LRRC34

gene
On this page

Also known as MGC27085

Summary

LRRC34 (leucine rich repeat containing 34, HGNC:28408) is a protein-coding gene on chromosome 3q26.2, encoding Leucine-rich repeat-containing protein 34 (Q8IZ02). Highly expressed in stem cells where it may be involved in regulation of pluripotency.

Predicted to be involved in cell differentiation. Predicted to act upstream of or within gene expression and telomere maintenance. Predicted to be located in cytoplasm and nucleolus.

Source: NCBI Gene 151827 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 75 total
  • Phenotypes (HPO): 1
  • MANE Select transcript: NM_001172779

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28408
Approved symbolLRRC34
Nameleucine rich repeat containing 34
Location3q26.2
Locus typegene with protein product
StatusApproved
AliasesMGC27085
Ensembl geneENSG00000171757
Ensembl biotypeprotein_coding
OMIM619037
Entrez151827

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 7 protein_coding, 5 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000446859, ENST00000518252, ENST00000520726, ENST00000522080, ENST00000522329, ENST00000522526, ENST00000522596, ENST00000522830, ENST00000524054, ENST00000524327, ENST00000528597, ENST00000602774, ENST00000895444, ENST00000895445, ENST00000942564

RefSeq mRNA: 6 — MANE Select: NM_001172779 NM_001172779, NM_001172780, NM_001363888, NM_001370608, NM_001370609, NM_153353

CCDS: CCDS3208, CCDS54672, CCDS87166

Canonical transcript exons

ENST00000446859 — 11 exons

ExonStartEnd
ENSE00001216849169812410169812904
ENSE00001360325169793003169793838
ENSE00001414252169796214169796369
ENSE00003466559169808628169808745
ENSE00003483931169807588169807709
ENSE00003492355169795485169795611
ENSE00003509284169807426169807490
ENSE00003536531169806848169806931
ENSE00003572982169800659169800754
ENSE00003618779169796745169796899
ENSE00003693383169804053169804181

Expression profiles

Bgee: expression breadth ubiquitous, 192 present calls, max score 97.21.

FANTOM5 (CAGE): breadth broad, TPM avg 2.1258 / max 78.0778, expressed in 767 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
455381.2786569
455370.4539243
455360.3021141
455350.091239

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bronchial epithelial cellCL:000232897.21gold quality
bronchusUBERON:000218595.77gold quality
spermCL:000001993.85gold quality
right uterine tubeUBERON:000130290.68gold quality
mucosa of paranasal sinusUBERON:000503090.07gold quality
olfactory segment of nasal mucosaUBERON:000538689.30gold quality
left testisUBERON:000453385.47gold quality
right testisUBERON:000453485.06gold quality
testisUBERON:000047384.47gold quality
oviduct epitheliumUBERON:000480483.29gold quality
ventricular zoneUBERON:000305382.03gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.52gold quality
calcaneal tendonUBERON:000370181.49gold quality
epithelium of nasopharynxUBERON:000195181.11gold quality
fallopian tubeUBERON:000388980.94gold quality
adult organismUBERON:000702380.82gold quality
adenohypophysisUBERON:000219680.72gold quality
pituitary glandUBERON:000000780.32gold quality
caput epididymisUBERON:000435879.55gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099179.47gold quality
nucleus accumbensUBERON:000188279.03gold quality
caudate nucleusUBERON:000187378.63gold quality
hypothalamusUBERON:000189877.43gold quality
Brodmann (1909) area 9UBERON:001354077.34gold quality
C1 segment of cervical spinal cordUBERON:000646977.21gold quality
right frontal lobeUBERON:000281076.65gold quality
anterior cingulate cortexUBERON:000983576.52gold quality
endothelial cellCL:000011575.97gold quality
adipose tissueUBERON:000101375.93gold quality
right coronary arteryUBERON:000162575.89gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting LRRC34, 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-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-428299.9975.366408
HSA-MIR-94499.8270.853042
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-494-3P99.7071.452795
HSA-MIR-46699.6770.852863
HSA-MIR-6513-3P99.5969.771102
HSA-MIR-432899.5771.064094
HSA-MIR-216B-5P97.1666.761126

Literature-anchored findings (GeneRIF, showing 2)

  • LRRC34 is a novel nucleolar protein that is predominantly expressed in pluripotent stem cells. (PMID:24991885)
  • Variants in LRRC34 reveal distinct mechanisms for predisposition to papillary thyroid carcinoma. (PMID:32051256)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriolrrc34ENSDARG00000062235
mus_musculusLrrc34ENSMUSG00000027702
rattus_norvegicusLrrc34ENSRNOG00000027935

Protein

Protein identifiers

Leucine-rich repeat-containing protein 34Q8IZ02 (reviewed: Q8IZ02)

All UniProt accessions (3): Q8IZ02, G3V115, H0YEZ4

UniProt curated annotations — full annotation on UniProt →

Function. Highly expressed in stem cells where it may be involved in regulation of pluripotency. In embryonic stem cells (ESCs), important for normal expression of the pluripotency regulators POU5F1/OCT4 and KLF4. Also important for expression of the ectodermal marker gene NES and the endodermal marker gene GATA4. Promotes stem cell proliferation in vitro.

Subunit / interactions. Interacts with NPM1 and NCL.

Subcellular location. Nucleus. Nucleolus. Cytoplasm.

Isoforms (2)

UniProt IDNamesCanonical?
Q8IZ02-21yes
Q8IZ02-32

RefSeq proteins (6): NP_001166250, NP_001166251, NP_001350817, NP_001357537, NP_001357538, NP_699184 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001611Leu-rich_rptRepeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR052201LRR-containing_regulatorFamily

Pfam: PF13516

UniProt features (11 total): sequence variant 3, repeat 2, sequence conflict 2, chain 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
8J07ELECTRON MICROSCOPY4.1

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IZ02-F186.220.76

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 45 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GOBP_TELOMERE_ORGANIZATION, chr3q26, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, GOCC_NUCLEOLUS, GOBP_DNA_METABOLIC_PROCESS, DODD_NASOPHARYNGEAL_CARCINOMA_DN, HATADA_METHYLATED_IN_LUNG_CANCER_UP, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, MIKKELSEN_ES_ICP_WITH_H3K4ME3, RAO_BOUND_BY_SALL4_ISOFORM_B, STK33_SKM_DN, ZNF436_TARGET_GENES, ZNF585B_TARGET_GENES

GO Biological Process (4): telomere maintenance (GO:0000723), gene expression (GO:0010467), cell differentiation (GO:0030154), biological_process (GO:0008150)

GO Molecular Function (2): molecular_function (GO:0003674), protein binding (GO:0005515)

GO Cellular Component (4): nucleolus (GO:0005730), cytoplasm (GO:0005737), cellular_component (GO:0005575), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA metabolic process1
telomere organization1
macromolecule biosynthetic process1
cellular developmental process1
binding1
nuclear lumen1
intracellular membraneless organelle1
intracellular anatomical structure1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

663 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRRC34MYNNQ9NPC7810
LRRC34LRRIQ4A6NIV6731
LRRC34ACTRT3Q9BYD9669
LRRC34LRRC31Q6UY01621
LRRC34LRRC23Q53EV4589
LRRC34INSYN2BA6NMK8573
LRRC34CCDC146Q8IYE0571
LRRC34RSPH14Q9UHP6504
LRRC34CFAP161Q6P656502
LRRC34STN1Q9H668500
LRRC34SPATA18Q8TC71482
LRRC34TSNAXIP1Q2TAA8480
LRRC34LYPD6Q86Y78475
LRRC34DNPEPQ9ULA0464
LRRC34CFAP57Q96MR6459

IntAct

4 interactions, top by confidence:

ABTypeScore
LILRB3FAM171A2psi-mi:“MI:0914”(association)0.350
SLC7A9CDC7psi-mi:“MI:0914”(association)0.350

BioGRID (7): LRRC34 (Biochemical Activity), LRRC34 (Affinity Capture-MS), LRRC34 (Affinity Capture-MS), LRRC34 (Proximity Label-MS), LRRC34 (Affinity Capture-MS), LRRC34 (Affinity Capture-MS), LRRC34 (Affinity Capture-RNA)

ESM2 similar proteins: A0JM56, A0JPI9, A2BFL2, A5PK13, A6H639, J9SQF3, O13066, P19686, P33402, Q02108, Q0VAA2, Q14BP6, Q15111, Q15813, Q3USB7, Q498T9, Q4R642, Q4V8D9, Q4ZHS0, Q5DU41, Q5FVQ9, Q5RAG3, Q5RBD9, Q5RJH2, Q5ZIJ9, Q5ZIU8, Q62688, Q68F79, Q6DN12, Q6GQN5, Q6NU09, Q6P9F7, Q6WRX3, Q7Z7L7, Q80ZJ6, Q8BG40, Q8CDU4, Q8CIR4, Q8CIV8, Q8HXA6

Diamond homologs: Q4V8D9, Q8IZ02, Q9DAM1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance60
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1876 predictions. Top by Δscore:

VariantEffectΔscore
3:169796213:CG:Cdonor_gain1.0000
3:169804047:ACT:Adonor_loss1.0000
3:169804048:CTC:Cdonor_loss1.0000
3:169804049:TCACC:Tdonor_loss1.0000
3:169804050:CAC:Cdonor_loss1.0000
3:169804051:A:ACdonor_gain1.0000
3:169804051:ACCAG:Adonor_loss1.0000
3:169804052:C:CCdonor_gain1.0000
3:169804177:TTCTT:Tacceptor_gain1.0000
3:169804178:TCTT:Tacceptor_loss1.0000
3:169804179:CTT:Cacceptor_gain1.0000
3:169804180:TT:Tacceptor_gain1.0000
3:169804181:TCTG:Tacceptor_loss1.0000
3:169804182:C:CCacceptor_gain1.0000
3:169804182:CTGA:Cacceptor_loss1.0000
3:169804183:T:Aacceptor_loss1.0000
3:169806846:A:ACdonor_gain1.0000
3:169806847:C:CCdonor_gain1.0000
3:169795483:A:ACdonor_gain0.9900
3:169795484:C:CCdonor_gain0.9900
3:169795628:C:CTacceptor_gain0.9900
3:169796212:A:ACdonor_gain0.9900
3:169796213:C:CCdonor_gain0.9900
3:169796304:T:TAdonor_gain0.9900
3:169804051:AC:Adonor_gain0.9900
3:169804052:CC:Cdonor_gain0.9900
3:169804052:CCAG:Cdonor_gain0.9900
3:169804121:TTCC:Tdonor_gain0.9900
3:169804122:TCC:Tdonor_gain0.9900
3:169804123:C:CTdonor_gain0.9900

AlphaMissense

3047 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:169796757:A:GL299P0.975
3:169800743:A:CS223R0.973
3:169800743:A:TS223R0.973
3:169800745:T:GS223R0.973
3:169796841:A:GL271P0.966
3:169796282:G:CN332K0.954
3:169796282:G:TN332K0.954
3:169804159:A:GL184P0.953
3:169796868:A:GL262S0.951
3:169796366:G:CN304K0.949
3:169796366:G:TN304K0.949
3:169800681:C:GR244P0.948
3:169796292:A:GL329P0.947
3:169804075:A:GL212S0.945
3:169804111:G:TA200D0.942
3:169804143:G:CN189K0.940
3:169804143:G:TN189K0.940
3:169795603:A:TV358E0.933
3:169796361:A:TI306K0.933
3:169796757:A:TL299H0.933
3:169804059:A:CC217W0.933
3:169796757:A:CL299R0.932
3:169796292:A:CL329R0.931
3:169800720:A:GL231P0.931
3:169795509:G:CN389K0.929
3:169795509:G:TN389K0.929
3:169795593:G:CN361K0.927
3:169795593:G:TN361K0.927
3:169796784:A:GL290P0.926
3:169806861:G:TA172D0.922

dbSNP variants (sampled 300 via entrez): RS1000282146 (3:169796966 A>G,T), RS1000644681 (3:169794815 AGTTG>A), RS1000915757 (3:169813918 T>C), RS1000942253 (3:169810201 A>C), RS1001161481 (3:169792967 A>C), RS1001248304 (3:169810406 GTT>G), RS1001263042 (3:169813650 T>A), RS1001316550 (3:169798131 A>G), RS1001522052 (3:169799587 G>A), RS1001945310 (3:169811358 T>C), RS1002041826 (3:169803955 AG>A), RS1002075731 (3:169814332 C>T), RS1002148818 (3:169812849 G>C), RS1002182548 (3:169807782 G>A,T), RS1002232225 (3:169805434 A>G)

Disease associations

OMIM: gene MIM:619037 | disease phenotypes: MIM:209850, MIM:213300

GenCC curated gene-disease

Mondo (2): autism (MONDO:0005260), Joubert syndrome (MONDO:0018772)

Orphanet (1): Isolated Joubert syndrome (Orphanet:475)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0000717Autism

GWAS associations

14 associations (top):

StudyTraitp-value
GCST001968_1Interstitial lung disease8.000000e-13
GCST002243_3Bladder cancer5.000000e-09
GCST002922_5Multiple myeloma and monoclonal gammopathy7.000000e-06
GCST004144_7Thyroid cancer3.000000e-08
GCST004600_195Eosinophil percentage of white cells6.000000e-15
GCST004617_90Eosinophil percentage of granulocytes5.000000e-15
GCST008721_1Chronic lymphocytic leukemia or multiple sclerosis2.000000e-09
GCST009597_108Multiple sclerosis2.000000e-11
GCST009758_14Idiopathic pulmonary fibrosis7.000000e-13
GCST012396_4Multiple myeloma3.000000e-08
GCST90002390_172Mean corpuscular hemoglobin2.000000e-12
GCST90002392_318Mean corpuscular volume6.000000e-11
GCST90002393_210Monocyte count3.000000e-09
GCST90002397_85Mean spheric corpuscular volume8.000000e-13

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0007991eosinophil percentage of leukocytes
EFO:0007996eosinophil percentage of granulocytes
EFO:0000768idiopathic pulmonary fibrosis
EFO:0004527mean corpuscular hemoglobin
EFO:0005091monocyte count

MeSH disease descriptors (1)

DescriptorNameTree numbers
D001321Autistic DisorderF03.625.164.113.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, increases expression, affects cotreatment6
trichostatin Aaffects cotreatment, decreases expression, increases expression3
(+)-JQ1 compounddecreases expression3
Air Pollutantsincreases expression, decreases expression, increases abundance3
mercuric bromidedecreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Smokeincreases abundance, increases expression2
Tretinoindecreases expression2
p-Chloromercuribenzoic Acidaffects cotreatment, decreases expression2
methylmercuric chloridedecreases expression1
bisphenol Aaffects cotreatment, increases methylation1
sodium arsenitedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment, decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
NSC 689534affects binding, decreases expression1
Temozolomidedecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Benzo(a)pyreneaffects methylation1
Cadmiumdecreases expression1
Carbamazepineaffects expression1
Coalincreases abundance, increases expression1
Copperaffects binding, decreases expression1
Endosulfanincreases expression1
Lipopolysaccharidesdecreases expression, affects response to substance, increases expression, affects cotreatment1
Nickeldecreases expression1
Rotenonedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Vanadatesdecreases expression1
Particulate Matterincreases abundance, decreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00211796PHASE4COMPLETEDDivalproex Sodium ER in Adult Autism
NCT00391261PHASE4COMPLETEDAn Open-label Trial of Metformin for Weight Control of Pediatric Patients on Antipsychotic Medications.
NCT00409747PHASE4COMPLETEDMinocycline to Treat Childhood Regressive Autism
NCT00576732PHASE4COMPLETEDA Study of the Effectiveness and Safety of Two Doses of Risperidone in the Treatment of Children and Adolescents With Autistic Disorder
NCT00844753PHASE4COMPLETEDAtomoxetine, Placebo and Parent Management Training in Autism
NCT01028820PHASE4COMPLETEDFMRI Brain Activation of Aripiprazole Treatment in Autism Spectrum Disorders
NCT01098383PHASE4UNKNOWNTreatment With Acetyl-Choline Esterase Inhibitors in Children With Autism Spectrum Disorders
NCT01333865PHASE4COMPLETEDA Study of Memantine Hydrochloride (Namenda®) for Cognitive and Behavioral Impairment in Adults With Autism Spectrum Disorders
NCT01337700PHASE4COMPLETEDMilnacipran in Autism and the Functional Locus Coeruleus and Noradrenergic Model of Autism
NCT01695200PHASE4COMPLETEDOmega-3 Fatty Acids in Autism Spectrum Disorders
NCT02069977PHASE4UNKNOWNStudy to Evaluate the Efficacy and Safety of Aripiprazole
NCT02096952PHASE4COMPLETEDMethylphenidate ER Liquid Formulation in Adults With ASD and ADHD
NCT02199925PHASE4UNKNOWNAn Open-Label Study to Evaluate the Efficacy of High-Dose Gammaplex in Children on the Autism Spectrum
NCT02235467PHASE4COMPLETEDMultisite Study: Parental Training Using Video Modelling to Develop Social Skills in Children With Autism
NCT02255565PHASE4COMPLETEDDose Response Effects of Quillivant XR in Children With ADHD and Autism: A Pilot Study
NCT02940574PHASE4COMPLETEDNeural and Behavioral Effects of Oxytocin in Autism Spectrum Disorders
NCT03333629PHASE4COMPLETEDPromoting Positive Outcomes for Individuals With ASD: Linking Early Detection, Treatment, and Long-term Outcomes
NCT03337646PHASE4COMPLETEDEvaluation of the Effect and Safety of Lisdexamfetamine in Children Aged 6-12 With ADHD and Autism
NCT03538431PHASE4COMPLETEDImproving Driving in Young People With Autism Spectrum Disorders
NCT03757585PHASE4COMPLETEDNatural Treatments for the Management of Emotional Dysregulation in Youth With Non-verbal Learning Disability (NVLD) and/or Autism Spectrum Disorders (ASD)
NCT04903353PHASE4COMPLETEDPragmatic Trial Comparing Weight Gain in Children With Autism Taking Risperidone Versus Aripiprazole
NCT05063656PHASE4COMPLETEDBiomarker-Driven Pharmacological Treatment of Adolescents With Autism Spectrum Disorder With Gabapentin
NCT05146245PHASE4UNKNOWNSafety and Pharmacokinetics of Antipsychotics in Children 2: Studying TDM in an RCT
NCT05916339PHASE4RECRUITINGAWARE: Management of ADHD in Autism Spectrum Disorder
NCT05954052PHASE4TERMINATEDA Study of Glutathione in Children With Autism Spectrum Disorder
NCT06853665PHASE4RECRUITINGThe TEAM Study - Treatment Efficacy for Autism/Attention Using Mixed Amphetamine
NCT07054697PHASE4COMPLETEDPilot-RCT With Individualized Homeopathic Treatment in the Children With Autism Spectrum Disorder
NCT07161804PHASE4COMPLETEDPilot RCT Using Homeopathic Medicines in ASD
NCT07439042PHASE4NOT_YET_RECRUITINGBuspirone for Anxiety in Autistic Youth
NCT00036231PHASE3TERMINATEDSynthetic Human Secretin in Children With Autism and Gastrointestinal Dysfunction
NCT00036244PHASE3COMPLETEDSynthetic Human Secretin in Children With Autism
NCT00065884PHASE3UNKNOWNValproate Response in Aggressive Autistic Adolescents
NCT00065962PHASE3COMPLETEDSecretin for the Treatment of Autism
NCT00252603PHASE3COMPLETEDGalantamine Versus Placebo in Childhood Autism
NCT00346736PHASE3COMPLETEDUse of Acupuncture In Children With Autistic Spectrum Disorder
NCT00352248PHASE3COMPLETEDRandomized Controlled Trial of Acupuncture Versus Sham Acupuncture in Autistic Spectrum Disorder
NCT00352352PHASE3COMPLETEDUse of Acupuncture In Children With Autistic Spectrum Disorder
NCT00355329PHASE3COMPLETEDRandomized Control Trial of Using Tongue Acupuncture in Autistic Spectrum Disorder Using PET Scan for Clinical Correlation
NCT00498173PHASE3COMPLETEDEffectiveness of Atomoxetine in Treating ADHD Symptoms in Children and Adolescents With Autism
NCT00541346PHASE3COMPLETEDA Pilot Study of Daytrana TM in Children With Autism Co-Morbid for Attention Deficit Hyperactivity Disorder (ADHD) Symptoms