TLNRD1

gene
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Also known as MGC99595

Summary

TLNRD1 (talin rod domain containing 1, HGNC:13519) is a protein-coding gene on chromosome 15q25.1, encoding Talin rod domain-containing protein 1 (Q9H1K6). Actin-binding protein which may have an oncogenic function and regulates cell proliferation, migration and invasion in cancer cells.

This gene encodes a protein that is regulated by micro RNA MiR-574-3, and is thought to have an oncogenic function in human bladder cancer. A similar gene in mouse is located in a chromosomal region critical for differentiation of mesoderm, which affects embryo patterning and the formation of heart, muscle, blood, skeleton and the urogenital system. The mouse gene is expressed in early development, and in the adult.

Source: NCBI Gene 59274 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 64 total
  • MANE Select transcript: NM_022566

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13519
Approved symbolTLNRD1
Nametalin rod domain containing 1
Location15q25.1
Locus typegene with protein product
StatusApproved
AliasesMGC99595
Ensembl geneENSG00000140406
Ensembl biotypeprotein_coding
OMIM615466
Entrez59274

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000267984

RefSeq mRNA: 1 — MANE Select: NM_022566 NM_022566

CCDS: CCDS10316

Canonical transcript exons

ENST00000267984 — 1 exons

ExonStartEnd
ENSE000009429348100092381005788

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 95.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.0157 / max 133.1378, expressed in 1809 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1480538.42811760
1480545.80001700
1480553.7876970

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ileal mucosaUBERON:000033195.64gold quality
lower lobe of lungUBERON:000894993.59gold quality
cardiac muscle of right atriumUBERON:000337991.34gold quality
left ventricle myocardiumUBERON:000656691.06gold quality
pericardiumUBERON:000240790.88gold quality
epithelium of mammary glandUBERON:000324490.82gold quality
mammary ductUBERON:000176590.81gold quality
pylorusUBERON:000116690.68gold quality
kidney epitheliumUBERON:000481990.11gold quality
pancreatic ductal cellCL:000207989.03gold quality
cerebellar vermisUBERON:000472088.89gold quality
cauda epididymisUBERON:000436088.72gold quality
cardia of stomachUBERON:000116288.68gold quality
corpus epididymisUBERON:000435988.65gold quality
pigmented layer of retinaUBERON:000178288.53gold quality
retinaUBERON:000096688.51gold quality
vena cavaUBERON:000408788.26gold quality
superficial temporal arteryUBERON:000161487.85gold quality
deciduaUBERON:000245087.05gold quality
upper arm skinUBERON:000426387.05silver quality
pharyngeal mucosaUBERON:000035587.00gold quality
parotid glandUBERON:000183186.96silver quality
synovial jointUBERON:000221786.74gold quality
cartilage tissueUBERON:000241886.43gold quality
colonic mucosaUBERON:000031786.30gold quality
myocardiumUBERON:000234986.26silver quality
tracheaUBERON:000312686.25gold quality
inferior vagus X ganglionUBERON:000536386.25gold quality
thymusUBERON:000237086.17gold quality
seminal vesicleUBERON:000099885.91gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes10.79
E-CURD-10no117.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

102 targeting TLNRD1, 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-9-5P100.0072.282361
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-480399.9871.993117
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-314899.9775.066478
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-314399.9371.963104
HSA-MIR-539-5P99.9370.302855
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-449299.8768.253611
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-5582-3P99.8672.484221
HSA-MIR-221-3P99.8671.561329
HSA-MIR-222-3P99.8671.351337

Literature-anchored findings (GeneRIF, showing 2)

  • Authors demonstrate that miR-574-3p is a miRNA with tumor suppressor function and that MESDC1 (which has a potential oncogenic function in BC) may be targeted by miR-574-3p. (PMID:22179486)
  • Talin rod domain-containing protein 1 (TLNRD1) is a novel actin-bundling protein which promotes filopodia formation. (PMID:34264272)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotlnrd1ENSDARG00000079017
mus_musculusTlnrd1ENSMUSG00000070462
rattus_norvegicusTlnrd1ENSRNOG00000012349
drosophila_melanogasterrheaFBGN0260442
caenorhabditis_eleganstln-1WBGENE00006771

Paralogs (2): TLN1 (ENSG00000137076), TLN2 (ENSG00000171914)

Protein

Protein identifiers

Talin rod domain-containing protein 1Q9H1K6 (reviewed: Q9H1K6)

Alternative names: Mesoderm development candidate 1

All UniProt accessions (1): Q9H1K6

UniProt curated annotations — full annotation on UniProt →

Function. Actin-binding protein which may have an oncogenic function and regulates cell proliferation, migration and invasion in cancer cells.

Subunit / interactions. May homodimerize. Interacts with F-actin.

Induction. Down-regulated by microRNA MIR574-3p.

RefSeq proteins (1): NP_072088* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR042799TLNRD1Family
IPR054082Talin_IBS2BDomain

Pfam: PF21896

UniProt features (21 total): helix 12, strand 3, initiator methionine 1, chain 1, turn 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
6XZ3X-RAY DIFFRACTION2.19
6XZ4X-RAY DIFFRACTION2.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H1K6-F188.400.79

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 (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 150 (showing top): AREB6_03, AP4_Q6, CREBP1_Q2, GGGTGGRR_PAX4_03, CAGCTG_AP4_Q5, CREB_Q4, HIF1_Q3, ATF4_Q2, GOMF_ACTIN_BINDING, LEF1_Q6, YAMAZAKI_TCEB3_TARGETS_UP, CCCNNGGGAR_OLF1_01, AP2_Q6_01, ATGTTTC_MIR494, GOCC_ACTIN_FILAMENT_BUNDLE

GO Biological Process (0):

GO Molecular Function (3): actin binding (GO:0003779), identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (1): stress fiber (GO:0001725)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoskeletal protein binding1
protein binding1
binding1
actomyosin1
contractile actin filament bundle1

Protein interactions and networks

STRING

484 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TLNRD1MESDQ14696548
TLNRD1VCLP18206413
TLNRD1KANK1Q14678383
TLNRD1ZNF736B4DX44370
TLNRD1TMC3Q7Z5M5367
TLNRD1ITGB8P26012348
TLNRD1SCAND1P57086344
TLNRD1NALCNQ8IZF0330
TLNRD1UTP3Q9NQZ2330
TLNRD1J3QSS9J3QSS9329
TLNRD1ZNF140P52738323
TLNRD1MOSMOQ8NHV5323
TLNRD1COX19Q49B96320
TLNRD1KANSL1LA0AUZ9317
TLNRD1ILKP57043310

IntAct

23 interactions, top by confidence:

ABTypeScore
CCM2KRIT1psi-mi:“MI:0914”(association)0.960
CCM2TLNRD1psi-mi:“MI:0915”(physical association)0.740
MAFKBACH1psi-mi:“MI:0914”(association)0.730
CDC123EIF2S2psi-mi:“MI:0914”(association)0.710
SH2B2TLNRD1psi-mi:“MI:0915”(physical association)0.560
TLNRD1PICK1psi-mi:“MI:0915”(physical association)0.560
TLNRD1TLNRD1psi-mi:“MI:0915”(physical association)0.560
TLNRD1KRIT1psi-mi:“MI:0914”(association)0.530
PLA2G5MANBApsi-mi:“MI:0914”(association)0.350
CCL15MLYCDpsi-mi:“MI:0914”(association)0.350
AVPR2ATP9Bpsi-mi:“MI:0914”(association)0.350
CHI3L1IGF1Rpsi-mi:“MI:0914”(association)0.350
IL12APTX3psi-mi:“MI:0914”(association)0.350
TLNRD1STK25psi-mi:“MI:0914”(association)0.350
TLNRD1SH2B2psi-mi:“MI:0915”(physical association)0.000
TLNRD1CCM2psi-mi:“MI:0915”(physical association)0.000
TLNRD1PICK1psi-mi:“MI:0915”(physical association)0.000
TLNRD1TLNRD1psi-mi:“MI:0915”(physical association)0.000

BioGRID (16): MESDC1 (Affinity Capture-RNA), MESDC1 (Two-hybrid), MESDC1 (Two-hybrid), MESDC1 (Two-hybrid), SH2B2 (Two-hybrid), MESDC1 (Positive Genetic), MESDC1 (Negative Genetic), CCM2 (Affinity Capture-MS), MESDC1 (Affinity Capture-MS), ITGB1BP1 (Affinity Capture-MS), MESDC1 (Affinity Capture-MS), KRIT1 (Affinity Capture-MS), MESDC1 (Affinity Capture-RNA), MESDC1 (Cross-Linking-MS (XL-MS)), ZNF257 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A3B6UES5, A0A3G2LGI8, D3ZHV2, G8JYB2, O46037, O60437, P0CE94, P0CE95, P11533, P12003, P18206, P19826, P26039, P26231, P26234, P30427, P33338, P35220, P35221, P54939, P85972, P90947, Q02328, Q03001, Q04615, Q15149, Q17162, Q3MHM6, Q54K81, Q54MH2, Q59I72, Q64727, Q6ZWR6, Q71LX4, Q8MSU4, Q91ZU6, Q95XZ0, Q9ERE8, Q9H1K6, Q9MBF8

Diamond homologs: Q9ERE8, Q9H1K6

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 significance59
Likely benign5
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

75 predictions. Top by Δscore:

VariantEffectΔscore
15:81001081:G:GTdonor_gain0.9900
15:81001148:G:GTdonor_gain0.9500
15:81001007:A:Tdonor_gain0.8700
15:81001006:G:GTdonor_gain0.8300
15:81001087:G:GTdonor_gain0.8200
15:81001081:G:Tdonor_gain0.8000
15:81001092:T:Gdonor_gain0.7800
15:81001091:T:TGdonor_gain0.7500
15:81001077:A:Tdonor_gain0.7400
15:81001086:G:Adonor_gain0.7300
15:81001090:G:Adonor_gain0.7300
15:81001238:G:GTdonor_gain0.6900
15:81001082:A:Tdonor_gain0.6800
15:81003298:GCTT:Gdonor_gain0.6700
15:81001084:GCGG:Gdonor_gain0.6600
15:81001089:T:TAdonor_gain0.6600
15:81001056:CCGAG:Cdonor_loss0.6500
15:81001057:CGAG:Cdonor_loss0.6500
15:81001058:GAGGT:Gdonor_loss0.6500
15:81001059:AGG:Adonor_loss0.6500
15:81001060:GGTG:Gdonor_loss0.6500
15:81001061:GTG:Gdonor_loss0.6500
15:81001062:T:Gdonor_loss0.6500
15:81001083:AGCG:Adonor_gain0.6300
15:81001148:G:Tdonor_gain0.6300
15:81001172:C:Tdonor_gain0.6300
15:81001063:G:GTdonor_gain0.5900
15:81001055:TCCGA:Tdonor_loss0.5800
15:81001323:G:Tdonor_gain0.5800
15:81001063:GAA:Gdonor_loss0.5700

AlphaMissense

2305 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:81002532:G:CK87N1.000
15:81002532:G:TK87N1.000
15:81002543:T:CI91T1.000
15:81003143:G:AG291D1.000
15:81002414:C:AA48D0.999
15:81002537:T:AL89H0.999
15:81002537:T:CL89P0.999
15:81002543:T:AI91N0.999
15:81002543:T:GI91S0.999
15:81002636:T:CL122P0.999
15:81002656:G:CA129P0.999
15:81002660:C:AA130D0.999
15:81002662:T:GY131D0.999
15:81002912:T:CF214S0.999
15:81003065:C:AA265D0.999
15:81003139:G:CG290R0.999
15:81003140:G:AG290D0.999
15:81003149:T:CM293T0.999
15:81003150:G:AM293I0.999
15:81003150:G:CM293I0.999
15:81003150:G:TM293I0.999
15:81003151:A:CS294R0.999
15:81003153:C:AS294R0.999
15:81003153:C:GS294R0.999
15:81003164:C:AA298D0.999
15:81003166:T:CC299R0.999
15:81003176:T:CL302P0.999
15:81003277:G:CG336R0.999
15:81003278:G:AG336D0.999
15:81003290:T:CL340P0.999

dbSNP variants (sampled 300 via entrez): RS1001066427 (15:81003631 C>T), RS1001604444 (15:81005747 A>G,T), RS1002230626 (15:81003992 T>A), RS1002361611 (15:80999372 G>A,C), RS1002412511 (15:80999137 T>C,G), RS1002456163 (15:81006050 T>C), RS1002817227 (15:81003063 C>A,T), RS1002881777 (15:81004243 T>G), RS1003557142 (15:81002201 C>A,T), RS1003938731 (15:81006044 A>C,G), RS1004325045 (15:81000628 G>C,T), RS1005037685 (15:81005663 A>C), RS1005588418 (15:81001541 G>C), RS1005817894 (15:80999783 G>A,C,T), RS1005849846 (15:81002756 A>G,T)

Disease associations

OMIM: gene MIM:615466 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): long QT syndrome (MONDO:0002442)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST005951_10Body mass index2.000000e-08
GCST010866_63Coronary artery disease4.000000e-10
GCST011365_109Myocardial infarction7.000000e-07

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004340body mass index

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008133Long QT SyndromeC14.280.067.565; C14.280.123.625; C16.131.240.400.715; C23.550.073.547

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, decreases methylation4
Benzo(a)pyreneincreases expression2
Nickelincreases expression2
Cyclosporineincreases expression2
Aflatoxin B1affects expression, increases expression2
aristolochic acid Iincreases expression1
bisphenol Faffects cotreatment, increases expression1
bisphenol Aincreases expression1
lead acetateincreases expression1
methylparabenincreases expression1
sodium arseniteincreases expression1
cobaltous chloridedecreases expression1
zinc chromatedecreases expression, increases abundance1
ferrous chloridedecreases expression1
cupric chlorideincreases expression1
cupric oxidedecreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression, increases abundance1
ICG 001decreases expression1
eprenetapoptaffects expression, affects reaction1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Vorinostatdecreases expression1
Acetaminophenincreases expression1
Coumestroldecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Estradiolaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Melphalanincreases expression1
Smokedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT02513940PHASE4COMPLETEDInfluence of Testosterone Administration on Drug-Induced QT Interval Prolongation and Torsades de Pointes
NCT03834883PHASE4COMPLETEDReducing the Risk of Drug-Induced QT Interval Lengthening in Women
NCT04169100PHASE4UNKNOWNNovel Form of Acquired Long QT Syndrome
NCT04675788PHASE4COMPLETEDNovel Approaches for Minimizing Drug-Induced QT Interval Lengthening
NCT01648205PHASE2COMPLETEDLong-term Efficacy Study of Sodium Channel Blocker in LQT3 Patients
NCT02412709PHASE2UNKNOWNLong QT Syndrome Screening in Newborns
NCT04581408PHASE2COMPLETEDMutation-specific Therapy for the Long QT Syndrome
NCT00316459PHASE1COMPLETEDStudy Evaluating the Effects of Multiple Oral Doses of ERB-041 on Cardiac Repolarization in Healthy Subjects
NCT01849003PHASE1COMPLETEDStudy of the Effect of GS-6615 in Subjects With LQT-3
NCT02365532PHASE1COMPLETEDEffect of Oral GS-6615 on Dofetilide-Induced QT Prolongation, Safety, and Tolerability in Healthy Adults
NCT02412098PHASE1COMPLETEDPharmacokinetics of Eleclazine in Adults With Normal and Impaired Hepatic Function
NCT02441829PHASE1COMPLETEDPharmacokinetics of Eleclazine in Adults With Normal and Impaired Renal Function
NCT05759962PHASE1COMPLETEDPhase 1 Study of LQT-1213 in Healthy Adults
NCT05906732PHASE1/PHASE2TERMINATEDStudy of LQT-1213 on QTc-induced Prolongation in Healthy Adult Subjects (Part1) and on Congenital Long QT in Patients Diagnosed With Type 2 or 3 Long QT Syndrome (Part 2).
NCT00005176Not specifiedCOMPLETEDLong QT Syndrome-Population Genetics and Cardiac Studies
NCT00005250Not specifiedCOMPLETEDLinkage Study of Long QT Syndrome In An Amish Kindred
NCT00005367Not specifiedCOMPLETEDEpidemiology of Long QTand Asian Sudden Death in Sleep
NCT00221832Not specifiedUNKNOWNMolecular Genetic Screening and Identification of Congenital Arrhythmogenic Diseases
NCT00292032Not specifiedCOMPLETEDRegistry of Unexplained Cardiac Arrest
NCT00335036Not specifiedTERMINATEDPediatric Lead Extractability and Survival Evaluation (PLEASE)
NCT00399412Not specifiedCOMPLETEDECG Signal Collection From Long QT Syndrome, Wide QRS Complexes, Heart Failure, and Cardiac Resynchronization Patients
NCT00488254Not specifiedCOMPLETEDThe Long QT Syndrome in Pregnancy
NCT00588965Not specifiedCOMPLETEDEffect of Beta-blocker Therapy on QTc Response in Exercise and Recovery in Normal Subjects
NCT01705925Not specifiedCOMPLETEDMulticenter Evaluation of Children and Young Adults With Genotype Positive Long QT Syndrome
NCT01903564Not specifiedCOMPLETEDFetal and Neonatal Magnetophysiology
NCT02082431Not specifiedCOMPLETEDDetermine the Incidence of Long QT Amongst a Large Cohort of Subjects Diagnosed With Unilateral or Bilateral Sensorineural Hearing Loss.
NCT02413450Not specifiedENROLLING_BY_INVITATIONDerivation of Human Induced Pluripotent Stem (iPS) Cells to Heritable Cardiac Arrhythmias
NCT02425189Not specifiedCOMPLETEDThe Canadian National Long QT Syndrome Registry
NCT02439645Not specifiedTERMINATEDA Registry to Determine the Clinical and Genetic Risk Factors for Torsade De Pointes
NCT02439658Not specifiedUNKNOWNGenetics of QT Prolongation With Antiarrhythmics
NCT02549664Not specifiedCOMPLETEDExercise in Genetic Cardiovascular Conditions
NCT02581241Not specifiedCOMPLETEDAbnormal QT-Response to the Sudden Tachycardia Provoked by Standing in Individuals With Drug-induced Long QT Syndrome
NCT02680080Not specifiedCOMPLETEDEffect of Grapefruit on QT Interval in Healthy Volunteers and Patients With Congenital Long QT Syndrome
NCT02775513Not specifiedUNKNOWNMetabolism of Patients With Genetically Caused Cardiac Arrhythmia
NCT02814981Not specifiedUNKNOWNHydroxyzine and Risk of Prolongation of QT Interval
NCT02876380Not specifiedCOMPLETEDProspective Identification of Long QT Syndrome in Fetal Life
NCT03182777Not specifiedCOMPLETEDSafety of Local Dental Anesthesia in Patients With Cardiac Channelopathies
NCT03544918Not specifiedCOMPLETEDPrevalence of Congenital Long QT Syndrome and Acquired QT Prolongation in a Hospital Cohort
NCT03642405Not specifiedUNKNOWNDrug-induced Repolarization ECG Changes
NCT03678311Not specifiedCOMPLETEDLong QT Syndrome and Sleep Apnea