TOR1AIP2

gene
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Also known as LULL1NET9IFRG15

Summary

TOR1AIP2 (torsin 1A interacting protein 2, HGNC:24055) is a protein-coding gene on chromosome 1q25.2, encoding Torsin-1A-interacting protein 2 (Q8NFQ8). Required for endoplasmic reticulum integrity.

One of the two protein isoforms encoded by this gene is a type II integral membrane protein found in the endoplasmic reticulum (ER). The encoded protein is a cofactor for the ATPase TorsinA, regulating the amount of TorsinA present in the ER compared to that found in the nuclear envelope. Defects in this protein are a cause of early onset primary dystonia, a neuromuscular disease. The other isoform encoded by this gene is an interferon alpha responsive protein whose cellular role has yet to be determined.

Source: NCBI Gene 163590 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 20 total — 1 pathogenic
  • MANE Select transcript: NM_001199260

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24055
Approved symbolTOR1AIP2
Nametorsin 1A interacting protein 2
Location1q25.2
Locus typegene with protein product
StatusApproved
AliasesLULL1, NET9, IFRG15
Ensembl geneENSG00000169905
Ensembl biotypeprotein_coding
OMIM614513
Entrez163590

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 24 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000367612, ENST00000474318, ENST00000482587, ENST00000483123, ENST00000495650, ENST00000609928, ENST00000894825, ENST00000894826, ENST00000894827, ENST00000894828, ENST00000894829, ENST00000894830, ENST00000894831, ENST00000894832, ENST00000894833, ENST00000894834, ENST00000894835, ENST00000894836, ENST00000894837, ENST00000894838, ENST00000936116, ENST00000936117, ENST00000942404, ENST00000942405, ENST00000942406, ENST00000942407

RefSeq mRNA: 9 — MANE Select: NM_001199260 NM_001199260, NM_001349931, NM_001349933, NM_001349934, NM_001349935, NM_001349936, NM_001349937, NM_022347, NM_145034

CCDS: CCDS1334, CCDS53439

Canonical transcript exons

ENST00000609928 — 7 exons

ExonStartEnd
ENSE00001120664179847535179847636
ENSE00001120667179850845179851363
ENSE00001231760179852632179852811
ENSE00002342499179877239179877373
ENSE00003703145179839976179846828
ENSE00003707494179865436179865854
ENSE00003707760179877693179877803

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 98.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 48.8428 / max 310.2371, expressed in 1820 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1609240.90181820
160917.78651756
160860.154524

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
adrenal tissueUBERON:001830398.31gold quality
jejunal mucosaUBERON:000039997.46gold quality
germinal epithelium of ovaryUBERON:000130496.62gold quality
parietal pleuraUBERON:000240095.71gold quality
amniotic fluidUBERON:000017395.69gold quality
pleuraUBERON:000097794.81gold quality
visceral pleuraUBERON:000240194.04gold quality
tibiaUBERON:000097993.84gold quality
esophagus squamous epitheliumUBERON:000692093.69gold quality
buccal mucosa cellCL:000233693.60gold quality
pericardiumUBERON:000240793.53gold quality
seminal vesicleUBERON:000099893.45gold quality
jejunumUBERON:000211593.18gold quality
tendon of biceps brachiiUBERON:000818892.87gold quality
epithelium of esophagusUBERON:000197692.80gold quality
placentaUBERON:000198792.80gold quality
deciduaUBERON:000245092.61gold quality
penisUBERON:000098992.26gold quality
tendonUBERON:000004391.95gold quality
lower lobe of lungUBERON:000894991.63gold quality
calcaneal tendonUBERON:000370191.61gold quality
stromal cell of endometriumCL:000225591.53gold quality
gingival epitheliumUBERON:000194991.45gold quality
duodenumUBERON:000211491.36gold quality
liverUBERON:000210791.23gold quality
islet of LangerhansUBERON:000000691.05gold quality
palpebral conjunctivaUBERON:000181291.01gold quality
gingivaUBERON:000182890.89gold quality
oocyteCL:000002390.76gold quality
medial globus pallidusUBERON:000247790.75gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NANOG, POU5F1

miRNA regulators (miRDB)

226 targeting TOR1AIP2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3163100.0077.238605
HSA-MIR-4262100.0073.263931
HSA-MIR-4533100.0069.482758
HSA-MIR-4776-3P100.0068.731340
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-3646100.0073.565283
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-656-3P100.0072.152788
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-366299.9973.825684
HSA-MIR-428299.9975.366408
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-480399.9871.993117

Literature-anchored findings (GeneRIF, showing 6)

  • identifed a novel transmembrane protein, lumenal domain like LAP1 (LULL1), which appears to interact with torsinA; it resides in the main endoplasmic reticulum. (PMID:15767459)
  • Data suggest that LULL1 regulates the distribution and activity of TorA within the ER and NE lumen and reveal functional defects in the mutant protein responsible for DYT1 dystonia. (PMID:19339278)
  • LAP1 and LULL1 as regulatory cofactors that are responsible for the activation of TorA’s ATPase activity. (PMID:23569223)
  • LAP1 and LULL1 regulate Torsin ATPase activity through an active site complementation mechanism. (PMID:25352667)
  • The Torsin Activator LULL1 Is Required for Efficient Growth of Herpes Simplex Virus 1. (PMID:26041288)
  • A comparison of these structures shows, in atomic detail, the subtle differences in TorsinADeltaE-LULL1 activator interactions that separate the healthy from the diseased state. (PMID:27490483)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriozgc:112962ENSDARG00000069102
danio_reriosi:dkeyp-82a1.6ENSDARG00000094336
mus_musculusTor1aip2ENSMUSG00000050565
rattus_norvegicusTor1aip2ENSRNOG00000024849

Paralogs (1): TOR1AIP1 (ENSG00000143337)

Protein

Protein identifiers

Torsin-1A-interacting protein 2Q8NFQ8 (reviewed: Q8NFQ8, Q9H496)

Alternative names: Lumenal domain-like LAP1

All UniProt accessions (4): Q8NFQ8, Q9H496, A0A096LNM1, A0A6B9D1Q5

UniProt curated annotations — full annotation on UniProt →

Function. Required for endoplasmic reticulum integrity. Regulates the distribution of TOR1A between the endoplasmic reticulum and the nuclear envelope as well as induces TOR1A, TOR1B and TOR3A ATPase activity.

Subunit / interactions. Interacts with TOR1A and TOR1B (ATP-bound).

Subcellular location. Endoplasmic reticulum membrane. Nucleus membrane.

Similarity. Belongs to the TOR1AIP family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8NFQ8-1TOR1AIP2yes
Q9H496-1IFRG15

RefSeq proteins (9): NP_001186189, NP_001336860, NP_001336862, NP_001336863, NP_001336864, NP_001336865, NP_001336866, NP_071742, NP_659471 (=MANE)

Domains & families (InterPro)

IDNameType
IPR008662TOIP1/2Family
IPR038599LAP1C-like_C_sfHomologous_superfamily
IPR046753TOIP1/2_CDomain
IPR046754TOIP1/2_NDomain

Pfam: PF05609, PF20443

UniProt features (41 total): helix 12, modified residue 7, strand 7, compositionally biased region 4, chain 2, topological domain 2, turn 2, region of interest 2, initiator methionine 1, glycosylation site 1, transmembrane region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
5J1SX-RAY DIFFRACTION1.4
5J1TX-RAY DIFFRACTION1.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NFQ8-F169.890.45
AF-Q9H496-F163.860.00

Antibody-complex structures (SAbDab): 25J1S, 5J1T

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 (7): 2, 13, 93, 120, 163, 176, 193

Glycosylation sites (1): 286

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 213 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, MAZ_Q6, GGGTGGRR_PAX4_03, OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, FOSTER_TOLERANT_MACROPHAGE_UP, DOANE_RESPONSE_TO_ANDROGEN_DN, LIAO_METASTASIS, TGANTCA_AP1_C, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, IK2_01, GOBP_REGULATION_OF_ATP_DEPENDENT_ACTIVITY, GOBP_MEMBRANE_ORGANIZATION

GO Biological Process (4): endoplasmic reticulum organization (GO:0007029), positive regulation of ATP-dependent activity (GO:0032781), membrane organization (GO:0061024), protein localization to nuclear envelope (GO:0090435)

GO Molecular Function (3): ATPase activator activity (GO:0001671), ATPase binding (GO:0051117), protein binding (GO:0005515)

GO Cellular Component (6): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), nuclear membrane (GO:0031965), nucleus (GO:0005634), endomembrane system (GO:0012505)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
ATP-dependent activity2
intracellular membrane-bounded organelle2
organelle membrane2
cellular anatomical structure2
organelle organization1
endomembrane system organization1
regulation of ATP-dependent activity1
positive regulation of molecular function1
cellular component organization1
protein localization to nucleus1
molecular function activator activity1
enzyme binding1
binding1
cytoplasm1
endomembrane system1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
nucleus1
nuclear envelope1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

758 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TOR1AIP2TOR1AO14656983
TOR1AIP2TOR1BO14657870
TOR1AIP2TOR3AQ9H497673
TOR1AIP2TOR2AQ5JU69654
TOR1AIP2SUN2Q9UH99643
TOR1AIP2SUN1O94901522
TOR1AIP2C6orf52Q5T4I8484
TOR1AIP2TDRD5Q8NAT2482
TOR1AIP2SNAPINO95295480
TOR1AIP2FAM163AQ96GL9468
TOR1AIP2CEP350Q5VT06464
TOR1AIP2TM7SF2O76062461
TOR1AIP2LRRC7Q96NW7446
TOR1AIP2TOR4AQ9NXH8439
TOR1AIP2SCCPDHQ8NBX0418

IntAct

92 interactions, top by confidence:

ABTypeScore
TOR1ATOR1AIP2psi-mi:“MI:0915”(physical association)0.810
TOR1ATOR1AIP2psi-mi:“MI:0407”(direct interaction)0.810
TOR1AIP2TOR1Apsi-mi:“MI:0407”(direct interaction)0.810
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
CFTRESYT2psi-mi:“MI:0914”(association)0.710
RAB15RAP1GDS1psi-mi:“MI:0914”(association)0.640
CANXPGRMC1psi-mi:“MI:0914”(association)0.570
TOR1AIP2TMEM223psi-mi:“MI:0914”(association)0.530
RPS2MPHOSPH10psi-mi:“MI:0914”(association)0.530
ABHD18HSPD1psi-mi:“MI:0914”(association)0.530
FAM174ABLTP3Bpsi-mi:“MI:0914”(association)0.530
APLNRSLC33A1psi-mi:“MI:0914”(association)0.530
TOR1ATOR1Bpsi-mi:“MI:0914”(association)0.530
TIMP3ZZEF1psi-mi:“MI:0914”(association)0.530
ARL6SART1psi-mi:“MI:0914”(association)0.510
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
TOR1Apsi-mi:“MI:0882”(atpase reaction)0.440
TOR1Bpsi-mi:“MI:0882”(atpase reaction)0.440
TOR1AIP2psi-mi:“MI:0882”(atpase reaction)0.440
PGRMC1psi-mi:“MI:0914”(association)0.350

BioGRID (777): TOR1AIP2 (Two-hybrid), TOR1B (Affinity Capture-Western), TOR1AIP2 (Reconstituted Complex), TOR1AIP2 (Affinity Capture-Western), TOR1A (Affinity Capture-Western), TOR1AIP2 (Co-purification), TOR1AIP2 (Affinity Capture-Western), TOR1AIP2 (Proximity Label-MS), TOR1AIP2 (Proximity Label-MS), TOR1AIP2 (Affinity Capture-MS), TOR1AIP2 (Proximity Label-MS), TOR1AIP2 (Affinity Capture-MS), SH3BP4 (Affinity Capture-MS), MCU (Affinity Capture-MS), TOR1AIP2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8HTT5, A1A4L4, A6QLD2, A8T6P4, F1N4E5, O02776, O35144, O60303, O88622, O94901, Q1LVK9, Q2M243, Q3UH68, Q3UQI9, Q3V0J1, Q4G0A6, Q5BLK4, Q5JTV8, Q5PQX1, Q5R7A3, Q5RF72, Q5RJ80, Q61029, Q6A037, Q6IRU7, Q6P1H6, Q6P752, Q71M44, Q76LL6, Q76N89, Q7T3T8, Q7T3T9, Q7TNY7, Q7TP65, Q80VH0, Q86W56, Q86XL3, Q8BVV7, Q8BYU6, Q8K3I4

Diamond homologs: F1N4E5, Q5JTV8, Q5PQX1, Q5R7A3, Q6P752, Q8BYU6, Q8NFQ8, Q921T2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 103 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Cargo trafficking to the periciliary membrane517.2×4e-04
Aggrephagy517.2×4e-04
HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand513.4×8e-04
Translocation of SLC2A4 (GLUT4) to the plasma membrane612.9×4e-04
Autophagy510.3×1e-03
Cilium Assembly69.1×8e-04
Macroautophagy58.0×3e-03
Neurotransmitter receptors and postsynaptic signal transmission57.0×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance2
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
253059NM_015602.4(TOR1AIP1):c.186del (p.Glu62fs)Pathogenic

SpliceAI

704 predictions. Top by Δscore:

VariantEffectΔscore
1:179877691:A:ACdonor_gain1.0000
1:179877692:C:CCdonor_gain1.0000
1:179877692:CA:Cdonor_gain0.9900
1:179877692:CAA:Cdonor_gain0.9900
1:179882977:GGTGA:Gdonor_loss0.9900
1:179882979:T:Gdonor_loss0.9900
1:179877687:A:ACdonor_gain0.9800
1:179877687:ACTT:Adonor_loss0.9800
1:179877688:C:CCdonor_gain0.9800
1:179877689:TTACA:Tdonor_loss0.9800
1:179877691:ACAA:Adonor_loss0.9800
1:179877692:CAAA:Cdonor_gain0.9800
1:179877692:CAAAT:Cdonor_gain0.9800
1:179882947:A:Tdonor_gain0.9800
1:179876207:A:Cacceptor_gain0.9700
1:179877684:TTTAC:Tdonor_loss0.9600
1:179877685:TTAC:Tdonor_loss0.9600
1:179877686:TAC:Tdonor_loss0.9600
1:179865570:CT:Cdonor_gain0.9500
1:179876206:CA:Cacceptor_gain0.9500
1:179882794:G:GTdonor_gain0.9500
1:179864981:A:Tacceptor_gain0.9400
1:179882974:GAAG:Gdonor_gain0.9400
1:179864980:C:CTacceptor_gain0.9300
1:179865569:A:ACdonor_gain0.9300
1:179865570:C:CCdonor_gain0.9300
1:179865570:CTCTG:Cdonor_gain0.9200
1:179876205:CCA:Cacceptor_gain0.9200
1:179882489:C:Gdonor_gain0.9100
1:179882990:G:GTdonor_gain0.9100

AlphaMissense

3113 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:179846145:A:GW447R0.998
1:179846145:A:TW447R0.998
1:179846114:A:TV457D0.997
1:179846143:C:AW447C0.997
1:179846143:C:GW447C0.997
1:179846317:A:CF389L0.997
1:179846317:A:TF389L0.997
1:179846319:A:GF389L0.997
1:179846336:T:AD383V0.997
1:179846338:A:CC382W0.997
1:179846339:C:TC382Y0.997
1:179846399:G:TA362D0.997
1:179846147:A:GL446P0.996
1:179846324:G:TA387D0.996
1:179846342:T:CY381C0.996
1:179846343:A:GY381H0.996
1:179846432:A:GL351P0.996
1:179846120:A:GL455P0.995
1:179846138:C:GR449P0.995
1:179846140:G:CS448R0.995
1:179846140:G:TS448R0.995
1:179846142:T:GS448R0.995
1:179846150:C:TG445E0.995
1:179846291:A:TV398D0.995
1:179846336:T:GD383A0.995
1:179846351:A:GF378S0.995
1:179846400:C:GA362P0.995
1:179846452:C:AK344N0.995
1:179846452:C:GK344N0.995
1:179846548:G:CS312R0.995

dbSNP variants (sampled 300 via entrez): RS1000055442 (1:179861835 C>T), RS1000060533 (1:179874355 A>C,G), RS1000338573 (1:179859949 A>C), RS1000363898 (1:179840579 T>G), RS1000376794 (1:179878481 C>T), RS1000410552 (1:179873947 T>C), RS1000416229 (1:179841098 C>T), RS1000429316 (1:179878820 G>A,C,T), RS1000447236 (1:179863676 G>A,C), RS1000470989 (1:179878941 G>C), RS1000979023 (1:179866700 C>T), RS1000995572 (1:179873866 T>C), RS1001044183 (1:179853312 T>C), RS1001050730 (1:179867000 G>C), RS1001171139 (1:179839549 C>T)

Disease associations

OMIM: gene MIM:614513 | disease phenotypes: MIM:617072

GenCC curated gene-disease

Mondo (1): autosomal recessive limb-girdle muscular dystrophy type 2Y (MONDO:0014900)

Orphanet (1): TOR1AIP1-related limb-girdle muscular dystrophy (Orphanet:424261)

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST010002_371Refractive error3.000000e-09

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
trichostatin Aaffects expression, increases expression2
Air Pollutantsaffects cotreatment, decreases expression, increases abundance2
Valproic Aciddecreases methylation, increases expression2
Aflatoxin B1decreases methylation, increases expression2
FR900359decreases phosphorylation1
urushiolincreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
bisphenol Adecreases expression1
sodium arsenitedecreases expression1
butyraldehydeincreases expression1
coumarinaffects phosphorylation1
methacrylaldehydeincreases abundance, affects cotreatment, decreases expression1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridineincreases expression1
pentabromodiphenyl etherdecreases expression1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)decreases expression1
Resveratrolincreases expression, affects cotreatment1
Acroleinincreases abundance, affects cotreatment, decreases expression1
Air Pollutants, Occupationaldecreases expression1
Benzo(a)pyreneincreases mutagenesis1
Caffeinedecreases phosphorylation1
Calcitriolincreases expression, affects cotreatment1
Estradiolincreases expression1
Hydrogen Peroxideincreases expression1
Nickeldecreases expression1
Ozoneaffects cotreatment, decreases expression, increases abundance1
Plant Extractsaffects cotreatment, increases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05989620Not specifiedRECRUITINGLong-Term Development of Muscular Dystrophy Outcome Assessments