NAA38

protein-coding

N-alpha-acetyltransferase 38, NatC auxiliary subunit, the group of LSm proteins|N-alpha-acetyltransferase subunits

Gene summary

Predicted to enable RNA binding activity. Involved in negative regulation of apoptotic process. Located in cytoplasm and nucleoplasm. Part of NatC complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

LSMD1

MANE transcript

NM_001320925.4

Inheritance

—

ClinVar variants

U:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.36

Max pathogenic AF

—

Genomic locus

chr17:7,856,685-7,885,238

External References & Databases

Ensembl (ENSG00000183011)

Transcript & Mutation Effects

hg38 • Region Span ~28.6 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 NAA38 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001320925.4. 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						0
missense			11 clinvar			11
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	11	0	0	11

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001320925.4	RefSeq	NP_001307854.1	3	MANE Select
ENST00000575771.6	Ensembl	ENSP00000460172.2	3	MANE Select
NM_001320924.3	RefSeq	NP_001307853.1	3	Standard
NM_001330111.2	RefSeq	NP_001317040.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Retrograde transport at the Trans-Golgi-Network
Intra-Golgi and retrograde Golgi-to-ER traffic

Biological Process

negative regulation of apoptotic process

Molecular Function

protein binding

Cellular Component

nucleus
cytoplasm
polysome
NatC complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000333775
Coding exons: 2
Length: 28554
Individuals with no LoFs: 123449
Homozygous LoFs: 15
Heterozygous LoFs: 2254
Defined: 125718
p: 0.00907

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.403	116	104	1.11	0.00000464	1069
Missense (PolyPhen)		19	26.792	0.70918		294
Synonymous	-1.65	61	46.7	1.31	0.00000210	398
Loss of Function	-0.802	8	5.90	1.36	2.56e-7	60

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0032	0.0028	notable
Latino/Admixed American	0.0066	0.0065	notable
Ashkenazi Jewish	0.016	0.015	notable
East Asian	0.00028	0.00027	rare
Finnish	0.0023	0.0023	notable
European (Non-Finnish)	0.016	0.015	notable
South Asian	0.0030	0.0027	notable
Other	0.012	0.011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Auxillary component of the N-terminal acetyltransferase C (NatC) complex which catalyzes acetylation of N-terminal methionine residues. {ECO:0000269|PubMed:19398576}.;

Recessive Scores

pRec: 0.0827

Intolerance Scores

LoFtool: 0.665
RVIS EVS: 0.08
RVIS percentile EVS: 59.43

Essentials

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

Gene Damage Prediction

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