LRRC45

gene
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Also known as MGC20806

Summary

LRRC45 (leucine rich repeat containing 45, HGNC:28302) is a protein-coding gene on chromosome 17q25.3, encoding Leucine-rich repeat-containing protein 45 (Q96CN5). Component of the proteinaceous fiber-like linker between two centrioles, required for centrosome cohesion.

Located in cytosol; microtubule organizing center; and plasma membrane.

Source: NCBI Gene 201255 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder (Moderate, GenCC) — +1 more curated relationship
  • GWAS associations: 2
  • Clinical variants (ClinVar): 192 total — 1 pathogenic
  • MANE Select transcript: NM_144999

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28302
Approved symbolLRRC45
Nameleucine rich repeat containing 45
Location17q25.3
Locus typegene with protein product
StatusApproved
AliasesMGC20806
Ensembl geneENSG00000169683
Ensembl biotypeprotein_coding
OMIM621312
Entrez201255

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000306688, ENST00000577638, ENST00000581227, ENST00000582083, ENST00000583302, ENST00000583383, ENST00000891005, ENST00000891006, ENST00000891007, ENST00000891008, ENST00000891009, ENST00000920878, ENST00000920879, ENST00000920880

RefSeq mRNA: 1 — MANE Select: NM_144999 NM_144999

CCDS: CCDS11797

Canonical transcript exons

ENST00000306688 — 17 exons

ExonStartEnd
ENSE000011630088202909382029185
ENSE000011630148202861382028683
ENSE000011630708202689982027011
ENSE000011630798202537982025507
ENSE000011631008202427882024339
ENSE000013220548203060982031151
ENSE000027298998202330582023863
ENSE000035097208203031982030466
ENSE000035182198202500082025178
ENSE000035225148202823482028311
ENSE000035386488202469382024763
ENSE000035657528202839782028508
ENSE000035898858203006582030238
ENSE000036092888202801182028146
ENSE000036173338202954382029635
ENSE000036521288202738682027444
ENSE000036813288202767482027751

Expression profiles

Bgee: expression breadth ubiquitous, 164 present calls, max score 92.71.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.2752 / max 36.7071, expressed in 1564 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1634454.03491556
1634460.2403125

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right uterine tubeUBERON:000130292.71gold quality
right hemisphere of cerebellumUBERON:001489092.14gold quality
cerebellar hemisphereUBERON:000224591.64gold quality
cerebellar cortexUBERON:000212991.44gold quality
mucosa of transverse colonUBERON:000499190.17gold quality
cerebellumUBERON:000203789.77gold quality
olfactory segment of nasal mucosaUBERON:000538687.50gold quality
granulocyteCL:000009487.14gold quality
right lobe of liverUBERON:000111486.73gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.50gold quality
ganglionic eminenceUBERON:000402384.69gold quality
apex of heartUBERON:000209884.40gold quality
tendon of biceps brachiiUBERON:000818884.26gold quality
body of stomachUBERON:000116183.67gold quality
ventricular zoneUBERON:000305383.65gold quality
cortical plateUBERON:000534383.64gold quality
right lobe of thyroid glandUBERON:000111983.10gold quality
lower esophagus mucosaUBERON:003583483.09gold quality
esophagus mucosaUBERON:000246982.54gold quality
minor salivary glandUBERON:000183082.51gold quality
transverse colonUBERON:000115782.39gold quality
right frontal lobeUBERON:000281082.09gold quality
spleenUBERON:000210681.62gold quality
metanephros cortexUBERON:001053381.56gold quality
small intestine Peyer’s patchUBERON:000345481.37gold quality
mouth mucosaUBERON:000372981.18gold quality
body of pancreasUBERON:000115081.12gold quality
skin of abdomenUBERON:000141680.99gold quality
saliva-secreting glandUBERON:000104480.85gold quality
stomachUBERON:000094580.72gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

1 targeting LRRC45, 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-1307-5P72.8961.085

Literature-anchored findings (GeneRIF, showing 1)

  • LRRC45 is a critical component of the proteinaceous linker between two centrioles and is required for centrosome cohesion. (PMID:24035387)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriolrrc45ENSDARG00000014005
mus_musculusLrrc45ENSMUSG00000025145
rattus_norvegicusLrrc45ENSRNOG00000045926

Paralogs (1): CEP83 (ENSG00000173588)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 45Q96CN5 (reviewed: Q96CN5)

All UniProt accessions (2): Q96CN5, J3KTD4

UniProt curated annotations — full annotation on UniProt →

Function. Component of the proteinaceous fiber-like linker between two centrioles, required for centrosome cohesion.

Subunit / interactions. Homomer. Interacts with CROCC/rootletin and CEP250. Interacts with CEP44. Interacts with CCDC102B (via N-terminus).

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome.

Post-translational modifications. Phosphorylated by NEK2 during misosis, phosphorylation reduces centrosomal localization which subsequently leads to centrosome separation.

RefSeq proteins (1): NP_659436* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001611Leu-rich_rptRepeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR052116Centro_Cilium_AssemblyFamily

Pfam: PF13516

UniProt features (9 total): repeat 6, chain 1, coiled-coil region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96CN5-F183.380.42

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): 661

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 66 (showing top): GOCC_MICROTUBULE_ORGANIZING_CENTER, GOCC_CENTROSOME, FISCHER_DREAM_TARGETS, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY, CHENG_IMPRINTED_BY_ESTRADIOL, E2F3_UP.V1_UP, ASH1L_TARGET_GENES, CEBPZ_TARGET_GENES, CREB3L4_TARGET_GENES, FOXN3_TARGET_GENES, HDAC4_TARGET_GENES, HSD17B8_TARGET_GENES, RBM34_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (8): centrosome (GO:0005813), cytosol (GO:0005829), plasma membrane (GO:0005886), ciliary basal body (GO:0036064), sperm midpiece (GO:0097225), sperm principal piece (GO:0097228), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
microtubule organizing center2
sperm flagellum2
binding1
centriole1
cytoplasm1
membrane1
cell periphery1
cilium1
intracellular anatomical structure1
intracellular membraneless organelle1

Protein interactions and networks

STRING

817 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRRC45CROCCQ5TZA2981
LRRC45CNTLNQ9NXG0924
LRRC45CEP250Q9BV73809
LRRC45CEP89Q96ST8782
LRRC45CDK5RAP2Q96SN8766
LRRC45SCLT1Q96NL6665
LRRC45CEP135Q66GS9642
LRRC45GAS2L1Q99501606
LRRC45CEP83Q9Y592605
LRRC45CEP164Q9UPV0603
LRRC45NEK2P51955597
LRRC45FBF1Q8TES7571
LRRC45ERICH5Q6P6B1543
LRRC45CCDC120Q96HB5511
LRRC45NEDD1Q8NHV4506

IntAct

46 interactions, top by confidence:

ABTypeScore
PRMT8SYNCRIPpsi-mi:“MI:0914”(association)0.830
KXD1LRRC45psi-mi:“MI:0915”(physical association)0.670
LRRC45KXD1psi-mi:“MI:0915”(physical association)0.670
CCDC89LRRC45psi-mi:“MI:0915”(physical association)0.670
LRRC45SSX2psi-mi:“MI:0915”(physical association)0.560
SSX7LRRC45psi-mi:“MI:0915”(physical association)0.560
LRRC45SSX7psi-mi:“MI:0915”(physical association)0.560
ALAS1LRRC45psi-mi:“MI:0915”(physical association)0.560
MCCLRRC45psi-mi:“MI:0915”(physical association)0.560
SSX2LRRC45psi-mi:“MI:0915”(physical association)0.560
LRRC45MID2psi-mi:“MI:0915”(physical association)0.560
HTTLRRC45psi-mi:“MI:0915”(physical association)0.560
SCLT1CCDC22psi-mi:“MI:0914”(association)0.420
LRRC45ANXA6psi-mi:“MI:0915”(physical association)0.400
LRRC45UPP1psi-mi:“MI:0915”(physical association)0.400
LRRC45PAK6psi-mi:“MI:0915”(physical association)0.400
LRRC45psi-mi:“MI:0915”(physical association)0.370
THAP11LRRC45psi-mi:“MI:0915”(physical association)0.370
LRRC45ZDHHC17psi-mi:“MI:0915”(physical association)0.370
ENTHD1C1orf226psi-mi:“MI:0914”(association)0.350
CKAP2WDR46psi-mi:“MI:0914”(association)0.350
H2APGNPATpsi-mi:“MI:0914”(association)0.350
PRMT8HNRNPRpsi-mi:“MI:0914”(association)0.350

BioGRID (22): LRRC45 (Two-hybrid), LRRC45 (Two-hybrid), LRRC45 (Two-hybrid), LRRC45 (Affinity Capture-MS), KXD1 (Two-hybrid), UPP1 (Affinity Capture-MS), LRRC45 (Two-hybrid), LRRC45 (Two-hybrid), MCC (Two-hybrid), CCDC89 (Two-hybrid), SSX7 (Two-hybrid), SSX2 (Two-hybrid), SSX2B (Two-hybrid), LRRC45 (Proximity Label-MS), LRRC45 (Affinity Capture-MS)

ESM2 similar proteins: A0JNH6, A1A5D9, A6NC98, A6NGB0, A6NI56, A7YH32, A9X1A5, B0KWC9, B1MTG4, B3EX63, B8JK76, F6XLV1, H7BZ55, P55937, P59242, Q08378, Q0P5D1, Q14980, Q29RS0, Q2KJ21, Q2TAC2, Q3TMW1, Q494R4, Q4QRL3, Q5RD60, Q5TZA2, Q60952, Q6PGZ0, Q6PHN1, Q6QZQ4, Q8CB62, Q8CHW5, Q8CJ40, Q8HZ57, Q8HZ58, Q8HZ59, Q8HZ60, Q8K2I2, Q8N137, Q8TD31

Diamond homologs: P29315, Q5ZI11, Q6B966, Q8CIM1, Q91VI7, Q96CN5

SIGNOR signaling

4 interactions.

AEffectBMechanism
LRRC45“up-regulates activity”CEP250binding
LRRC45“up-regulates activity”CROCCbinding
NEK2“down-regulates activity”LRRC45phosphorylation
CCDC102B“up-regulates activity”LRRC45binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance133
Likely benign35
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3393451NM_144999.4(LRRC45):c.1402-2A>GPathogenic

SpliceAI

2315 predictions. Top by Δscore:

VariantEffectΔscore
17:82023860:G:GTdonor_gain1.0000
17:82023860:GAAGG:Gdonor_loss1.0000
17:82023861:A:Tdonor_gain1.0000
17:82023861:AAG:Adonor_loss1.0000
17:82023864:GTG:Gdonor_loss1.0000
17:82023865:T:Gdonor_loss1.0000
17:82024575:G:GTdonor_gain1.0000
17:82024687:TCCTA:Tacceptor_loss1.0000
17:82024689:CTA:Cacceptor_loss1.0000
17:82024690:TA:Tacceptor_loss1.0000
17:82024691:AG:Aacceptor_gain1.0000
17:82024692:GG:Gacceptor_gain1.0000
17:82024761:GAG:Gdonor_gain1.0000
17:82024995:T:TAacceptor_gain1.0000
17:82024995:TGCA:Tacceptor_loss1.0000
17:82024996:GCAG:Gacceptor_loss1.0000
17:82024997:CAG:Cacceptor_loss1.0000
17:82024998:A:AGacceptor_gain1.0000
17:82024998:AGC:Aacceptor_loss1.0000
17:82024999:G:Aacceptor_loss1.0000
17:82024999:G:GCacceptor_gain1.0000
17:82024999:GC:Gacceptor_gain1.0000
17:82024999:GCC:Gacceptor_gain1.0000
17:82024999:GCCT:Gacceptor_gain1.0000
17:82024999:GCCTC:Gacceptor_gain1.0000
17:82025112:A:Gdonor_gain1.0000
17:82025124:G:GTdonor_gain1.0000
17:82025174:GCTGG:Gdonor_gain1.0000
17:82025175:C:Gdonor_gain1.0000
17:82025177:GG:Gdonor_gain1.0000

AlphaMissense

4346 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
17:82025018:C:AN124K0.994
17:82025018:C:GN124K0.994
17:82025392:T:AN182K0.994
17:82025392:T:GN182K0.994
17:82024698:C:AN96K0.990
17:82024698:C:GN96K0.990
17:82025013:T:AW123R0.990
17:82025013:T:CW123R0.990
17:82025108:C:AN154K0.990
17:82025108:C:GN154K0.990
17:82025391:A:TN182I0.990
17:82025476:C:AN210K0.990
17:82025476:C:GN210K0.990
17:82025098:T:AL151H0.987
17:82025098:T:CL151P0.986
17:82025387:T:AW181R0.986
17:82025387:T:CW181R0.986
17:82025391:A:CN182T0.986
17:82030753:T:AV654D0.986
17:82025015:G:CW123C0.985
17:82025015:G:TW123C0.985
17:82025382:T:CL179P0.984
17:82025017:A:TN124I0.982
17:82025390:A:TN182Y0.981
17:82025113:T:CI156T0.980
17:82025390:A:CN182H0.979
17:82025017:A:CN124T0.976
17:82025106:A:TN154Y0.976
17:82025412:G:AG189D0.976
17:82025016:A:TN124Y0.974

dbSNP variants (sampled 300 via entrez): RS1000218612 (17:82027580 A>C,G,T), RS1000334058 (17:82023022 C>A,G,T), RS1000585646 (17:82026285 G>A), RS1000661885 (17:82021823 G>C), RS1000956484 (17:82026560 T>C), RS1001041313 (17:82029451 C>A,G,T), RS1001060305 (17:82031245 C>G,T), RS1001547112 (17:82023238 C>G), RS1001581258 (17:82023073 C>A,G), RS1001611613 (17:82031546 GCCCCGCCAGCCGCGCGGCCGGGCGCC>G), RS1001885566 (17:82022158 G>A), RS1001916894 (17:82021892 C>T), RS1002121413 (17:82023441 C>T), RS1002573889 (17:82028274 C>G,T), RS1002809921 (17:82026799 C>T)

Disease associations

OMIM: gene MIM:621312 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorderModerateAutosomal recessive
ciliopathyLimitedAutosomal recessive

Mondo (2): ciliopathy (MONDO:0005308), neurodevelopmental disorder (MONDO:0700092)

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST010002_133Refractive error2.000000e-50
GCST011053_11Neuroblastoma (pediatric)3.000000e-17

MeSH disease descriptors (1)

DescriptorNameTree numbers
D065886Neurodevelopmental DisordersF03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, decreases expression3
Cyclosporinedecreases expression2
FR900359decreases phosphorylation1
bisphenol Aaffects expression1
methylparabenincreases expression1
sulforaphanedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
aflatoxin B2increases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
abrinedecreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
NSC 689534affects binding, decreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Atrazinedecreases expression1
Benzo(a)pyreneincreases methylation1
Caffeinedecreases phosphorylation1
Calcitrioldecreases expression, affects cotreatment1
Cannabidioldecreases expression1
Catechinaffects cotreatment, increases expression1
Cisplatinaffects cotreatment, increases expression1
Copperaffects binding, decreases expression1
Lipopolysaccharidesdecreases expression, affects response to substance, increases expression1
Oxygendecreases expression1
Testosteroneaffects cotreatment, decreases expression1
Tobacco Smoke Pollutiondecreases expression1
Urethanedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT00068224Not specifiedCOMPLETEDClinical and Molecular Investigations Into Ciliopathies
NCT04874909Not specifiedCOMPLETEDClassification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT01783041PHASE2/PHASE3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385PHASE2/PHASE3RECRUITINGFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098EARLY_PHASE1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504Not specifiedRECRUITINGStudying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784Not specifiedUNKNOWNHigh Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791Not specifiedCOMPLETEDNutrition and Pregnancy Intervention Study
NCT01942525Not specifiedUNKNOWNInfluence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170Not specifiedCOMPLETEDEtiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649Not specifiedACTIVE_NOT_RECRUITINGEnhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191Not specifiedTERMINATEDBiomarkers, Neurodevelopment and Preterm Infants
NCT02690675Not specifiedCOMPLETEDIron Supplement Effect on Child Development
NCT02694003Not specifiedCOMPLETEDBetter Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894Not specifiedCOMPLETEDFamily Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674Not specifiedUNKNOWNGood Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157Not specifiedCOMPLETEDAnalyzing Retinal Microanatomy in ROP
NCT02898298Not specifiedCOMPLETEDPositive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780Not specifiedUNKNOWNIntroduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293Not specifiedCOMPLETEDn-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644Not specifiedCOMPLETEDImproving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991Not specifiedUNKNOWNEarly Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189Not specifiedTERMINATEDEffect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028Not specifiedCOMPLETEDDevelopmental Origins of Mental Health Disorders
NCT03148782Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104Not specifiedCOMPLETEDNeurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375Not specifiedRECRUITINGSQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism