NAA25

N-alpha-acetyltransferase 25, NatB auxiliary subunit, the group of N-alpha-acetyltransferase subunits|MicroRNA protein coding host genes

Basic information

Region (hg38): 12:112026689-112108796

Previous symbols: [ "C12orf30" ]

Links

ENSG00000111300 ∙ NCBI:80018 ∙ OMIM:612755 ∙ HGNC:25783 ∙ Uniprot:Q14CX7 ∙ 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 NAA25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAA25 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			38	2		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	39	3	0

Variants in NAA25

This is a list of pathogenic ClinVar variants found in the NAA25 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-112033277-G-A		not specified	Uncertain significance (Oct 04, 2024)
12-112033288-T-C		not specified	Uncertain significance (Jul 09, 2021)
12-112033348-A-C		not specified	Uncertain significance (Aug 09, 2021)
12-112033351-T-C		not specified	Uncertain significance (Aug 17, 2022)
12-112033364-T-A		not specified	Uncertain significance (Feb 16, 2023)
12-112033384-G-A			Likely benign (Oct 30, 2018)
12-112039259-T-G		not specified	Uncertain significance (Nov 08, 2022)
12-112039269-T-C		not specified	Uncertain significance (Jun 22, 2023)
12-112039290-C-T		not specified	Uncertain significance (Jan 08, 2024)
12-112040501-T-G		not specified	Uncertain significance (Mar 01, 2024)
12-112042096-T-A		not specified	Uncertain significance (May 15, 2024)
12-112042102-C-A		not specified	Uncertain significance (Jan 03, 2024)
12-112043120-T-C		not specified	Likely benign (Dec 13, 2022)
12-112043641-A-G		not specified	Uncertain significance (Dec 10, 2024)
12-112043707-C-T			Likely benign (Jul 31, 2018)
12-112043708-G-A		not specified	Uncertain significance (Jan 03, 2024)
12-112043731-G-C		not specified	Uncertain significance (Apr 05, 2023)
12-112043779-C-A		not specified	Uncertain significance (Sep 26, 2023)
12-112043824-G-A		not specified	Uncertain significance (Dec 12, 2023)
12-112047754-G-C		not specified	Uncertain significance (May 05, 2023)
12-112048326-G-A		not specified	Uncertain significance (Nov 14, 2024)
12-112048335-G-T		not specified	Uncertain significance (Mar 01, 2024)
12-112048442-G-A		not specified	Uncertain significance (Nov 13, 2024)
12-112053565-T-C		not specified	Uncertain significance (Mar 16, 2024)
12-112053591-G-A			Likely benign (Aug 28, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAA25	protein_coding	protein_coding	ENST00000261745	24	82327

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.52e-8	125725	0	13	125738	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.45	289	508	0.569	0.0000260	6389
Missense in Polyphen		62	140.85	0.44017		1784
Synonymous	0.903	164	179	0.914	0.00000893	1782
Loss of Function	6.85	2	58.5	0.0342	0.00000324	716

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000373	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Non-catalytic subunit of the NatB complex which catalyzes acetylation of the N-terminal methionine residues of peptides beginning with Met-Asp-Glu. May play a role in normal cell-cycle progression. {ECO:0000269|PubMed:18570629}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.236
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.371
• hipred: Y
• hipred_score: 0.673
• ghis: 0.552

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Naa25

Gene ontology

• Biological process: N-terminal peptidyl-methionine acetylation
• Cellular component: cytoplasm;Golgi apparatus;cytosol;NatB complex
• Molecular function: peptide alpha-N-acetyltransferase activity