ACTRT2

gene
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Also known as Arp-T2ARPM2FLJ25424

Summary

ACTRT2 (actin related protein T2, HGNC:24026) is a protein-coding gene on chromosome 1p36.32, encoding Actin-related protein T2 (Q8TDY3).

The protein encoded by this intronless gene belongs to the actin family. Studies have shown that this protein may be involved in cytoskeletal organization similar to other cytoplasmic actin-related protein (ARP) subfamily members. Antibody raised against the human protein has been used to detect the protein by immunoblotting and immunofluorescence microscopy, demonstrating its specific synthesis in the testis, late in spermatid differentiation, and its localization in the calyx.

Source: NCBI Gene 140625 — RefSeq curated summary.

At a glance

  • GWAS associations: 11
  • Clinical variants (ClinVar): 100 total — 11 pathogenic
  • MANE Select transcript: NM_080431

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24026
Approved symbolACTRT2
Nameactin related protein T2
Location1p36.32
Locus typegene with protein product
StatusApproved
AliasesArp-T2, ARPM2, FLJ25424
Ensembl geneENSG00000169717
Ensembl biotypeprotein_coding
OMIM608535
Entrez140625

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000378404

RefSeq mRNA: 1 — MANE Select: NM_080431 NM_080431

CCDS: CCDS45

Canonical transcript exons

ENST00000378404 — 1 exons

ExonStartEnd
ENSE0000147736330214673022903

Expression profiles

Bgee: expression breadth broad, 31 present calls, max score 96.67.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1568 / max 148.8580, expressed in 7 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
2730.14207
2013250.00763
2720.00733

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left testisUBERON:000453396.67gold quality
right testisUBERON:000453496.58gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099195.97gold quality
testisUBERON:000047393.53gold quality
spermCL:000001988.47gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.10gold quality
adult organismUBERON:000702384.52gold quality
pancreatic ductal cellCL:000207972.40silver quality
upper arm skinUBERON:000426365.53gold quality
left ventricle myocardiumUBERON:000656664.85gold quality
cardiac muscle of right atriumUBERON:000337964.76gold quality
epithelial cell of pancreasCL:000008356.15gold quality
quadriceps femorisUBERON:000137756.14gold quality
epithelium of nasopharynxUBERON:000195156.10gold quality
pericardiumUBERON:000240755.87gold quality
myocardiumUBERON:000234955.82gold quality
kidney epitheliumUBERON:000481955.47gold quality
vastus lateralisUBERON:000137955.37gold quality
superficial temporal arteryUBERON:000161455.04gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450254.90gold quality
parotid glandUBERON:000183154.38gold quality
mucosa of paranasal sinusUBERON:000503054.35gold quality
deltoidUBERON:000147653.26gold quality
tibialis anteriorUBERON:000138551.41silver quality
oocyteCL:000002349.67gold quality
nasal cavity epitheliumUBERON:000538448.81gold quality
layer of synovial tissueUBERON:000761648.00gold quality
ileal mucosaUBERON:000033147.15silver quality
body of tongueUBERON:001187647.08gold quality
cauda epididymisUBERON:000436046.66gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-GEOD-134144yes31.68
E-ANND-3no0.66

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

  • Describes the discovery of two actin-related proteins as major components in a cytoskeletal, nonmotile structure of bull spermatozoa, suggesting that certain members of this family of proteins may serve functions other than nucleation of actin filaments. (PMID:12243744)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusActrt2ENSMUSG00000051276
rattus_norvegicusActrt2ENSRNOG00000012586

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), ACTL9 (ENSG00000181786), ACTG1 (ENSG00000184009), ACTRT3 (ENSG00000184378), ACTL7A (ENSG00000187003), ACTL10 (ENSG00000288649)

Protein

Protein identifiers

Actin-related protein T2Q8TDY3 (reviewed: Q8TDY3)

Alternative names: Actin-related protein M2

All UniProt accessions (1): Q8TDY3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Cytoskeleton.

Similarity. Belongs to the actin family.

RefSeq proteins (1): NP_536356* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR004000ActinFamily
IPR020902Actin/actin-like_CSConserved_site
IPR043129ATPase_NBDHomologous_superfamily

Pfam: PF00022

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TDY3-F193.420.85

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, MARTINEZ_RB1_TARGETS_UP, MARTINEZ_RB1_AND_TP53_TARGETS_UP, GOMF_STRUCTURAL_CONSTITUENT_OF_CYTOSKELETON, GOMF_STRUCTURAL_MOLECULE_ACTIVITY, chr1p36, ZNF436_TARGET_GENES, GSE13229_IMM_VS_INTMATURE_NKCELL_UP, GSE13485_DAY3_VS_DAY21_YF17D_VACCINE_PBMC_DN, GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_DN, GSE10211_UV_INACT_SENDAI_VS_LIVE_SENDAI_VIRUS_TRACHEAL_EPITHELIAL_CELLS_UP, GSE17721_PAM3CSK4_VS_GADIQUIMOD_6H_BMDC_DN, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_12H_ACT_CD4_TCELL_DN, GOCC_ACTIN_CYTOSKELETON, GSE8921_UNSTIM_0H_VS_TLR1_2_STIM_MONOCYTE_3H_UP

GO Biological Process (0):

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

GO Cellular Component (3): actin cytoskeleton (GO:0015629), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1
cytoskeleton1
intracellular anatomical structure1
cellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

2100 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ACTRT2OR2T34Q8NGX1542
ACTRT2OR10J1P30954516
ACTRT2TSACCQ96A04507
ACTRT2C22orf23Q9BZE7507
ACTRT2PRDM16Q9HAZ2495
ACTRT2ACTL9Q8TC94478
ACTRT2CATSPERTQ53TS8474
ACTRT2CFAP161Q6P656462
ACTRT2FAM186BQ8IYM0453
ACTRT2TMEM247A6NEH6452
ACTRT2ACTRT1Q8TDG2449
ACTRT2PRR30Q53SZ7447
ACTRT2GKAP1Q5VSY0447
ACTRT2SLC67A1-ASQ8N1D0447
ACTRT2CAPZA3Q96KX2444

IntAct

3 interactions, top by confidence:

ABTypeScore
ACTRT2PDCL3psi-mi:“MI:0915”(physical association)0.500
ACTRT2ACSL4psi-mi:“MI:0914”(association)0.350

BioGRID (10): PDCL3 (Affinity Capture-MS), CCT6A (Affinity Capture-MS), CCT6B (Affinity Capture-MS), CCT2 (Affinity Capture-MS), CCT7 (Affinity Capture-MS), ACSL4 (Affinity Capture-MS), SLC25A19 (Affinity Capture-MS), CCT3 (Affinity Capture-MS), TCP1 (Affinity Capture-MS), ACTRT2 (Cross-Linking-MS (XL-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: A2BDB0, O13419, O18499, O18500, O18840, O42161, O74258, O93400, P02576, P02578, P07830, P10365, P10984, P10988, P10989, P10993, P12432, P14883, P17304, P20359, P26197, P27131, P29751, P30162, P41340, P48465, P48975, P50138, P53455, P53485, P53500, P53505, P53689, P60009, P60010, P60011, P60706, P60707, P60708, P60709

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic11
Likely pathogenic0
Uncertain significance81
Likely benign7
Benign0

Top pathogenic / likely-pathogenic (11)

Variant IDHGVSClassification
148513GRCh38/hg38 1p36.32-36.31(chr1:2906020-5336116)x1Pathogenic
1808734GRCh37/hg19 1p36.33-36.32(chr1:2173570-5023430)x1Pathogenic
3063066GRCh37/hg19 1p36.33-36.31(chr1:1959612-5471235)x1Pathogenic
443115GRCh37/hg19 1p36.33-36.32(chr1:1415800-5007235)x1Pathogenic
565062GRCh37/hg19 1p36.33-36.32(chr1:2190850-3503606)x1Pathogenic
58040GRCh38/hg38 1p36.32(chr1:2659405-3273322)x3Pathogenic
58319GRCh38/hg38 1p36.33-36.32(chr1:1482278-3152536)x1Pathogenic
58321GRCh38/hg38 1p36.32(chr1:2683403-4729121)x1Pathogenic
625765GRCh37/hg19 1p36.33-36.31(chr1:1471075-5831645)Pathogenic
638130GRCh37/hg19 1p36.33-36.32(chr1:2261222-5304873)x1Pathogenic
666432GRCh37/hg19 1p36.33-36.32(chr1:1723651-3444846)x1Pathogenic

SpliceAI

46 predictions. Top by Δscore:

VariantEffectΔscore
1:3022549:A:AGdonor_gain0.6500
1:3022406:G:Tdonor_gain0.5800
1:3022491:C:Gdonor_gain0.5800
1:3022406:G:GTdonor_gain0.5700
1:3022562:G:GTdonor_gain0.5200
1:3022577:G:Tdonor_gain0.4900
1:3022349:C:Gdonor_gain0.4600
1:3022543:A:Gdonor_gain0.4600
1:3022577:G:GTdonor_gain0.4600
1:3022544:G:GGdonor_gain0.4400
1:3022398:GTCC:Gdonor_gain0.4000
1:3022399:TCCT:Tdonor_gain0.4000
1:3022395:G:GTdonor_gain0.3900
1:3022638:G:GTdonor_gain0.3600
1:3022698:T:TAdonor_gain0.3300
1:3022699:G:GAdonor_gain0.3200
1:3022405:GGGA:Gdonor_gain0.3100
1:3022662:G:GTdonor_gain0.3100
1:3022154:G:GAdonor_gain0.3000
1:3021597:G:GTdonor_gain0.2800
1:3022197:G:GCacceptor_gain0.2800
1:3021597:G:Tdonor_gain0.2700
1:3022477:T:Adonor_gain0.2700
1:3022220:A:AGacceptor_gain0.2600
1:3022221:G:GGacceptor_gain0.2600
1:3022547:T:Adonor_gain0.2600
1:3022695:C:Aacceptor_gain0.2600
1:3022110:G:GTdonor_gain0.2500
1:3022153:T:TAdonor_gain0.2500
1:3022374:G:GTdonor_gain0.2500

AlphaMissense

2473 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:3022161:A:CS159R0.974
1:3022163:C:AS159R0.974
1:3022163:C:GS159R0.974
1:3022533:A:CS283R0.971
1:3022535:C:AS283R0.971
1:3022535:C:GS283R0.971
1:3022710:T:AW342R0.970
1:3022710:T:CW342R0.970
1:3022337:A:CK217N0.967
1:3022337:A:TK217N0.967
1:3022068:T:CF128L0.963
1:3022070:C:AF128L0.963
1:3022070:C:GF128L0.963
1:3022758:T:AW358R0.960
1:3022758:T:CW358R0.960
1:3022627:G:CR314P0.956
1:3022746:T:CF354L0.956
1:3022748:C:AF354L0.956
1:3022748:C:GF354L0.956
1:3022815:T:CF377L0.951
1:3022817:C:AF377L0.951
1:3022817:C:GF377L0.951
1:3021752:A:CK22N0.949
1:3021752:A:TK22N0.949
1:3022476:T:CF264L0.945
1:3022478:C:AF264L0.945
1:3022478:C:GF264L0.945
1:3022189:C:AP168H0.941
1:3022630:T:CL315P0.934
1:3022525:T:AV280D0.932

dbSNP variants (sampled 300 via entrez): RS1000415473 (1:3022307 G>A), RS1000783590 (1:3019639 C>T), RS1001000664 (1:3021108 T>A), RS1002720697 (1:3023286 G>A), RS1002770605 (1:3021579 A>T), RS1004385684 (1:3022955 GGCCCTGACAGTGAATCTGTGAAGTGTCTTGGTCCACACCC>G), RS1004549796 (1:3019733 C>T), RS1004621741 (1:3019575 G>A,T), RS1006784944 (1:3021905 C>A), RS1007207452 (1:3023054 A>G), RS1008782805 (1:3019900 G>A), RS1010732877 (1:3019933 C>T), RS1011232692 (1:3023027 G>A,T), RS1011744431 (1:3023260 G>A,C), RS1012258936 (1:3022512 C>G,T)

Disease associations

OMIM: gene MIM:608535 | disease phenotypes: MIM:607872

GenCC curated gene-disease

Mondo (2): chromosome 1p36 deletion syndrome (MONDO:0011929), intellectual disability (MONDO:0001071)

Orphanet (2): 1p36 deletion syndrome (Orphanet:1606), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

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

GWAS associations

11 associations (top):

StudyTraitp-value
GCST003901_7Cognitive decline (age-related)1.000000e-06
GCST004749_57Lung cancer in ever smokers4.000000e-06
GCST005194_148Coronary artery disease2.000000e-07
GCST005951_35Body mass index4.000000e-08
GCST006288_592Heel bone mineral density6.000000e-14
GCST006288_699Heel bone mineral density1.000000e-07
GCST006288_95Heel bone mineral density1.000000e-06
GCST006979_848Heel bone mineral density7.000000e-47
GCST010866_12Coronary artery disease6.000000e-12
GCST012295_7Schizophrenia, bipolar disorder or recurrent major depressive disorder x sex interaction7.000000e-06
GCST012319_9LDL levels x SSRI levels (escitalopram or citalopram) interaction in schizophrenia or bipolar disorder5.000000e-06

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0009270heel bone mineral density
EFO:0004952disease recurrence
EFO:0008343sex interaction measurement
EFO:0004611low density lipoprotein cholesterol measurement

MeSH disease descriptors (2)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
C535362Chromosome 1p36 Deletion Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsaffects methylation, increases abundance, decreases expression, increases expression3
bisphenol Adecreases expression1
sodium arseniteincreases expression1
3,4,5,3’,4’-pentachlorobiphenyldecreases expression1
perfluorooctanoic aciddecreases expression1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
Benzo(a)pyrenedecreases methylation, affects methylation1
Coalincreases abundance, increases expression1
Folic Aciddecreases expression1
Ozoneaffects methylation, increases abundance1
Smokeincreases abundance, increases expression1
Valproic Acidincreases methylation1
Particulate Matterincreases abundance, decreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT02381457Not specifiedCOMPLETEDSNP-based Microdeletion and Aneuploidy RegisTry (SMART)
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394Not specifiedUNKNOWNFCT With Young Children With ID in the UK: A Feasibility Project V.1
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): chromosome 1p36 deletion syndrome