LMNTD1

gene
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Also known as FLJ36004Pas1c1

Summary

LMNTD1 (lamin tail domain containing 1, HGNC:26683) is a protein-coding gene on chromosome 12p12.1, encoding Lamin tail domain-containing protein 1 (Q8N9Z9).

Predicted to act upstream of or within cell population proliferation. Predicted to be located in intermediate filament and nucleus. Predicted to be active in cytoplasm and nuclear envelope.

Source: NCBI Gene 160492 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 64 total
  • MANE Select transcript: NM_001145728

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26683
Approved symbolLMNTD1
Namelamin tail domain containing 1
Location12p12.1
Locus typegene with protein product
StatusApproved
AliasesFLJ36004, Pas1c1
Ensembl geneENSG00000152936
Ensembl biotypeprotein_coding
OMIM617254
Entrez160492

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 11 protein_coding

ENST00000282881, ENST00000413632, ENST00000445693, ENST00000458174, ENST00000538178, ENST00000539523, ENST00000539744, ENST00000540106, ENST00000542224, ENST00000543629, ENST00000545543

RefSeq mRNA: 8 — MANE Select: NM_001145728 NM_001145727, NM_001145728, NM_001145729, NM_001256266, NM_001352232, NM_001352233, NM_001352234, NM_152590

CCDS: CCDS44847, CCDS44848, CCDS44849, CCDS58218, CCDS8704

Canonical transcript exons

ENST00000458174 — 10 exons

ExonStartEnd
ENSE000010079262551985825520075
ENSE000011332922551879525518967
ENSE000011896722552609925526218
ENSE000013748262550373825503800
ENSE000017790042555287125552989
ENSE000022766342547608225476460
ENSE000023076652555306925553283
ENSE000034622652554637425546554
ENSE000035001292554932625549546
ENSE000036238952552676925526955

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 85.50.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3738 / max 44.2381, expressed in 116 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1301880.248581
1301890.055217
1301900.049913
1301850.00983
1301860.00834
1301870.00201

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130285.50gold quality
olfactory segment of nasal mucosaUBERON:000538682.36gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047379.11gold quality
left testisUBERON:000453375.81gold quality
right testisUBERON:000453474.51gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099173.58gold quality
testisUBERON:000047373.45gold quality
buccal mucosa cellCL:000233667.80silver quality
islet of LangerhansUBERON:000000666.55gold quality
bronchial epithelial cellCL:000232864.43gold quality
bronchusUBERON:000218563.34gold quality
fallopian tubeUBERON:000388962.25gold quality
nasal cavity mucosaUBERON:000182660.75gold quality
mucosa of paranasal sinusUBERON:000503059.47gold quality
corpus callosumUBERON:000233658.26gold quality
spermCL:000001958.00silver quality
smooth muscle tissueUBERON:000113557.27gold quality
left uterine tubeUBERON:000130355.46gold quality
mucosa of transverse colonUBERON:000499155.21gold quality
hypothalamusUBERON:000189853.68gold quality
adenohypophysisUBERON:000219653.09gold quality
right lungUBERON:000216752.52gold quality
amygdalaUBERON:000187652.51gold quality
C1 segment of cervical spinal cordUBERON:000646952.45gold quality
pituitary glandUBERON:000000752.41gold quality
pancreasUBERON:000126451.39gold quality
spinal cordUBERON:000224051.31gold quality
caudate nucleusUBERON:000187351.22gold quality
rectumUBERON:000105251.02gold quality
adrenal tissueUBERON:001830349.27gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.18

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting LMNTD1, 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-314899.9775.066478
HSA-MIR-568099.9169.833421
HSA-MIR-449599.8272.083080
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-6892-3P99.6866.401178
HSA-MIR-10394-5P99.6566.831852
HSA-MIR-120599.6566.761826
HSA-MIR-4690-5P99.6566.24813
HSA-MIR-58799.6470.862611
HSA-MIR-32599.5866.55358
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-444199.4966.563216
HSA-MIR-94099.3766.142064
HSA-MIR-431199.3170.473041
HSA-MIR-6893-5P99.3166.252119
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-6510-5P99.1466.591081
HSA-MIR-807099.0769.301303
HSA-MIR-427099.0266.261987
HSA-MIR-1213598.9970.261814
HSA-MIR-374A-3P98.8767.821531
HSA-MIR-6754-5P98.6065.541627
HSA-MIR-4766-3P98.4867.941347
HSA-MIR-6865-3P97.5464.67684
HSA-MIR-6503-3P93.8766.39348

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
mus_musculusLmntd1ENSMUSG00000054966
rattus_norvegicusLmntd1ENSRNOG00000015910
caenorhabditis_elegansWBGENE00002067

Paralogs (68): KRT33A (ENSG00000006059), VIM (ENSG00000026025), KRT31 (ENSG00000094796), NEFM (ENSG00000104722), KRT23 (ENSG00000108244), KRT37 (ENSG00000108417), KRT32 (ENSG00000108759), KRT18 (ENSG00000111057), LMNB1 (ENSG00000113368), KRT36 (ENSG00000126337), KRT17 (ENSG00000128422), GFAP (ENSG00000131095), KRT34 (ENSG00000131737), KRT33B (ENSG00000131738), NES (ENSG00000132688), PRPH (ENSG00000135406), KRT85 (ENSG00000135443), KRT7 (ENSG00000135480), KRT71 (ENSG00000139648), INA (ENSG00000148798), LMNA (ENSG00000160789), KRT84 (ENSG00000161849), KRT82 (ENSG00000161850), KRT80 (ENSG00000167767), KRT1 (ENSG00000167768), KRT24 (ENSG00000167916), KRT8 (ENSG00000170421), KRT78 (ENSG00000170423), KRT86 (ENSG00000170442), KRT75 (ENSG00000170454), KRT6C (ENSG00000170465), KRT4 (ENSG00000170477), KRT74 (ENSG00000170484), KRT72 (ENSG00000170486), KRT83 (ENSG00000170523), BFSP2 (ENSG00000170819), KRT19 (ENSG00000171345), KRT15 (ENSG00000171346), KRT38 (ENSG00000171360), KRT13 (ENSG00000171401)

Protein

Protein identifiers

Lamin tail domain-containing protein 1Q8N9Z9 (reviewed: Q8N9Z9)

Alternative names: Intermediate filament tail domain-containing protein 1

All UniProt accessions (7): Q8N9Z9, F5H3Q3, F5H5I3, F5H719, F5H8G2, H0YFE3, H0YFH5

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the intermediate filament family.

Isoforms (5)

UniProt IDNamesCanonical?
Q8N9Z9-11yes
Q8N9Z9-22
Q8N9Z9-33
Q8N9Z9-44
Q8N9Z9-55

RefSeq proteins (8): NP_001139199, NP_001139200, NP_001139201, NP_001243195, NP_001339161, NP_001339162, NP_001339163, NP_689803 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001322Lamin_tail_domDomain
IPR036415Lamin_tail_dom_sfHomologous_superfamily
IPR042840LMNTD1Family

Pfam: PF00932

UniProt features (16 total): sequence variant 5, splice variant 5, sequence conflict 2, chain 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N9Z9-F156.950.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 53 (showing top): TGACCTY_ERR1_Q2, GOCC_NUCLEAR_ENVELOPE, GOCC_INTERMEDIATE_FILAMENT_CYTOSKELETON, chr12p12, TCANNTGAY_SREBP1_01, ER_Q6_01, GOCC_ORGANELLE_ENVELOPE, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, RAO_BOUND_BY_SALL4_ISOFORM_B, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, ZWANG_CLASS_2_TRANSIENTLY_INDUCED_BY_EGF, GOCC_SUPRAMOLECULAR_POLYMER, ZBTB18_TARGET_GENES

GO Biological Process (1): cell population proliferation (GO:0008283)

GO Molecular Function (0):

GO Cellular Component (4): nuclear envelope (GO:0005635), cytoplasm (GO:0005737), intermediate filament (GO:0005882), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular process1
nucleus1
endomembrane system1
organelle envelope1
intracellular anatomical structure1
cellular anatomical structure1
intermediate filament cytoskeleton1
polymeric cytoskeletal fiber1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

686 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LMNTD1IRAG2Q12912543
LMNTD1LRRC74BQ6ZQY2528
LMNTD1LRRC18Q8N456510
LMNTD1DNAI7Q6TDU7477
LMNTD1ETFRF1Q6IPR1474
LMNTD1RASSF8Q8NHQ8471
LMNTD1GPR87Q9BY21468
LMNTD1ATP6AP1LQ52LC2461
LMNTD1CSRNP3Q8WYN3453
LMNTD1DTHD1Q6ZMT9439
LMNTD1WDR48Q8TAF3435
LMNTD1FAM114A2Q9NRY5411
LMNTD1LRRC46Q96FV0410
LMNTD1SHCBP1LQ9BZQ2410
LMNTD1BCAT1P54687393

IntAct

2 interactions, top by confidence:

ABTypeScore
Ppsi-mi:“MI:0914”(association)0.350

BioGRID (3): BRCA1 (Two-hybrid), LMNTD1 (Proximity Label-MS), APP (Reconstituted Complex)

ESM2 similar proteins: A2VE56, A6QPH9, I3LHS8, O08781, O14545, O54836, P0C6S7, Q14CM0, Q3SZY7, Q3U2E2, Q497H0, Q4R3D6, Q4R970, Q58D05, Q5F3F2, Q5FWF5, Q5R7S6, Q5RDJ2, Q5U2M7, Q5VT97, Q66J85, Q68FE8, Q69Z69, Q6DGF4, Q6FIF0, Q6N043, Q6P2K3, Q70EL2, Q7Z6G8, Q8BIZ1, Q8IWR0, Q8K214, Q8K387, Q8N7W2, Q8N9Z9, Q8NA31, Q8ND82, Q8QFX1, Q91YD3, Q96B23

Diamond homologs: A0A125S9M5, P11048, P14733, Q4R899, Q8N9Z9, Q9D4C1, A0A125S9M6, A6QQJ3, O76011, O77788, P02542, P02545, P04260, P04261, P04263, P05785, P07197, P08552, P08553, P08928, P09010, P10999, P12839, P13648, P14731, P14732, P15331, P16053, P16275, P20700, P21619, P21807, P21910, P23239, P23565, P35616, P41219, P46660, P48671, P48672

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance54
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1894 predictions. Top by Δscore:

VariantEffectΔscore
12:25503734:TTAC:Tdonor_loss1.0000
12:25503735:TACCT:Tdonor_loss1.0000
12:25503736:A:ACdonor_gain1.0000
12:25503736:AC:Adonor_gain1.0000
12:25503737:C:CTdonor_gain1.0000
12:25503737:CC:Cdonor_gain1.0000
12:25503737:CCT:Cdonor_gain1.0000
12:25503799:CC:Cacceptor_gain1.0000
12:25503800:CC:Cacceptor_gain1.0000
12:25503801:C:CCacceptor_gain1.0000
12:25526097:A:ACdonor_gain1.0000
12:25526098:C:CCdonor_gain1.0000
12:25526760:TATAC:Tdonor_loss1.0000
12:25526761:ATAC:Adonor_loss1.0000
12:25526762:TACT:Tdonor_loss1.0000
12:25526763:ACTC:Adonor_loss1.0000
12:25526765:TCA:Tdonor_loss1.0000
12:25526767:A:ACdonor_gain1.0000
12:25526767:A:Tdonor_loss1.0000
12:25526768:C:CAdonor_gain1.0000
12:25526768:CT:Cdonor_gain1.0000
12:25526768:CTGTT:Cdonor_gain1.0000
12:25526785:G:Adonor_gain1.0000
12:25526951:GAGAA:Gacceptor_gain1.0000
12:25526952:AGAA:Aacceptor_gain1.0000
12:25526953:GAA:Gacceptor_gain1.0000
12:25526954:AA:Aacceptor_gain1.0000
12:25526956:C:CCacceptor_gain1.0000
12:25526956:CTAGA:Cacceptor_loss1.0000
12:25526957:T:Gacceptor_loss1.0000

AlphaMissense

2677 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:25526809:A:GF192S0.994
12:25526851:A:GL178P0.993
12:25520069:C:GA248P0.991
12:25526851:A:TL178H0.991
12:25526217:A:TV206E0.988
12:25526808:G:CF192L0.988
12:25526808:G:TF192L0.988
12:25526810:A:GF192L0.988
12:25526118:A:GL239P0.987
12:25526167:A:GW223R0.987
12:25526167:A:TW223R0.987
12:25526215:A:GW207R0.987
12:25526215:A:TW207R0.987
12:25526848:T:GQ179P0.986
12:25526213:C:AW207C0.985
12:25526213:C:GW207C0.985
12:25526851:A:CL178R0.985
12:25520068:G:TA248E0.984
12:25526816:A:CY190D0.984
12:25526845:T:GQ180P0.984
12:25526899:A:GL162P0.984
12:25526118:A:TL239Q0.983
12:25526809:A:CF192C0.983
12:25526148:A:GF229S0.980
12:25526892:G:CN164K0.980
12:25526892:G:TN164K0.980
12:25526212:C:GA208P0.978
12:25526118:A:CL239R0.976
12:25526935:A:TI150K0.976
12:25526172:A:GF221S0.974

dbSNP variants (sampled 300 via entrez): RS1000005853 (12:25555812 T>C), RS1000010909 (12:25601573 C>A), RS1000023981 (12:25523836 A>G,T), RS1000035930 (12:25570918 C>T), RS1000039449 (12:25561287 T>C), RS1000093333 (12:25520327 A>C), RS1000139663 (12:25523376 C>A,T), RS1000145834 (12:25565322 G>C), RS1000150402 (12:25562466 C>G,T), RS1000154865 (12:25476223 A>G), RS1000159327 (12:25578003 C>A,G), RS1000187137 (12:25496537 G>T), RS1000206582 (12:25564681 G>A), RS1000223845 (12:25642397 C>A,T), RS1000254321 (12:25545284 T>C)

Disease associations

OMIM: gene MIM:617254 | disease phenotypes: MIM:189800

GenCC curated gene-disease

Mondo (1): preeclampsia (MONDO:0005081)

Orphanet (1): Preeclampsia (Orphanet:275555)

HPO phenotypes

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

GWAS associations

7 associations (top):

StudyTraitp-value
GCST003927_3Dysmenorrheic pain6.000000e-07
GCST007136_2Resistant hypertension2.000000e-07
GCST009144_15Disease progression in age-related macular degeneration (adjusted for baseline)3.000000e-06
GCST010120_2Urinary volume5.000000e-06
GCST010725_34Malaria6.000000e-06
GCST010725_77Malaria2.000000e-06
GCST90011898_14Alanine aminotransferase levels3.000000e-08

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007889dysmenorrheic pain measurement
EFO:1002006treatment-resistant hypertension
EFO:0008336disease progression measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
D011225Pre-EclampsiaC12.050.703.395.249

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases methylation1
testosterone undecanoateaffects cotreatment, increases expression1
perfluorooctanoic acidaffects cotreatment, decreases expression1
perfluorooctane sulfonic acidaffects cotreatment, decreases expression1
perfluorohexanesulfonic acidaffects cotreatment, decreases expression1
abrineincreases expression1
Arsenicaffects methylation1
Calcitriolincreases expression1
Tobacco Smoke Pollutiondecreases expression1
Levonorgestrelaffects cotreatment, increases expression1
Asbestos, Crocidoliteaffects methylation1
Antirheumatic Agentsdecreases expression1
Okadaic Acidincreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00117546PHASE4UNKNOWNCardiovascular and Autonomic Reactivity in Women With a History of Pre-eclampsia
NCT00567957PHASE4UNKNOWNRemifentanil for General Anesthesia in Preeclamptics
NCT01030627PHASE4COMPLETEDTreatment Approaches to Preeclampsia
NCT01352234PHASE4COMPLETEDComparison of Doses of Acetylsalicylic Acid in Women With Previous History of Preeclampsia
NCT01361425PHASE4UNKNOWNAnti-Hypertensive Treatment In Stable Pregnant Women With Severe Pre-Eclampsia (Metildopape)
NCT01729468PHASE4COMPLETEDPrevention of Pre-eclampsia and SGA by Low-Dose Aspirin in Nulliparous Women With Abnormal First-trimester Uterine Artery Dopplers
NCT01761916PHASE4COMPLETEDClonidine Versus Captopril for Treatment of Postpartum Very High Blood Pressure
NCT01912677PHASE4COMPLETEDOral Antihypertensive Regimens for Management of Hypertension in Pregnancy
NCT02025426PHASE4TERMINATEDPhenylephrine Versus Ephedrine in Pre-eclampsia
NCT02091401PHASE4COMPLETEDA Trial Comparing Treatment With the Springfusor Infusion Pump to the IV Magnesium Sulfate Regimen
NCT02163655PHASE4COMPLETEDDiuretics for Postpartum High Blood Pressure in Preeclampsia
NCT02338687PHASE4COMPLETEDLow Dose Calcium to Prevent Preeclampsia
NCT02396030PHASE4TERMINATEDDifferent Schemes of Magnesium Sulfate for Preeclampsia
NCT02531490PHASE4UNKNOWNEarly Vascular Adjustments During Hypertensive Pregnancy
NCT02699827PHASE4COMPLETEDAdding MgSO4 to Epidural Levobupivacaine in CS for Patients With Preeclampsia
NCT02835339PHASE4COMPLETEDMagnesium Sulfate in Obese Preeclamptics
NCT02891174PHASE4COMPLETEDThe Effect of Ibuprofen on Post-partum Blood Pressure in Women With Hypertensive Disorders of Pregnancy
NCT02911701PHASE4COMPLETEDEffect of Acetaminophen on Postpartum Blood Pressure Control in Preeclampsia With Severe Features
NCT03171480PHASE4COMPLETEDUse of Nitrous Oxide Donor for Labor Induction in Women With PreEclampsia
NCT03233880PHASE4UNKNOWNImpact of Antichlamydial Treatment on the Rate of Preeclampsia
NCT03237000PHASE4UNKNOWNEffect of Administering Intravenous Magnesium Sulfate on Fetal Cardiotocography and Neonatal Outcome in Preeclamptic Patients
NCT03506724PHASE4COMPLETEDResponse to Anti-hypertensives in Pregnant and Postpartum Patients
NCT03674606PHASE4COMPLETEDTrial of Early Screening Test for Pre-eclampsia and Growth Restriction
NCT03735433PHASE4TERMINATEDThe Effect of Two Aspirin Dosing Strategies for Obese Women at High Risk for Preeclampsia
NCT03824119PHASE4UNKNOWNPostpartum NSAIDS and Maternal Hypertension
NCT04051567PHASE4UNKNOWNLow-dose Aspirin for Prevention of Adverse Pregnancy Outcomes in Twin Pregnancies
NCT04077853PHASE4COMPLETEDProgesterone in Expectantly Managed Early-onset Preeclampsia
NCT04158830PHASE4WITHDRAWNAspirin (ASA) Therapy and Preeclampsia Prevention
NCT04424693PHASE4UNKNOWNComparing the Incidence of Preeclampsia Between Pregnant Women Receiving Tdap Vaccinations at Week 28 or at Week 36
NCT04631627PHASE4UNKNOWNEarly Prediction and Randomised Prevention of Preeclampsia With Low Dose Aspirin in Chinese Cohort
NCT04656665PHASE4UNKNOWNThe Effectiveness of Aspirin on Preventing Pre-eclampsia
NCT04797949PHASE4WITHDRAWNAdherence to Universal Aspirin Compared to Screening Indicated Aspirin for Prevention of Preeclampsia
NCT04908982PHASE4UNKNOWNAspirin for the Prevention of Preeclampsia in Women With Stage 1 Hypertension
NCT05221164PHASE4UNKNOWN162 mg of Aspirin for Prevention of Preeclampsia
NCT05294952PHASE4UNKNOWNco Ihibtory Receptor in Preeclampsia
NCT05514847PHASE4ACTIVE_NOT_RECRUITINGLow Dose Aspirin for Preterm Preeclampsia Preventionmg/day Dose in High-risk Patients
NCT05586373PHASE4COMPLETEDIbuprofen vs Dipyrone After C-section in Preeclampsia
NCT06069102PHASE4COMPLETEDOptimal Blood Pressure Treatment Thresholds Postpartum
NCT06107335PHASE4NOT_YET_RECRUITINGEffect of Albumin Versus Routine Care on Hemodynamic Response and Stability in Patients With Preeclampsia Guided by a Non-invasive Hemodynamic Monitoring System During Cesarean Delivery With Spinal Anesthesia
NCT06281665PHASE4RECRUITINGTreatment With Aspirin After Preeclampsia: TAP Trial
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): preeclampsia