NATD1

Summary

NATD1 (N-acetyltransferase domain containing 1, HGNC:30770) is a protein-coding gene on chromosome 17p11.2, encoding Protein NATD1 (Q8N6N6).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_152914

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30770
Approved symbol	NATD1
Name	N-acetyltransferase domain containing 1
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC33894, Gtlf3b
Ensembl gene	ENSG00000274180
Ensembl biotype	protein_coding
Entrez	256302

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000611551

RefSeq mRNA: 1 — MANE Select: NM_152914 NM_152914

Canonical transcript exons

ENST00000611551 — 3 exons

Exon	Start	End
ENSE00003715885	21244106	21244224
ENSE00003724970	21253159	21253410
ENSE00003739371	21238870	21243429

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 95.01.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.4309 / max 295.3658, expressed in 1668 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164927	4.4444	1376
164928	2.9864	1396

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
tibialis anterior	UBERON:0001385	95.01	gold quality
amniotic fluid	UBERON:0000173	93.97	gold quality
pancreatic ductal cell	CL:0002079	92.22	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	90.77	gold quality
blood	UBERON:0000178	90.71	gold quality
trabecular bone tissue	UBERON:0002483	89.08	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.73	gold quality
gastrocnemius	UBERON:0001388	88.17	gold quality
muscle of leg	UBERON:0001383	87.88	gold quality
left ventricle myocardium	UBERON:0006566	87.81	gold quality
cardiac muscle of right atrium	UBERON:0003379	87.79	gold quality
quadriceps femoris	UBERON:0001377	87.28	gold quality
tendon of biceps brachii	UBERON:0008188	86.38	gold quality
vastus lateralis	UBERON:0001379	86.10	gold quality
skeletal muscle tissue	UBERON:0001134	85.97	gold quality
deltoid	UBERON:0001476	85.36	silver quality
muscle tissue	UBERON:0002385	85.07	gold quality
apex of heart	UBERON:0002098	84.81	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.27	gold quality
biceps brachii	UBERON:0001507	83.73	gold quality
oviduct epithelium	UBERON:0004804	82.98	gold quality
granulocyte	CL:0000094	82.93	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	82.48	gold quality
adipose tissue	UBERON:0001013	81.82	gold quality
heart left ventricle	UBERON:0002084	81.75	gold quality
cardiac ventricle	UBERON:0002082	81.19	gold quality
leukocyte	CL:0000738	81.13	gold quality
subcutaneous adipose tissue	UBERON:0002190	80.91	gold quality
monocyte	CL:0000576	80.88	gold quality
palpebral conjunctiva	UBERON:0001812	80.53	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.53

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

169 targeting NATD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4745-5P	99.98	65.95	1028
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-652-5P	99.91	67.49	505
HSA-MIR-4648	99.91	67.00	710

Literature-anchored findings (GeneRIF, showing 1)

• Development of A Continuous Fluorescence-Based Assay for N-Terminal Acetyltransferase D. (PMID:33435607)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	natd1	ENSDARG00000038281
danio_rerio	im:6904045	ENSDARG00000115174
mus_musculus	Natd1	ENSMUSG00000018931
rattus_norvegicus	Natd1	ENSRNOG00000089004
drosophila_melanogaster	CG32163	FBGN0052163
caenorhabditis_elegans		WBGENE00014226

Protein

Protein identifiers

Protein NATD1 — Q8N6N6 (reviewed: Q8N6N6)

Alternative names: N-acetyltransferase domain-containing protein 1

All UniProt accessions (1): Q8N6N6

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NATD1 family.

RefSeq proteins (1): NP_690878* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR016181	Acyl_CoA_acyltransferase	Homologous_superfamily
IPR031165	GNAT_YJDJ	Domain
IPR045057	Gcn5-rel_NAT	Family

Pfam: PF14542

UniProt features (4 total): chain 1, domain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N6N6-F1	89.56	0.76

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 111 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN, CUI_TCF21_TARGETS_2_DN, DODD_NASOPHARYNGEAL_CARCINOMA_DN, BRUINS_UVC_RESPONSE_MIDDLE, LEE_BMP2_TARGETS_UP, FEVR_CTNNB1_TARGETS_UP, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK, CSR_EARLY_UP.V1_DN, DACH1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

314 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NATD1	DHRS7B	Q6IAN0	480
NATD1	DRC3	Q9H069	474
NATD1	DRG2	P55039	400
NATD1	NT5M	Q9NPB1	398
NATD1	MED9	Q9NWA0	394
NATD1	SNX29	Q8TEQ0	388
NATD1	FKBP7	Q9Y680	387
NATD1	CCER1	Q8TC90	386
NATD1	OLFML2B	Q68BL8	371
NATD1	TRIM41	Q8WV44	363
NATD1	COPS3	Q9UNS2	351
NATD1	ATPAF2	Q8N5M1	348
NATD1	UBXN4	Q92575	347
NATD1	SMCR8	Q8TEV9	340
NATD1	ATF7IP2	Q5U623	314

IntAct

36 interactions, top by confidence:

A	B	Type	Score
NATD1	ADAMTSL4	psi-mi:“MI:0915”(physical association)	0.720
NATD1	NIF3L1	psi-mi:“MI:0915”(physical association)	0.720
ADAMTSL4	NATD1	psi-mi:“MI:0915”(physical association)	0.720
NATD1	TRAF2	psi-mi:“MI:0915”(physical association)	0.560
NATD1	IKZF3	psi-mi:“MI:0915”(physical association)	0.560
IKZF3	NATD1	psi-mi:“MI:0915”(physical association)	0.560
TRAF2	NATD1	psi-mi:“MI:0915”(physical association)	0.560
NATD1	PICK1	psi-mi:“MI:0915”(physical association)	0.560
PLEKHG4	NATD1	psi-mi:“MI:0915”(physical association)	0.560
INCA1	NATD1	psi-mi:“MI:0915”(physical association)	0.560
NATD1	ZNF426	psi-mi:“MI:0915”(physical association)	0.560
NATD1	E6	psi-mi:“MI:0915”(physical association)	0.370
NATD1	PCNA	psi-mi:“MI:0915”(physical association)	0.370
ADAMTSL4	NATD1	psi-mi:“MI:0915”(physical association)	0.370
ARMC8	VWA8	psi-mi:“MI:0914”(association)	0.350
GID8	PGRMC1	psi-mi:“MI:0914”(association)	0.350
NATD1	ADAMTSL4	psi-mi:“MI:0915”(physical association)	0.000
NATD1	NIF3L1	psi-mi:“MI:0915”(physical association)	0.000
NATD1	PICK1	psi-mi:“MI:0915”(physical association)	0.000
NATD1	PLEKHG4	psi-mi:“MI:0915”(physical association)	0.000
NATD1	INCA1	psi-mi:“MI:0915”(physical association)	0.000
NATD1	ZNF426	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): NATD1 (Two-hybrid), NATD1 (Two-hybrid), NATD1 (Two-hybrid), NATD1 (Two-hybrid), NATD1 (Two-hybrid), ADAMTSL4 (Two-hybrid), NATD1 (Biochemical Activity), NATD1 (Two-hybrid), NATD1 (Two-hybrid), NATD1 (Two-hybrid), NATD1 (Two-hybrid), NATD1 (Two-hybrid), NATD1 (Two-hybrid), NATD1 (Affinity Capture-MS), NATD1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B4XBG9, A0A1B5L8S2, A0A1V6PAA5, A2Y953, A4HE59, A4I1F7, A6QL79, B8DN19, O00170, O08915, O97628, P08487, P10686, P19174, Q0CCX8, Q12931, Q2KI24, Q2KNB7, Q2TBI4, Q3ULF4, Q4PMC9, Q4Q9X8, Q5D014, Q5FWY5, Q5N127, Q5XHZ0, Q5XI79, Q5ZHX9, Q5ZI74, Q5ZJI6, Q62077, Q66IM5, Q6IP48, Q754C9, Q7TT47, Q7YRC1, Q8N6N6, Q8WYJ6, Q924K1, Q95MN9

Diamond homologs: A6QL79, Q5D014, Q5ZJI6, Q66IM5, Q6IP48, Q8N6N6, Q9DBW3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

540 predictions. Top by Δscore:

Variant	Effect	Δscore
17:21243316:CGG:C	donor_gain	1.0000
17:21243426:CGGC:C	acceptor_gain	1.0000
17:21243427:GGCC:G	acceptor_loss	1.0000
17:21243428:GCCT:G	acceptor_loss	1.0000
17:21243430:C:CA	acceptor_loss	1.0000
17:21243430:C:CC	acceptor_gain	1.0000
17:21243431:T:C	acceptor_loss	1.0000
17:21243438:C:CT	acceptor_gain	1.0000
17:21243438:C:T	acceptor_gain	1.0000
17:21243439:G:T	acceptor_gain	1.0000
17:21244101:CCTA:C	donor_loss	1.0000
17:21244103:TAC:T	donor_loss	1.0000
17:21244104:ACC:A	donor_loss	1.0000
17:21244220:ACATC:A	acceptor_gain	1.0000
17:21244221:CATC:C	acceptor_gain	1.0000
17:21244221:CATCC:C	acceptor_gain	1.0000
17:21244222:ATC:A	acceptor_gain	1.0000
17:21244223:TC:T	acceptor_gain	1.0000
17:21244223:TCC:T	acceptor_loss	1.0000
17:21244224:CC:C	acceptor_gain	1.0000
17:21244225:C:CC	acceptor_gain	1.0000
17:21244225:CT:C	acceptor_loss	1.0000
17:21244226:T:C	acceptor_loss	1.0000
17:21244232:T:C	acceptor_gain	1.0000
17:21244232:T:TC	acceptor_gain	1.0000
17:21253153:CCTTA:C	donor_loss	1.0000
17:21253154:CTTAC:C	donor_loss	1.0000
17:21253155:TTAC:T	donor_loss	1.0000
17:21253156:TA:T	donor_loss	1.0000
17:21253157:A:AC	donor_gain	1.0000

AlphaMissense

717 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:21253175:G:C	F30L	0.999
17:21253175:G:T	F30L	0.999
17:21253176:A:G	F30S	0.999
17:21253177:A:G	F30L	0.999
17:21243380:C:T	C92Y	0.998
17:21243381:A:G	C92R	0.998
17:21243425:G:T	A77D	0.998
17:21244110:G:T	A74D	0.998
17:21244113:A:T	L73H	0.998
17:21244122:G:T	A70D	0.998
17:21244203:A:G	L43P	0.998
17:21243375:A:G	Y94H	0.997
17:21244113:A:G	L73P	0.997
17:21244167:A:G	L55P	0.997
17:21244209:G:T	A41D	0.997
17:21253176:A:C	F30C	0.997
17:21243374:T:C	Y94C	0.996
17:21243379:G:C	C92W	0.996
17:21243415:G:C	F80L	0.996
17:21243415:G:T	F80L	0.996
17:21243417:A:G	F80L	0.996
17:21244122:G:A	A70V	0.996
17:21244152:A:T	V60D	0.996
17:21253170:A:T	V32D	0.996
17:21243380:C:A	C92F	0.995
17:21243392:G:T	A88D	0.995
17:21243398:A:G	L86P	0.995
17:21244134:C:T	G66E	0.995
17:21244153:C:G	V60L	0.995
17:21244173:A:T	V53E	0.995

dbSNP variants (sampled 300 via entrez): RS1000032782 (17:21251766 G>A,T), RS1000129931 (17:21246222 A>G), RS1000191915 (17:21254532 GTCTC>G,GTCTCTC), RS1000250086 (17:21238596 C>A), RS1000270880 (17:21241122 G>C), RS1000362994 (17:21251531 G>A), RS1000622030 (17:21246552 T>G), RS1000677523 (17:21242549 G>A), RS1000868939 (17:21249222 G>A,C), RS1000968610 (17:21245071 G>A), RS1001007111 (17:21242240 T>C), RS1001148862 (17:21252142 C>T), RS1001178644 (17:21252422 G>C), RS1001259438 (17:21239509 G>A), RS1001337401 (17:21246847 T>C,G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST004621_187	Red cell distribution width	8.000000e-09
GCST004628_15	Immature fraction of reticulocytes	8.000000e-18
GCST005951_14	Body mass index	5.000000e-10
GCST90002387_23	Immature fraction of reticulocytes	2.000000e-43
GCST90002404_151	Red cell distribution width	4.000000e-23

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0009188	Red cell distribution width
EFO:0007986	reticulocyte count
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	increases expression	2
Benzo(a)pyrene	affects methylation	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
GSK-J4	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases methylation	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
perfluorooctane sulfonic acid	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Acetaminophen	increases expression	1
Coumestrol	decreases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	increases expression	1
Estradiol	decreases expression	1
Methapyrilene	increases methylation	1
Niclosamide	increases expression	1
Smoke	decreases expression	1
Thimerosal	decreases expression	1
Urethane	increases expression	1
Gold Compounds	increases expression	1
Cadmium Chloride	increases expression	1
Acrylamide	decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_SG08	HAP1 NATD1 (-) 1	Cancer cell line	Male
CVCL_SG09	HAP1 NATD1 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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