LRRC47

gene
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Also known as KIAA1185RP1-286D6.3

Summary

LRRC47 (leucine rich repeat containing 47, HGNC:29207) is a protein-coding gene on chromosome 1p36.32, encoding Leucine-rich repeat-containing protein 47 (Q8N1G4).

Enables RNA binding activity. Predicted to be involved in phenylalanyl-tRNA aminoacylation.

Source: NCBI Gene 57470 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 81 total
  • Druggable target: yes
  • MANE Select transcript: NM_020710

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29207
Approved symbolLRRC47
Nameleucine rich repeat containing 47
Location1p36.32
Locus typegene with protein product
StatusApproved
AliasesKIAA1185, RP1-286D6.3
Ensembl geneENSG00000130764
Ensembl biotypeprotein_coding
OMIM619154
Entrez57470

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000378251, ENST00000462356, ENST00000479239, ENST00000855510, ENST00000855511, ENST00000855512, ENST00000931368, ENST00000931369, ENST00000931370, ENST00000931371, ENST00000971585

RefSeq mRNA: 1 — MANE Select: NM_020710 NM_020710

CCDS: CCDS51

Canonical transcript exons

ENST00000378251 — 7 exons

ExonStartEnd
ENSE0000089620837839963784111
ENSE0000089621037850873785203
ENSE0000089621337868493787310
ENSE0000112255237785593781336
ENSE0000147685337958623796498
ENSE0000363804637826613782763
ENSE0000369148437815123781601

Expression profiles

Bgee: expression breadth ubiquitous, 287 present calls, max score 98.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 32.3468 / max 189.5829, expressed in 1816 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
996332.34681816

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277198.55gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451197.90gold quality
endothelial cellCL:000011597.89gold quality
gluteal muscleUBERON:000200097.70gold quality
Brodmann (1909) area 23UBERON:001355497.69gold quality
quadriceps femorisUBERON:000137797.66gold quality
tibialis anteriorUBERON:000138597.66gold quality
vastus lateralisUBERON:000137997.65gold quality
gingival epitheliumUBERON:000194997.43gold quality
deltoidUBERON:000147697.13gold quality
triceps brachiiUBERON:000150997.07gold quality
gingivaUBERON:000182897.03gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450296.89gold quality
skeletal muscle tissueUBERON:000113496.82gold quality
gastrocnemiusUBERON:000138896.73gold quality
cerebellar vermisUBERON:000472096.72gold quality
body of tongueUBERON:001187696.72gold quality
muscle organUBERON:000163096.57gold quality
metanephric glomerulusUBERON:000473696.54gold quality
palpebral conjunctivaUBERON:000181296.36gold quality
muscle of legUBERON:000138396.34gold quality
muscle tissueUBERON:000238596.24gold quality
esophagus squamous epitheliumUBERON:000692096.24gold quality
tibiaUBERON:000097996.22gold quality
renal glomerulusUBERON:000007496.19gold quality
mammalian vulvaUBERON:000099796.17gold quality
biceps brachiiUBERON:000150796.17gold quality
seminal vesicleUBERON:000099896.01gold quality
tongueUBERON:000172395.97gold quality
nippleUBERON:000203095.97gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes8.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting LRRC47, 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-371B-5P99.9975.344759
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-589-3P99.9169.622088
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-383-3P99.8565.841359
HSA-MIR-629-3P99.8567.991875
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-4713-5P99.7867.801794
HSA-MIR-129999.7771.242389
HSA-MIR-1273H-5P99.7766.322471
HSA-MIR-2116-3P99.7464.32889
HSA-MIR-30B-3P99.7065.762325
HSA-MIR-3689A-3P99.7065.732306
HSA-MIR-3689B-3P99.7065.712311
HSA-MIR-3689C99.7065.712311
HSA-MIR-6779-5P99.7065.762363
HSA-MIR-875-3P99.6369.472548
HSA-MIR-613499.6365.681537
HSA-MIR-7106-5P99.5367.473574

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriolrrc47ENSDARG00000053138
mus_musculusLrrc47ENSMUSG00000029028
rattus_norvegicusLrrc47ENSRNOG00000024796
caenorhabditis_elegansY54E10A.6WBGENE00021828

Paralogs (1): FARSB (ENSG00000116120)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 47Q8N1G4 (reviewed: Q8N1G4)

All UniProt accessions (2): Q8N1G4, J3KRP5

RefSeq proteins (1): NP_065761* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR005146B3/B4_tRNA-bdDomain
IPR020825Phe-tRNA_synthase-like_B3/B4Homologous_superfamily
IPR025875Leu-rich_rpt_4Repeat
IPR032675LRR_dom_sfHomologous_superfamily
IPR045060Phe-tRNA-ligase_IIc_bsuFamily

Pfam: PF12799, PF13855

UniProt features (62 total): strand 20, helix 13, repeat 7, turn 7, modified residue 6, sequence variant 3, region of interest 2, initiator methionine 1, chain 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
6ZXGELECTRON MICROSCOPY2.6
6ZXEELECTRON MICROSCOPY3
6ZXDELECTRON MICROSCOPY3.2
8XP3ELECTRON MICROSCOPY3.4
6ZXFELECTRON MICROSCOPY3.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N1G4-F177.500.27

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 (6): 2, 315, 431, 509, 518, 520

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 67 (showing top): GOBP_AMINO_ACID_ACTIVATION, GOBP_TRNA_METABOLIC_PROCESS, GOBP_TRANSLATION, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, TIEN_INTESTINE_PROBIOTICS_24HR_UP, HAN_SATB1_TARGETS_DN, SENESE_HDAC3_TARGETS_DN, GOMF_LIGASE_ACTIVITY_FORMING_CARBON_OXYGEN_BONDS, chr1p36, KRIEG_KDM3A_TARGETS_NOT_HYPOXIA, GOMF_CATALYTIC_ACTIVITY_ACTING_ON_RNA, GOMF_CATALYTIC_ACTIVITY_ACTING_ON_A_TRNA, CEBPZ_TARGET_GENES, DACH1_TARGET_GENES, MAFG_TARGET_GENES

GO Biological Process (1): phenylalanyl-tRNA aminoacylation (GO:0006432)

GO Molecular Function (3): RNA binding (GO:0003723), phenylalanine-tRNA ligase activity (GO:0004826), protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
tRNA aminoacylation for protein translation1
nucleic acid binding1
aminoacyl-tRNA ligase activity1
binding1

Protein interactions and networks

STRING

2752 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRRC47RIOK1Q9BRS2612
LRRC47EIF1ADQ8N9N8549
LRRC47CCDC27Q2M243520
LRRC47PJA2O43164487
LRRC47C1orf54Q8WWF1465
LRRC47EIF3CLB5ME19449
LRRC47C1orf174Q8IYL3447
LRRC47CEP104O60308445
LRRC47RIOK2Q9BVS4440
LRRC47SPRYD3Q8NCJ5412
LRRC47RBMS2Q15434406
LRRC47XPO1O14980404
LRRC47KCNH2Q12809403
LRRC47MICU2Q8IYU8403
LRRC47OLA1Q9NTK5402
LRRC47CPSF2Q9P2I0402

IntAct

70 interactions, top by confidence:

ABTypeScore
MED4MED19psi-mi:“MI:0914”(association)0.900
MED20MED19psi-mi:“MI:0914”(association)0.840
CUL4BCOPS2psi-mi:“MI:0914”(association)0.790
RIOK1PRMT5psi-mi:“MI:0914”(association)0.710
LRRC47gagpsi-mi:“MI:0915”(physical association)0.500
LRRC47PLOD1psi-mi:“MI:0915”(physical association)0.400
GNAT3psi-mi:“MI:0915”(physical association)0.400
JUNpsi-mi:“MI:0914”(association)0.350
JUNTPM3psi-mi:“MI:0914”(association)0.350
MAPTC11orf98psi-mi:“MI:0914”(association)0.350
MAPTPOTEFpsi-mi:“MI:0914”(association)0.350
TNFRSF10ANAP1L4psi-mi:“MI:0914”(association)0.350
COPS5FBLL1psi-mi:“MI:0914”(association)0.350
COPS6DDX3Xpsi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
TNIP3RNH1psi-mi:“MI:0914”(association)0.350
USP32psi-mi:“MI:0914”(association)0.350
USP42KPNA3psi-mi:“MI:0914”(association)0.350
BABAM1PYCR3psi-mi:“MI:0914”(association)0.350
ORF4CTDNEP1psi-mi:“MI:0914”(association)0.350
SHTN1psi-mi:“MI:0914”(association)0.350
TNFRSF10Apsi-mi:“MI:0914”(association)0.350
RIN3psi-mi:“MI:0914”(association)0.350
PAK4SNRPEpsi-mi:“MI:0914”(association)0.350
PAK4MCM5psi-mi:“MI:0914”(association)0.350
MAP1LC3Apsi-mi:“MI:0914”(association)0.350
MAP1LC3Bpsi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350

BioGRID (150): EIF2A (Co-fractionation), LRRC47 (Co-fractionation), LRRC47 (Co-fractionation), LRRC47 (Co-fractionation), LRRC47 (Co-fractionation), NAPRT (Co-fractionation), PSMB6 (Co-fractionation), LRRC47 (Affinity Capture-MS), LRRC47 (Proximity Label-MS), LRRC47 (Affinity Capture-MS), LRRC47 (Affinity Capture-MS), LRRC47 (Proximity Label-MS), LRRC47 (Proximity Label-MS), LRRC47 (Affinity Capture-MS), LRRC47 (Affinity Capture-MS)

ESM2 similar proteins: A0A8P0N4K0, A2AB59, B4F7F3, D3YZU1, D3ZD05, O35681, O75427, O95382, P22455, P22607, P40748, P55144, P70218, Q06418, Q14160, Q1LZH7, Q2PS20, Q32P44, Q495M9, Q4ACU6, Q4H4B6, Q505F5, Q5F488, Q61851, Q63ZY3, Q6P9K8, Q6TLK4, Q6ZUM4, Q7KRY7, Q80T11, Q80U72, Q8BH60, Q8BX02, Q8N1G4, Q8TE68, Q8VC03, Q8VHK1, Q8VHK2, Q8WXD9, Q8WXE0

Diamond homologs: A0B993, A1QZU9, A1RYS1, A2ST82, A3CT77, A4FWS3, A4YIL0, A6UPQ4, A6UWT1, A6VGJ4, A7I615, A9AA58, B0R807, B1L7C0, B2S0L6, B5RM71, B5RPL7, B6YTJ3, B7J278, B8GEX4, B9LU47, C3MJ88, C3MYY0, C3N028, C3N8B1, C3NMS5, C4KJ68, C5A5Z0, C6A237, O26864, O28848, O42849, O73984, P57694, P94283, P95960, Q0W0X4, Q12YP2, Q19713, Q2FLL1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 96 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
SARS-CoV-2 modulates host translation machinery516.2×8e-04
Influenza Infection512.7×2e-03
SARS-CoV-1 Infection612.4×7e-04
Signaling by ROBO receptors610.8×9e-04
SARS-CoV-2-host interactions610.3×9e-04
SARS-CoV-2 Infection78.2×9e-04
Major pathway of rRNA processing in the nucleolus and cytosol98.1×4e-04
SARS-CoV Infections75.6×5e-03

GO biological processes:

GO termPartnersFoldFDR
cytoplasmic translation612.9×1e-03
positive regulation of cell growth510.7×6e-03
positive regulation of canonical Wnt signaling pathway59.0×1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance65
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1343 predictions. Top by Δscore:

VariantEffectΔscore
1:3781600:ACC:Aacceptor_loss1.0000
1:3781601:CCT:Cacceptor_gain1.0000
1:3781602:C:CCacceptor_gain1.0000
1:3781602:C:Tacceptor_gain1.0000
1:3781603:T:Cacceptor_gain1.0000
1:3781603:T:TCacceptor_gain1.0000
1:3782656:CCTA:Cdonor_loss1.0000
1:3782657:CTACC:Cdonor_loss1.0000
1:3782660:C:Adonor_loss1.0000
1:3782673:A:ACdonor_gain1.0000
1:3782674:C:CCdonor_gain1.0000
1:3782759:GGTAT:Gacceptor_gain1.0000
1:3782760:GTAT:Gacceptor_gain1.0000
1:3782761:TAT:Tacceptor_gain1.0000
1:3782762:AT:Aacceptor_gain1.0000
1:3782763:TCTG:Tacceptor_loss1.0000
1:3782764:C:CAacceptor_loss1.0000
1:3782764:C:CCacceptor_gain1.0000
1:3782765:T:Aacceptor_loss1.0000
1:3782766:G:Cacceptor_gain1.0000
1:3784108:CAAT:Cacceptor_gain1.0000
1:3784112:C:CCacceptor_gain1.0000
1:3787064:T:TAdonor_gain1.0000
1:3787070:C:CAdonor_gain1.0000
1:3787073:T:TAdonor_gain1.0000
1:3787079:T:TAdonor_gain1.0000
1:3787093:T:TAdonor_gain1.0000
1:3787160:C:CAdonor_gain1.0000
1:3787306:AACGT:Aacceptor_gain1.0000
1:3787307:ACGT:Aacceptor_gain1.0000

AlphaMissense

3707 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:3781560:A:CS485R0.998
1:3781560:A:TS485R0.998
1:3781562:T:GS485R0.998
1:3787290:G:CN212K0.998
1:3787290:G:TN212K0.998
1:3795910:G:CN189K0.998
1:3795910:G:TN189K0.998
1:3795988:A:CN163K0.998
1:3795988:A:TN163K0.998
1:3796150:G:CN109K0.998
1:3796150:G:TN109K0.998
1:3796151:T:AN109I0.998
1:3796313:A:GL55S0.998
1:3781144:A:CY566D0.997
1:3781539:G:CC492W0.997
1:3795866:A:TL204H0.997
1:3796060:G:CN139K0.997
1:3796060:G:TN139K0.997
1:3796061:T:AN139I0.997
1:3796175:A:TL101H0.997
1:3796222:G:CN85K0.997
1:3796222:G:TN85K0.997
1:3796238:A:TL80H0.997
1:3781540:C:TC492Y0.996
1:3785163:G:TA373D0.996
1:3787221:G:CN235K0.996
1:3787221:G:TN235K0.996
1:3787291:T:AN212I0.996
1:3795989:T:AN163I0.996
1:3796062:T:CN139D0.996

dbSNP variants (sampled 300 via entrez): RS1000010436 (1:3784824 C>T), RS1000388489 (1:3794820 C>G), RS1000488149 (1:3789941 G>A), RS1000515827 (1:3790105 G>A), RS1000625061 (1:3786066 C>T), RS1000671680 (1:3781231 T>C), RS1000915190 (1:3795211 T>C), RS1000916168 (1:3780943 T>G), RS1000960846 (1:3785781 A>G), RS1001101341 (1:3786245 C>T), RS1001566744 (1:3782182 A>G), RS1001819343 (1:3780719 C>T), RS1001985844 (1:3796662 C>G,T), RS1002032431 (1:3784909 C>A,T), RS1002094263 (1:3791171 G>A,C,T)

Disease associations

OMIM: gene MIM:619154 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

StudyTraitp-value
GCST001524_16Visceral adipose tissue/subcutaneous adipose tissue ratio2.000000e-06
GCST001525_13Visceral fat2.000000e-06
GCST001525_2Visceral fat2.000000e-06
GCST002041_1Blood trace element (Cu levels)5.000000e-10
GCST004621_2Red cell distribution width7.000000e-21
GCST90002383_142Hematocrit9.000000e-10

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004767visceral:subcutaneous adipose tissue ratio
EFO:0005267serum copper measurement
EFO:0009188Red cell distribution width
EFO:0004348hematocrit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066357 (SINGLE PROTEIN)

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

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.04Kd9.132nMCHEMBL5653589
8.04ED509.132nMCHEMBL5653589
7.68Kd20.68nMCHEMBL3752910
7.68ED5020.68nMCHEMBL3752910

PubChem BioAssay actives

2 with measured affinity, of 4 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148666: Binding affinity to human LRRC47 incubated for 45 mins by Kinobead based pull down assaykd0.0091uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148666: Binding affinity to human LRRC47 incubated for 45 mins by Kinobead based pull down assaykd0.0207uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression2
aristolochic acid Iincreases expression1
FR900359affects phosphorylation1
bisphenol Aincreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, decreases expression1
sodium arseniteaffects cotreatment, increases abundance, increases expression1
cobaltous chlorideincreases expression1
perfluorooctanoic aciddecreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
coumarinaffects phosphorylation1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic aciddecreases expression1
perfluorohexanesulfonic aciddecreases expression1
bisphenol Sincreases expression1
bisphenol AFincreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1
Sunitinibincreases expression1
Adeninedecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Cadmiumdecreases expression1
Caffeineincreases phosphorylation1
Cisplatindecreases expression1
Colchicinedecreases expression1
Doxorubicinincreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651708BindingBinding affinity to human LRRC47 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.