NAA25

protein-coding

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

Gene summary

This gene encodes the auxiliary subunit of the heteromeric N-terminal acetyltransferase B complex. This complex acetylates methionine residues that are followed by acidic or asparagine residues.[provided by RefSeq, Mar 2010]

Previous symbols:

C12orf30

MANE transcript

NM_024953.4

Inheritance

—

ClinVar variants

U:84B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr12:112,026,689-112,108,796

External References & Databases

Ensembl (ENSG00000111300)

Transcript & Mutation Effects

hg38 • Region Span ~82.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NAA25 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 78

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024953.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar		4
missense			77 clinvar	4 clinvar		81
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	84	6	0	90

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024953.4	RefSeq	NP_079229.2	24	MANE Select
ENST00000261745.9	Ensembl	ENSP00000261745.4	24	MANE Select
ENST00000547133.1	Ensembl	ENSP00000447676.1	5	Standard
ENST00000549711.5	Ensembl	ENSP00000448200.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

N-terminal peptidyl-methionine acetylation

Molecular Function

peptide alpha-N-acetyltransferase activity

Cellular Component

cytoplasm
Golgi apparatus
cytosol
NatB complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261745
Coding exons: 24
Length: 82327
Individuals with no LoFs: 125725
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125738
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.45	289	508	0.569	0.0000260	6389
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000037	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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