NAA30

N-alpha-acetyltransferase 30, NatC catalytic subunit, the group of GCN5 related N-acetyltransferases|N-alpha-acetyltransferase subunits

Basic information

Region (hg38): 14:57390544-57415906

Previous symbols: [ "C14orf35", "NAT12" ]

Links

ENSG00000139977 ∙ NCBI:122830 ∙ OMIM:617989 ∙ HGNC:19844 ∙ Uniprot:Q147X3 ∙ 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 NAA30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA30 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in NAA30

This is a list of pathogenic ClinVar variants found in the NAA30 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-57391015-C-T		not specified	Uncertain significance (Apr 07, 2023)
14-57391025-T-C		not specified	Likely benign (Apr 07, 2023)
14-57391045-C-T		not specified	Uncertain significance (Nov 10, 2024)
14-57391086-G-C		not specified	Uncertain significance (Jan 31, 2022)
14-57391165-C-T		not specified	Uncertain significance (May 18, 2023)
14-57391247-C-T		not specified	Uncertain significance (Feb 22, 2023)
14-57391249-G-C		not specified	Uncertain significance (Jun 30, 2022)
14-57391345-G-T		not specified	Uncertain significance (Apr 13, 2023)
14-57391360-G-A		not specified	Uncertain significance (Dec 19, 2023)
14-57391405-G-A		not specified	Uncertain significance (Aug 05, 2024)
14-57391409-C-A		Lethal multiystemic syndrome	Likely pathogenic (-)
14-57391442-C-A		not specified	Uncertain significance (Aug 22, 2023)
14-57391445-C-T		not specified	Uncertain significance (Jul 19, 2023)
14-57391465-G-A		not specified	Uncertain significance (Dec 05, 2022)
14-57391477-G-C		not specified	Uncertain significance (Dec 13, 2023)
14-57391526-C-T		not specified	Uncertain significance (Jan 23, 2023)
14-57391534-G-T		not specified	Uncertain significance (Jun 13, 2024)
14-57391666-G-A		not specified	Uncertain significance (Apr 15, 2024)
14-57396817-C-G		not specified	Uncertain significance (Aug 10, 2021)
14-57399863-G-A		not specified	Uncertain significance (Oct 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA30	protein_coding	protein_coding	ENST00000556492	4	25374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0132	125691	0	2	125693	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.61	142	207	0.685	0.00000990	2306
Missense in Polyphen		9	45.412	0.19819		539
Synonymous	-0.587	96	89.0	1.08	0.00000454	749
Loss of Function	3.35	0	13.1	0.00	6.31e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000182	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the N-terminal acetyltransferase C (NatC) complex. Catalyzes acetylation of the N-terminal methionine residues of peptides beginning with Met-Leu-Ala and Met-Leu-Gly. Necessary for the lysosomal localization and function of ARL8B sugeesting that ARL8B is a NatC substrate. {ECO:0000269|PubMed:19398576}.
• Pathway: Metapathway biotransformation Phase I and II;Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.159
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.419
• hipred: Y
• hipred_score: 0.710
• ghis: 0.595

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• 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: Naa30

Gene ontology

• Biological process: N-terminal peptidyl-methionine acetylation
• Cellular component: nucleus;cytoplasm;cytosol;polysome;NatC complex
• Molecular function: peptide alpha-N-acetyltransferase activity;protein binding