ACTRT3

Summary

ACTRT3 (actin related protein T3, HGNC:24022) is a protein-coding gene on chromosome 3q26.2, encoding Actin-related protein T3 (Q9BYD9).

Predicted to be located in cytoplasm; cytoskeleton; and male germ cell nucleus. Predicted to be active in actin cytoskeleton.

Source: NCBI Gene 84517 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 69 total — 1 pathogenic
• MANE Select transcript: NM_032487

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24022
Approved symbol	ACTRT3
Name	actin related protein T3
Location	3q26.2
Locus type	gene with protein product
Status	Approved
Aliases	ARPM1
Ensembl gene	ENSG00000184378
Ensembl biotype	protein_coding
OMIM	608534
Entrez	84517

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000330368, ENST00000956146

RefSeq mRNA: 1 — MANE Select: NM_032487 NM_032487

CCDS: CCDS3206

Canonical transcript exons

ENST00000330368 — 2 exons

Exon	Start	End
ENSE00001292725	169769321	169769561
ENSE00001326845	169766921	169768350

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 94.22.

FANTOM5 (CAGE): breadth broad, TPM avg 0.8165 / max 115.0267, expressed in 398 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
45532	0.2859	116
45531	0.2699	77
45533	0.2607	91

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	94.22	gold quality
left testis	UBERON:0004533	93.12	gold quality
right testis	UBERON:0004534	92.86	gold quality
testis	UBERON:0000473	91.10	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.54	gold quality
adult organism	UBERON:0007023	86.53	gold quality
endothelial cell	CL:0000115	74.56	silver quality
stromal cell of endometrium	CL:0002255	73.52	gold quality
calcaneal tendon	UBERON:0003701	70.04	gold quality
mucosa of stomach	UBERON:0001199	68.76	gold quality
right lobe of liver	UBERON:0001114	68.21	gold quality
thoracic aorta	UBERON:0001515	66.58	gold quality
descending thoracic aorta	UBERON:0002345	66.44	gold quality
islet of Langerhans	UBERON:0000006	66.33	gold quality
ascending aorta	UBERON:0001496	66.23	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	66.06	gold quality
left uterine tube	UBERON:0001303	65.93	gold quality
smooth muscle tissue	UBERON:0001135	65.92	gold quality
lower esophagus muscularis layer	UBERON:0035833	65.53	gold quality
lower esophagus	UBERON:0013473	65.49	gold quality
left coronary artery	UBERON:0001626	63.97	gold quality
right coronary artery	UBERON:0001625	63.95	gold quality
liver	UBERON:0002107	63.71	gold quality
omental fat pad	UBERON:0010414	63.59	gold quality
peritoneum	UBERON:0002358	63.57	gold quality
mucosa of transverse colon	UBERON:0004991	63.53	gold quality
adipose tissue of abdominal region	UBERON:0007808	63.23	gold quality
prefrontal cortex	UBERON:0000451	63.09	gold quality
metanephros cortex	UBERON:0010533	63.09	gold quality
right atrium auricular region	UBERON:0006631	63.03	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting ACTRT3, 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-96-5P	99.95	72.80	2140
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-494-3P	99.70	71.45	2795
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-182-3P	99.57	67.57	825
HSA-MIR-6853-3P	99.36	70.79	1558
HSA-MIR-4652-3P	99.33	70.02	2742
HSA-MIR-888-5P	99.30	70.15	1855
HSA-MIR-26B-3P	98.71	67.49	1102
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-660-5P	98.16	68.27	680
HSA-MIR-4733-5P	97.75	67.44	866
HSA-MIR-7976	95.75	65.67	1186
HSA-MIR-324-5P	95.68	65.20	560
HSA-MIR-874-3P	95.02	65.66	806

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Actrt3	ENSMUSG00000037737
rattus_norvegicus	Actrt3	ENSRNOG00000027908

Paralogs (26): ACTR6 (ENSG00000075089), ACTB (ENSG00000075624), ACTL6B (ENSG00000077080), ACTR5 (ENSG00000101442), ACTR3C (ENSG00000106526), ACTA2 (ENSG00000107796), ACTR8 (ENSG00000113812), ACTR1B (ENSG00000115073), ACTR3 (ENSG00000115091), ACTL8 (ENSG00000117148), ACTRT1 (ENSG00000123165), ACTR10 (ENSG00000131966), ACTR3B (ENSG00000133627), ACTL6A (ENSG00000136518), ACTR2 (ENSG00000138071), ACTR1A (ENSG00000138107), ACTA1 (ENSG00000143632), ACTL7B (ENSG00000148156), ACTC1 (ENSG00000159251), ACTG2 (ENSG00000163017), ACTBL2 (ENSG00000169067), ACTRT2 (ENSG00000169717), ACTL9 (ENSG00000181786), ACTG1 (ENSG00000184009), ACTL7A (ENSG00000187003), ACTL10 (ENSG00000288649)

Protein

Protein identifiers

Actin-related protein T3 — Q9BYD9 (reviewed: Q9BYD9)

Alternative names: Actin-related protein M1

All UniProt accessions (1): Q9BYD9

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with PFN3.

Subcellular location. Cytoplasm. Cytoskeleton. Nucleus.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the actin family.

RefSeq proteins (1): NP_115876* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004000	Actin	Family
IPR020902	Actin/actin-like_CS	Conserved_site
IPR043129	ATPase_NBD	Homologous_superfamily

Pfam: PF00022

UniProt features (4 total): sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BYD9-F1	94.47	0.90

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 46 (showing top): chr3q26, GOCC_GERM_CELL_NUCLEUS, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOMF_STRUCTURAL_CONSTITUENT_OF_CYTOSKELETON, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, BRUINS_UVC_RESPONSE_EARLY_LATE, MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN, WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D, FOXN3_TARGET_GENES, SIPA1_TARGET_GENES, ZBTB12_TARGET_GENES, ZSCAN2_TARGET_GENES, MIR96_5P, MIR1271_5P

GO Biological Process (0):

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

GO Cellular Component (5): male germ cell nucleus (GO:0001673), cytoplasm (GO:0005737), actin cytoskeleton (GO:0015629), nucleus (GO:0005634), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
germ cell nucleus	1
intracellular anatomical structure	1
cellular anatomical structure	1
cytoskeleton	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

2100 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ACTRT3	LRRIQ4	A6NIV6	730
ACTRT3	MYNN	Q9NPC7	722
ACTRT3	LRRC34	Q8IZ02	669
ACTRT3	PFN3	P60673	584
ACTRT3	ZNF888	P0CJ79	510
ACTRT3	LRRC31	Q6UY01	479
ACTRT3	CFAP161	Q6P656	438
ACTRT3	MYLK2	Q9H1R3	414
ACTRT3	ACRBP	Q8NEB7	410
ACTRT3	ODF2	Q5BJF6	406
ACTRT3	TNP1	P09430	374
ACTRT3	INSYN2B	A6NMK8	366
ACTRT3	IZUMO4	Q1ZYL8	366
ACTRT3	RNF113B	Q8IZP6	358
ACTRT3	B4DL54	B4DL54	358
ACTRT3	SERTAD3	Q9UJW9	358

IntAct

3 interactions, top by confidence:

A	B	Type	Score
ACTRT3	PDCL3	psi-mi:“MI:0915”(physical association)	0.500
PDCL3	POTEF	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): PDCL3 (Affinity Capture-MS), ACTRT3 (Affinity Capture-MS)

ESM2 similar proteins: A0JNU3, A2AKE7, A6H603, A6QQ74, D3ZBP4, F1MH07, O43542, Q149M9, Q2T9W4, Q2TA43, Q2V057, Q32KZ2, Q32L91, Q3ZBE0, Q49HH9, Q49KI5, Q4QR76, Q4R317, Q4R6Q3, Q4R821, Q5JWF8, Q5REQ1, Q5XIK1, Q641W9, Q643R3, Q68FW7, Q6AY16, Q6NVG1, Q76HM9, Q86U10, Q8CG27, Q8K4F6, Q8TC94, Q8TDG2, Q8TDY3, Q8TDZ2, Q8VCZ9, Q8VDP3, Q8VEI3, Q95JK8

Diamond homologs: A2XLF2, A3C6D7, A5DQP9, B5X2S3, D2I1E3, O74258, P02580, P0C539, P0C540, P0C542, P0CJ46, P0CJ47, P10988, P10990, P10992, P10993, P11426, P12432, P12433, P14235, P17128, P18602, P20360, P24902, P30165, P30172, P30173, P45889, P45891, P46258, P53477, P53496, P53504, P59679, P60009, P60010, P60011, P69002, P69003, P86287

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	66
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
40977	NC_000003.12:g.169764745_169767720del	Pathogenic

SpliceAI

115 predictions. Top by Δscore:

Variant	Effect	Δscore
3:169768346:GGTAA:G	acceptor_gain	1.0000
3:169768348:TAA:T	acceptor_gain	1.0000
3:169768348:TAAC:T	acceptor_loss	1.0000
3:169768349:AA:A	acceptor_gain	1.0000
3:169768351:C:CC	acceptor_gain	1.0000
3:169768351:C:CG	acceptor_loss	1.0000
3:169768353:G:C	acceptor_gain	1.0000
3:169769316:GGTAC:G	donor_loss	1.0000
3:169769317:GTACC:G	donor_loss	1.0000
3:169769318:TACC:T	donor_loss	1.0000
3:169769319:A:C	donor_loss	1.0000
3:169768347:GTAA:G	acceptor_gain	0.9900
3:169768353:G:GC	acceptor_gain	0.9900
3:169768350:ACTGT:A	acceptor_gain	0.9800
3:169768351:C:A	acceptor_gain	0.9800
3:169768347:GTAAC:G	acceptor_gain	0.9700
3:169768348:TAACT:T	acceptor_gain	0.9700
3:169768349:AACT:A	acceptor_gain	0.9700
3:169768352:T:A	acceptor_gain	0.9700
3:169768364:A:T	acceptor_gain	0.9700
3:169769319:A:AC	donor_gain	0.9600
3:169769320:C:CC	donor_gain	0.9600
3:169768363:C:CT	acceptor_gain	0.9400
3:169769345:T:TA	donor_gain	0.8900
3:169769321:C:G	donor_loss	0.6700
3:169769337:T:TA	donor_gain	0.6600
3:169768347:G:C	acceptor_gain	0.5400
3:169769320:CCTG:C	donor_gain	0.5300
3:169769340:T:TA	donor_gain	0.5300
3:169768883:T:C	acceptor_gain	0.5200

AlphaMissense

2469 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:169767915:C:A	K212N	0.991
3:169767915:C:G	K212N	0.991
3:169767542:A:G	W337R	0.989
3:169767542:A:T	W337R	0.989
3:169767625:C:G	R309P	0.989
3:169767717:G:C	S278R	0.988
3:169767717:G:T	S278R	0.988
3:169767719:T:G	S278R	0.988
3:169768298:A:G	W85R	0.986
3:169768298:A:T	W85R	0.986
3:169767903:A:C	C216W	0.984
3:169767504:G:C	F349L	0.982
3:169767504:G:T	F349L	0.982
3:169767506:A:G	F349L	0.982
3:169767988:A:G	L188P	0.982
3:169768000:A:G	L184P	0.982
3:169768105:C:T	G149D	0.982
3:169768207:C:G	R115P	0.982
3:169767658:C:A	G298V	0.980
3:169767659:C:A	G298W	0.980
3:169767532:C:T	G340D	0.977
3:169768096:A:G	L152P	0.977
3:169769466:C:G	A19P	0.977
3:169767574:A:T	V326D	0.975
3:169768068:A:C	S161R	0.975
3:169768068:A:T	S161R	0.975
3:169768070:T:G	S161R	0.975
3:169769467:C:A	K18N	0.975
3:169769467:C:G	K18N	0.975
3:169767474:A:C	F359L	0.974

dbSNP variants (sampled 300 via entrez): RS1000090994 (3:169769736 A>C,G), RS1000369014 (3:169770039 G>A), RS1000800661 (3:169770197 A>G), RS1002635219 (3:169767696 G>T), RS1003501596 (3:169769205 T>C,G), RS1005379261 (3:169769109 T>G), RS1006356195 (3:169771418 T>A,G), RS1006508464 (3:169766750 G>C), RS1008509039 (3:169769698 C>G,T), RS1009112835 (3:169768694 A>AT), RS1011104756 (3:169766996 T>C), RS1011467742 (3:169768754 T>C), RS1011553679 (3:169767240 C>T), RS1011702614 (3:169766620 C>A), RS1011854255 (3:169768562 C>G)

Disease associations

OMIM: gene MIM:608534 | disease phenotypes: MIM:127550

GenCC curated gene-disease

Mondo (1): dyskeratosis congenita, autosomal dominant 1 (MONDO:0007485)

Orphanet (1): Dyskeratosis congenita (Orphanet:1775)

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST002243_3	Bladder cancer	5.000000e-09
GCST002514_2	Melanoma	7.000000e-07
GCST004606_105	Eosinophil count	2.000000e-12
GCST004623_30	Neutrophil percentage of granulocytes	6.000000e-14
GCST004624_37	Sum eosinophil basophil counts	9.000000e-11
GCST004744_12	Lung adenocarcinoma	5.000000e-06
GCST005991_7	Platelet count	3.000000e-08
GCST009391_1557	Metabolite levels	4.000000e-06
GCST009391_2043	Metabolite levels	9.000000e-06
GCST009391_48	Metabolite levels	2.000000e-06
GCST012396_4	Multiple myeloma	3.000000e-08

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004842	eosinophil count
EFO:0007994	neutrophil percentage of granulocytes
EFO:0005090	basophil count
EFO:0004309	platelet count
EFO:0009776	ornithine measurement
EFO:0009777	citrulline measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C565079	Dyskeratosis Congenita, Autosomal Dominant (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	decreases expression, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Valproic Acid	affects expression, decreases expression	2
methylmercuric chloride	decreases expression	1
arsenite	affects binding, increases reaction	1
methylparaben	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
tobacco tar	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
CGP 52608	affects binding, increases reaction	1
Decitabine	decreases expression, decreases reaction	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, increases expression	1
Cannabidiol	decreases expression	1
Cisplatin	decreases expression	1
Drugs, Chinese Herbal	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Naphthoquinones	increases expression	1
Smoke	decreases reaction, decreases expression	1
Cadmium Chloride	increases abundance, increases expression	1
Genistein	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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