglia calcification, idiopathic, 9, autosomal recessive	Pathogenic (Apr 16, 2024)
16-3483377-G-A		not specified	Uncertain significance (Oct 02, 2023)
16-3483377-G-C		not specified	Uncertain significance (Nov 15, 2021)
16-3483407-G-A		not specified	Uncertain significance (Jan 22, 2024)
16-3483416-C-T		Basal ganglia calcification, idiopathic, 9, autosomal recessive	Pathogenic (Apr 16, 2024)
16-3483453-A-C		Basal ganglia calcification, idiopathic, 9, autosomal recessive	Pathogenic (Apr 16, 2024)
16-3483457-C-G		not specified	Uncertain significance (Aug 01, 2024)
16-3483540-A-G		not specified	Uncertain significance (Apr 03, 2023)
16-3483552-C-G		not specified	Uncertain significance (Nov 13, 2023)
16-3483592-G-A			Uncertain significance (Jan 01, 2017)
16-3484706-A-C		not specified	Uncertain significance (Jun 05, 2024)
16-3484763-G-A		not specified	Likely benign (Feb 10, 2022)
16-3484780-C-G			Benign (Dec 04, 2017)
16-3484781-A-G		not specified	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA60	protein_coding	protein_coding	ENST00000407558	5	43353

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.517	0.480	124630	0	9	124639	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.929	111	142	0.781	0.00000813	1577
Missense in Polyphen		13	39.609	0.32821		458
Synonymous	0.0606	59	59.6	0.990	0.00000400	452
Loss of Function	2.44	2	10.6	0.189	5.12e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000950	0.0000928
European (Non-Finnish)	0.0000370	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: N-alpha-acetyltransferase that specifically mediates the acetylation of N-terminal residues of the transmembrane proteins, with a strong preference for N-termini facing the cytosol (PubMed:25732826). Displays N-terminal acetyltransferase activity towards a range of N-terminal sequences including those starting with Met-Lys, Met-Val, Met-Ala and Met-Met (PubMed:21750686, PubMed:25732826, PubMed:27550639, PubMed:27320834). Required for normal chromosomal segregation during anaphase (PubMed:21750686). May also show histone acetyltransferase activity; such results are however unclear in vivo and would require additional experimental evidences (PubMed:21981917). {ECO:0000269|PubMed:21750686, ECO:0000269|PubMed:25732826, ECO:0000269|PubMed:27320834, ECO:0000269|PubMed:27550639, ECO:0000305|PubMed:21981917}.

Recessive Scores

• pRec: 0.0989

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.314
• ghis: 0.520

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: Naa60

Gene ontology

• Biological process: nucleosome assembly;N-terminal protein amino acid acetylation;chromosome segregation;cell population proliferation;N-terminal peptidyl-methionine acetylation;histone H3 acetylation;histone H4 acetylation
• Cellular component: Golgi membrane
• Molecular function: peptide alpha-N-acetyltransferase activity;H4 histone acetyltransferase activity;protein homodimerization activity