NAA38

Summary

NAA38 (N-alpha-acetyltransferase 38, NatC auxiliary subunit, HGNC:28212) is a protein-coding gene on chromosome 17p13.1, encoding N-alpha-acetyltransferase 38, NatC auxiliary subunit (Q9BRA0). Auxillary component of the N-terminal acetyltransferase C (NatC) complex which catalyzes acetylation of N-terminal methionine residues.

Predicted to enable RNA binding activity. Involved in negative regulation of apoptotic process. Located in cytoplasm and nucleoplasm. Part of NatC complex.

Source: NCBI Gene 84316 — RefSeq curated summary.

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_001320925

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28212
Approved symbol	NAA38
Name	N-alpha-acetyltransferase 38, NatC auxiliary subunit
Location	17p13.1
Locus type	gene with protein product
Status	Approved
Aliases	MGC14151, PFAAP2
Ensembl gene	ENSG00000183011
Ensembl biotype	protein_coding
OMIM	617990
Entrez	84316

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 7 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000333775, ENST00000570555, ENST00000575071, ENST00000575208, ENST00000575771, ENST00000576384, ENST00000576861, ENST00000917337

RefSeq mRNA: 4 — MANE Select: NM_001320925 NM_001320924, NM_001320925, NM_001330111, NM_032356

CCDS: CCDS11122, CCDS82059, CCDS82060, CCDS82062

Canonical transcript exons

ENST00000575771 — 3 exons

Exon	Start	End
ENSE00002670388	7857383	7857559
ENSE00002677426	7856685	7856843
ENSE00003488318	7857015	7857198

Expression profiles

Bgee: expression breadth ubiquitous, 254 present calls, max score 97.88.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 83.8634 / max 1001.4679, expressed in 1822 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164321	54.9795	1816
164322	24.2411	1802
164327	2.9057	1359
164328	0.8846	520
164323	0.4116	166
164325	0.2130	79
164324	0.2019	78
164326	0.0260	5

Top tissues by expression

255 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
prefrontal cortex	UBERON:0000451	97.88	gold quality
putamen	UBERON:0001874	97.68	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.64	gold quality
amygdala	UBERON:0001876	97.62	gold quality
right testis	UBERON:0004534	97.62	gold quality
nucleus accumbens	UBERON:0001882	97.58	gold quality
anterior cingulate cortex	UBERON:0009835	97.55	gold quality
left testis	UBERON:0004533	97.49	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.48	gold quality
caudate nucleus	UBERON:0001873	97.38	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	97.37	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.32	gold quality
apex of heart	UBERON:0002098	97.28	gold quality
mucosa of transverse colon	UBERON:0004991	97.26	gold quality
hypothalamus	UBERON:0001898	97.17	gold quality
right adrenal gland	UBERON:0001233	97.16	gold quality
left adrenal gland cortex	UBERON:0035825	97.06	gold quality
right adrenal gland cortex	UBERON:0035827	97.06	gold quality
left adrenal gland	UBERON:0001234	97.02	gold quality
right frontal lobe	UBERON:0002810	96.78	gold quality
adenohypophysis	UBERON:0002196	96.59	gold quality
adrenal cortex	UBERON:0001235	96.57	gold quality
spinal cord	UBERON:0002240	96.48	gold quality
frontal cortex	UBERON:0001870	96.38	gold quality
neocortex	UBERON:0001950	96.22	gold quality
substantia nigra	UBERON:0002038	96.21	gold quality
pituitary gland	UBERON:0000007	96.19	gold quality
endothelial cell	CL:0000115	96.14	gold quality
left coronary artery	UBERON:0001626	96.14	gold quality
gastrocnemius	UBERON:0001388	96.11	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 7.

Experiment	Marker?	Max mean expression
E-MTAB-10042	yes	1163.63
E-HCAD-6	yes	623.72
E-HCAD-4	yes	558.17
E-GEOD-125970	yes	42.49
E-CURD-112	yes	32.75
E-CURD-122	yes	17.41
E-MTAB-9067	no	1231.55
E-MTAB-8884	no	682.26
E-ANND-5	no	584.37
E-MTAB-8205	no	500.08
E-HCAD-31	no	2.87
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Molecular role of NAA38 in thermostability and catalytic activity of the human NatC N-terminal acetyltransferase. (PMID:36638802)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	naa38	ENSDARG00000099122
mus_musculus	Naa38	ENSMUSG00000059278
rattus_norvegicus	Naa38	ENSRNOG00000090113
drosophila_melanogaster	Sbat	FBGN0051950
caenorhabditis_elegans	natc-3	WBGENE00021682

Protein

Protein identifiers

N-alpha-acetyltransferase 38, NatC auxiliary subunit — Q9BRA0 (reviewed: Q9BRA0)

Alternative names: LSM domain-containing protein 1, Phosphonoformate immuno-associated protein 2

All UniProt accessions (5): A0A0B4J297, Q9BRA0, I3L310, I3L3Z2, I3L4V0

UniProt curated annotations — full annotation on UniProt →

Function. Auxillary component of the N-terminal acetyltransferase C (NatC) complex which catalyzes acetylation of N-terminal methionine residues. N-terminal acetylation protects proteins from ubiquitination and degradation by the N-end rule pathway.

Subunit / interactions. Component of the N-terminal acetyltransferase C (NatC) complex, which is composed of NAA35, NAA38 and NAA30.

Subcellular location. Cytoplasm. Nucleus.

Similarity. Belongs to the snRNP Sm proteins family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BRA0-1	1	yes
Q9BRA0-2	2

RefSeq proteins (4): NP_001307853, NP_001307854, NP_001317040, NP_115732 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001163	Sm_dom_euk/arc	Domain
IPR010920	LSM_dom_sf	Homologous_superfamily
IPR034110	LSMD1_Sm	Domain
IPR047575	Sm	Domain
IPR050914	snRNP_SmB/NAA38-like	Family

Pfam: PF01423

UniProt features (12 total): modified residue 4, initiator methionine 1, chain 1, splice variant 1, sequence variant 1, domain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7MX2	ELECTRON MICROSCOPY	3.64

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRA0-F1	79.47	0.58

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 2, 22, 25, 29

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-6811440	Retrograde transport at the Trans-Golgi-Network
R-HSA-199991	Membrane Trafficking
R-HSA-5653656	Vesicle-mediated transport
R-HSA-6811442	Intra-Golgi and retrograde Golgi-to-ER traffic

MSigDB gene sets: 207 (showing top): RNGTGGGC_UNKNOWN, PAL_PRMT5_TARGETS_UP, LFA1_Q6, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, REACTOME_MEMBRANE_TRAFFICKING, SOX9_B1, GATA3_01, TCF11_01, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, HU_GENOTOXIC_DAMAGE_24HR, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN, TGGAAA_NFAT_Q4_01, GOCC_TRANSFERASE_COMPLEX, GOCC_N_TERMINAL_PROTEIN_ACETYLTRANSFERASE_COMPLEX

GO Biological Process (1): negative regulation of apoptotic process (GO:0043066)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), NatC complex (GO:0031417)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	1
Vesicle-mediated transport	1
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
apoptotic process	1
regulation of apoptotic process	1
negative regulation of programmed cell death	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
N-terminal protein acetyltransferase complex	1

Protein interactions and networks

STRING

1739 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NAA38	NAA35	Q5VZE5	982
NAA38	NAA30	Q147X3	842
NAA38	SYS1	Q8N2H4	621
NAA38	NAA50	Q9GZZ1	594
NAA38	NAA15	Q9BXJ9	545
NAA38	LSM10	Q969L4	535
NAA38	LSM5	Q9Y4Y9	515
NAA38	LSM3	P62310	500
NAA38	LSM6	P62312	499
NAA38	EPM2AIP1	Q7L775	491
NAA38	CYB5D1	Q6P9G0	475
NAA38	SAT2	Q96F10	471
NAA38	LSM1	O15116	470
NAA38	LSM7	Q9UK45	467
NAA38	LSM12	Q3MHD2	446

IntAct

26 interactions, top by confidence:

A	B	Type	Score
NAA30	NAA35	psi-mi:“MI:0914”(association)	0.740
NAA38	PDE9A	psi-mi:“MI:0915”(physical association)	0.560
PRR20C	NAA38	psi-mi:“MI:0915”(physical association)	0.560
NAA38	N4BP2L2	psi-mi:“MI:0915”(physical association)	0.560
NAA38	PRR20C	psi-mi:“MI:0915”(physical association)	0.560
N4BP2L2	NAA38	psi-mi:“MI:0915”(physical association)	0.560
PDE9A	NAA38	psi-mi:“MI:0915”(physical association)	0.560
NAA38	ATN1	psi-mi:“MI:0915”(physical association)	0.560
NAA38	KLK6	psi-mi:“MI:0915”(physical association)	0.560
NAA38	NAA35	psi-mi:“MI:0915”(physical association)	0.560
ASCC1	NAA38	psi-mi:“MI:0915”(physical association)	0.400
PRNP	CARNS1	psi-mi:“MI:0914”(association)	0.350
SOX2	DDX39A	psi-mi:“MI:0914”(association)	0.350
NAA38	EIF3H	psi-mi:“MI:0914”(association)	0.350
NAA38	PRORP	psi-mi:“MI:0914”(association)	0.350
NAA30	ATP1A3	psi-mi:“MI:0914”(association)	0.350
NAA30	PAPSS1	psi-mi:“MI:0914”(association)	0.350
NAA30	RPL26	psi-mi:“MI:0403”(colocalization)	0.350

BioGRID (39): NAA38 (Two-hybrid), NAA38 (Two-hybrid), PRR20A (Two-hybrid), API5 (Co-fractionation), LSM7 (Co-fractionation), MLLT4 (Co-fractionation), NAA38 (Co-fractionation), NAA38 (Co-fractionation), NAA38 (Co-fractionation), NAA38 (Co-fractionation), NAA38 (Co-fractionation), NAA38 (Co-fractionation), NAA38 (Co-fractionation), NAA38 (Co-fractionation), NAA38 (Co-fractionation)

ESM2 similar proteins: A2BIG9, A4IGZ4, A6H8I2, B8JKF4, D2GXY4, G2TRR1, O14036, O15116, O74499, O80396, P23059, P47017, P53905, P87173, Q02260, Q06217, Q08DB2, Q0IIM8, Q38E83, Q4R804, Q54HF6, Q54W83, Q55EX5, Q5E9Z8, Q6AZT2, Q6C7U0, Q6DJ48, Q6E0V2, Q6GQ67, Q6NU60, Q6NW58, Q7PWB1, Q8IPZ7, Q8LFL8, Q8N2I9, Q8VC85, Q945P8, Q94C95, Q9BRA0, Q9CQQ8

Diamond homologs: A2BIG9, A4IGZ4, O43080, O95777, P91918, Q10163, Q3ZCE0, Q55A45, Q5RCP3, Q6GQ67, Q6NU60, Q6ZWM4, Q8IPZ7, Q9BRA0, Q9D2U5, O15116, O26745, P14678, P17136, P27048, P40018, P63162, P63163, P63164, Q05856, Q0W8R9, Q12U30, Q17QN3, Q54W83, Q58DW4, Q5E9Z8, Q5R6I0, Q60HD3, Q8VC85, Q9N1Q0, Q9PV94, Q9TU66, Q9TU67, Q9YEQ5, Q8VYI0

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
NAA38	“form complex”	NatC	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

18 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	15
Likely benign	1
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

753 predictions. Top by Δscore:

Variant	Effect	Δscore
17:7857006:GGCAC:G	donor_loss	1.0000
17:7857007:GCAC:G	donor_loss	1.0000
17:7857008:CACT:C	donor_loss	1.0000
17:7857009:ACTG:A	donor_loss	1.0000
17:7857010:CTGA:C	donor_loss	1.0000
17:7857011:TGAC:T	donor_loss	1.0000
17:7857012:GAC:G	donor_loss	1.0000
17:7857013:ACCCG:A	donor_loss	1.0000
17:7857014:CCCGA:C	donor_gain	1.0000
17:7858291:AAGG:A	donor_gain	1.0000
17:7858292:AGG:A	donor_gain	1.0000
17:7858293:GG:G	donor_gain	1.0000
17:7858293:GGG:G	donor_gain	1.0000
17:7858294:GG:G	donor_gain	1.0000
17:7858295:G:GG	donor_gain	1.0000
17:7858296:T:A	donor_loss	1.0000
17:7858400:A:AG	acceptor_gain	1.0000
17:7858400:AAG:A	acceptor_gain	1.0000
17:7858400:AAGG:A	acceptor_gain	1.0000
17:7858401:A:G	acceptor_gain	1.0000
17:7858475:GAGAC:G	donor_gain	1.0000
17:7858477:GAC:G	donor_gain	1.0000
17:7858480:G:GG	donor_gain	1.0000
17:7858485:T:G	donor_gain	1.0000
17:7859441:T:G	acceptor_gain	1.0000
17:7884954:G:GT	donor_gain	1.0000
17:7857013:A:AC	donor_gain	0.9900
17:7857013:AC:A	donor_gain	0.9900
17:7857014:C:CC	donor_gain	0.9900
17:7857014:CC:C	donor_gain	0.9900

AlphaMissense

799 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:7856783:A:T	I109N	1.000
17:7856792:C:T	G106E	1.000
17:7856801:A:C	M103R	1.000
17:7856801:A:T	M103K	1.000
17:7856804:G:T	A102D	1.000
17:7856807:A:G	L101P	1.000
17:7856810:C:T	G100D	1.000
17:7856811:C:G	G100R	1.000
17:7857047:A:G	L78P	1.000
17:7857050:A:C	I77S	1.000
17:7857050:A:G	I77T	1.000
17:7857050:A:T	I77N	1.000
17:7857053:A:T	V76D	1.000
17:7857055:A:C	N75K	1.000
17:7857055:A:T	N75K	1.000
17:7857067:G:C	D71E	1.000
17:7857067:G:T	D71E	1.000
17:7857068:T:A	D71V	1.000
17:7857068:T:C	D71G	1.000
17:7857068:T:G	D71A	1.000
17:7857069:C:G	D71H	1.000
17:7857073:G:C	C69W	1.000
17:7857074:C:T	C69Y	1.000
17:7857075:A:G	C69R	1.000
17:7857080:A:G	F67S	1.000
17:7857086:C:A	G65V	1.000
17:7857086:C:T	G65D	1.000
17:7857087:C:G	G65R	1.000
17:7857092:A:G	L63P	1.000
17:7857104:T:A	D59V	1.000

dbSNP variants (sampled 300 via entrez): RS1000065053 (17:7864545 C>T), RS1000378794 (17:7856253 C>G,T), RS1000406116 (17:7875996 A>G), RS1000481168 (17:7880669 A>G), RS1000570951 (17:7869044 G>A,T), RS1000617531 (17:7862935 A>G), RS1000828452 (17:7860120 T>C), RS1000940754 (17:7860588 G>A,T), RS1001005411 (17:7869377 C>T), RS1001103782 (17:7867259 G>A,T), RS1001242583 (17:7881216 T>C), RS1001352322 (17:7857096 T>C), RS1001390412 (17:7874187 A>C), RS1001421229 (17:7874589 T>C), RS1001472853 (17:7866931 C>T)

Disease associations

OMIM: gene MIM:617990 | disease phenotypes: MIM:618205

GenCC curated gene-disease

Mondo (1): Snijders Blok-Campeau syndrome (MONDO:0032600)

Orphanet (1): CHD3-related developmental delay-speech delay-intellectual disability-abnormalities of vision-facial dysmorphism syndrome (Orphanet:599082)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST004613_60	Sum neutrophil eosinophil counts	2.000000e-09
GCST004614_56	Granulocyte count	2.000000e-09
GCST004626_139	Myeloid white cell count	3.000000e-09
GCST006190_14	Diastolic blood pressure x smoking status (ever vs never) interaction (2df test)	7.000000e-18
GCST006190_56	Diastolic blood pressure x smoking status (ever vs never) interaction (2df test)	2.000000e-21
GCST006192_58	Systolic blood pressure x smoking status (ever vs never) interaction (2df test)	2.000000e-12
GCST006192_85	Systolic blood pressure x smoking status (ever vs never) interaction (2df test)	3.000000e-07
GCST006193_47	Diastolic blood pressure x smoking status (current vs non-current) interaction (2df test)	4.000000e-18
GCST006193_85	Diastolic blood pressure x smoking status (current vs non-current) interaction (2df test)	1.000000e-20
GCST006195_36	Systolic blood pressure x smoking status (current vs non-current) interaction (2df test)	4.000000e-07
GCST006195_77	Systolic blood pressure x smoking status (current vs non-current) interaction (2df test)	2.000000e-12
GCST006288_283	Heel bone mineral density	2.000000e-11
GCST006288_51	Heel bone mineral density	6.000000e-07
GCST006979_803	Heel bone mineral density	2.000000e-38
GCST007930_181	Medication use (agents acting on the renin-angiotensin system)	1.000000e-08
GCST010703_158	Brain morphology (MOSTest)	3.000000e-09
GCST90002395_241	Mean platelet volume	9.000000e-13
GCST90002398_263	Neutrophil count	7.000000e-10

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004833	neutrophil count
EFO:0004842	eosinophil count
EFO:0007987	granulocyte count
EFO:0006336	diastolic blood pressure
EFO:0006527	smoking status measurement
EFO:0006335	systolic blood pressure
EFO:0009270	heel bone mineral density
EFO:0009931	Agents acting on the renin-angiotensin system use measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects cotreatment, increases expression, affects expression, decreases expression	6
Air Pollutants	affects cotreatment, increases abundance, increases expression, decreases expression	3
sodium arsenite	decreases expression, increases expression	2
Cyclosporine	decreases expression	2
Particulate Matter	decreases expression, increases abundance	2
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
alpha-pinene	increases expression, increases abundance, affects cotreatment	1
beta-lapachone	decreases expression	1
methylparaben	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
methacrylaldehyde	affects cotreatment, increases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
K 7174	decreases expression	1
ICG 001	decreases expression	1
NSC 689534	increases expression, affects binding	1
Acrolein	affects cotreatment, increases expression, increases abundance	1
Aspirin	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	decreases expression	1
Copper	affects binding, increases expression	1
Doxorubicin	increases expression	1
Estradiol	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Hydralazine	affects cotreatment, increases expression	1
Hydrogen Peroxide	affects expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects cotreatment, increases expression, increases abundance	1
Thiram	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.