LRRC4C

gene
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Also known as KIAA1580NGL-1

Summary

LRRC4C (leucine rich repeat containing 4C, HGNC:29317) is a protein-coding gene on chromosome 11p12, encoding Leucine-rich repeat-containing protein 4C (Q9HCJ2). May promote neurite outgrowth of developing thalamic neurons.

NGL1 is a specific binding partner for netrin G1 (NTNG1; MIM 608818), which is a member of the netrin family of axon guidance molecules (Lin et al., 2003 [PubMed 14595443]).

Source: NCBI Gene 57689 — RefSeq curated summary.

At a glance

  • GWAS associations: 26
  • Clinical variants (ClinVar): 70 total
  • MANE Select transcript: NM_001258419

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29317
Approved symbolLRRC4C
Nameleucine rich repeat containing 4C
Location11p12
Locus typegene with protein product
StatusApproved
AliasesKIAA1580, NGL-1
Ensembl geneENSG00000148948
Ensembl biotypeprotein_coding
OMIM608817
Entrez57689

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 18 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000278198, ENST00000527150, ENST00000528697, ENST00000530763, ENST00000533474, ENST00000534577, ENST00000901039, ENST00000901040, ENST00000901041, ENST00000901042, ENST00000901043, ENST00000901044, ENST00000966813, ENST00000966814, ENST00000966815, ENST00000966816, ENST00000966817, ENST00000966818, ENST00000966819

RefSeq mRNA: 2 — MANE Select: NM_001258419 NM_001258419, NM_020929

CCDS: CCDS31464

Canonical transcript exons

ENST00000528697 — 7 exons

ExonStartEnd
ENSE000021477014145943141459652
ENSE000021496884064814240648278
ENSE000021627524014080140140853
ENSE000021778874093363540933723
ENSE000021977084031962840319721
ENSE000021993374024151940241598
ENSE000038443024011420940116334

Expression profiles

Bgee: expression breadth ubiquitous, 206 present calls, max score 96.78.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6277 / max 244.0114, expressed in 230 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1194120.5157134
1194060.3103105
1194130.218280
1194070.148469
1194050.113768
1194020.109652
1194140.082850
1194030.067737
1194010.040214
1194040.021310

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277196.78gold quality
buccal mucosa cellCL:000233696.04gold quality
Brodmann (1909) area 23UBERON:001355495.86gold quality
Brodmann (1909) area 46UBERON:000648395.74gold quality
entorhinal cortexUBERON:000272895.22gold quality
postcentral gyrusUBERON:000258194.51gold quality
parietal lobeUBERON:000187294.48gold quality
superior frontal gyrusUBERON:000266194.25gold quality
ventral tegmental areaUBERON:000269192.46gold quality
superior vestibular nucleusUBERON:000722792.01gold quality
occipital lobeUBERON:000202191.82gold quality
lateral globus pallidusUBERON:000247691.66gold quality
primary visual cortexUBERON:000243691.57gold quality
medulla oblongataUBERON:000189691.53gold quality
substantia nigra pars reticulataUBERON:000196690.47gold quality
temporal lobeUBERON:000187189.32gold quality
trigeminal ganglionUBERON:000167588.72gold quality
frontal cortexUBERON:000187088.55gold quality
substantia nigra pars compactaUBERON:000196588.55gold quality
prefrontal cortexUBERON:000045188.35gold quality
neocortexUBERON:000195087.76gold quality
subthalamic nucleusUBERON:000190687.70gold quality
dorsolateral prefrontal cortexUBERON:000983487.60gold quality
cerebral cortexUBERON:000095687.52gold quality
dorsal plus ventral thalamusUBERON:000189787.40gold quality
endothelial cellCL:000011587.39silver quality
dorsal root ganglionUBERON:000004487.15gold quality
corpus callosumUBERON:000233686.88gold quality
ponsUBERON:000098886.69gold quality
inferior vagus X ganglionUBERON:000536386.32gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-HCAD-35yes7201.35
E-HCAD-30yes7035.07
E-GEOD-180759yes5760.13
E-HCAD-25yes5505.16
E-GEOD-84465yes298.34
E-ANND-3no5.63

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting LRRC4C, 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-806899.9873.852376
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-219A-5P99.9173.36735
HSA-MIR-627-3P99.9071.423316
HSA-MIR-153-5P99.8973.866317
HSA-MIR-129-5P99.8870.263273
HSA-MIR-4782-3P99.8873.31735
HSA-MIR-6766-3P99.8873.38732
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-5010-3P99.8370.602357
HSA-MIR-4760-5P99.8069.881619
HSA-MIR-494-3P99.7071.452795
HSA-MIR-806199.6369.441411
HSA-MIR-510-3P99.5470.062965
HSA-MIR-548G-3P99.4868.672159
HSA-MIR-513A-3P99.3970.633620
HSA-MIR-513C-3P99.3970.633620
HSA-MIR-3606-3P99.1169.843254
HSA-MIR-93698.8770.511124
HSA-MIR-508-3P98.6669.62887
HSA-MIR-59998.3266.991037
HSA-MIR-4445-5P97.2166.16832
HSA-MIR-428897.1167.231636
HSA-MIR-569497.0667.70682
HSA-MIR-34697.0166.97662
HSA-MIR-597-5P96.8267.57732
HSA-MIR-616-3P96.8266.99784
HSA-MIR-59296.5967.59817
HSA-MIR-63296.0867.17798

Literature-anchored findings (GeneRIF, showing 4)

  • NGL-1 is most abundant in the striatum and the cerebral cortex–the intermediate and final targets, of thalamocortical axons; surface-bound NGL-1 stimulates, but soluble NGL-1 disrupts, the growth of embryonic thalamic axons. (PMID:14595443)
  • netrin-G1 functions as an important component of the NGL-1 receptor to promote TCA outgrowth and that membrane-bound netrins can participate in receiving axonal signaling pathways. (PMID:14595443)
  • Interaction between the tripartite NGL-1, netrin-G1 and LAR adhesion complex promotes development of excitatory synapses. (PMID:23986473)
  • These data suggest that the proband’s autism may be due to the inheritance of disruptions in both DPP6 and LRRC4C, and may highlight the importance of the netrin G family and potassium channel interacting molecules in neurodevelopmental disorders. (PMID:27759917)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriolrrc4cbENSDARG00000016739
danio_reriolrrc4caENSDARG00000113411
mus_musculusLrrc4cENSMUSG00000050587
rattus_norvegicusLrrc4cENSRNOG00000029798

Paralogs (22): DCN (ENSG00000011465), RTN4R (ENSG00000040608), ASPN (ENSG00000106819), FLRT3 (ENSG00000125848), FLRT1 (ENSG00000126500), LRRC4 (ENSG00000128594), LRRC4B (ENSG00000131409), PODNL1 (ENSG00000132000), LRTM1 (ENSG00000144771), LRRTM1 (ENSG00000162951), LRRC15 (ENSG00000172061), PODN (ENSG00000174348), LRRTM4 (ENSG00000176204), BGN (ENSG00000182492), LRRC19 (ENSG00000184434), FLRT2 (ENSG00000185070), GP1BA (ENSG00000185245), RTN4RL1 (ENSG00000185924), RTN4RL2 (ENSG00000186907), NYX (ENSG00000188937), LRRC66 (ENSG00000188993), LRRTM3 (ENSG00000198739)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 4CQ9HCJ2 (reviewed: Q9HCJ2)

Alternative names: Netrin-G1 ligand

All UniProt accessions (2): Q9HCJ2, E9PLP4

UniProt curated annotations — full annotation on UniProt →

Function. May promote neurite outgrowth of developing thalamic neurons.

Subunit / interactions. Interacts with NTNG1 and WHRN.

Subcellular location. Postsynaptic cell membrane.

Tissue specificity. Highly expressed in the cerebral cortex, including frontal, parietal and occipital lobes. Putamen, amygdala, hippocampus and medulla oblongata show moderate expression. Caudate nucleus and thalamus express small amounts, whereas other brain regions show very weak or no expression.

Domain organisation. The LRR region is both necessary and sufficient for the interaction with NTNG1.

RefSeq proteins (2): NP_001245348, NP_065980 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000372LRRNTDomain
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013098Ig_I-setDomain
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR032675LRR_dom_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR050541LRR_TM_domain-containingFamily

Pfam: PF00560, PF07679, PF13855

UniProt features (49 total): strand 22, repeat 9, turn 7, domain 3, helix 2, signal peptide 1, chain 1, region of interest 1, modified residue 1, disulfide bond 1, transmembrane region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3ZYJX-RAY DIFFRACTION3.25

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HCJ2-F175.920.55

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): 631

Disulfide bonds (1): 375–426

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): MODULE_255, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, MODULE_317, GOBP_NEUROGENESIS, GOBP_CELL_CELL_SIGNALING, GOBP_CELL_CELL_ADHESION, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_SYNAPTIC_SIGNALING, GOBP_REGULATION_OF_NEURON_PROJECTION_DEVELOPMENT, GOBP_CELL_PROJECTION_ORGANIZATION, RIGGI_EWING_SARCOMA_PROGENITOR_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, SENESE_HDAC3_TARGETS_DN, GOCC_POSTSYNAPSE

GO Biological Process (3): regulation of axonogenesis (GO:0050770), modulation of chemical synaptic transmission (GO:0050804), synaptic membrane adhesion (GO:0099560)

GO Molecular Function (3): cell adhesion molecule binding (GO:0050839), cell-cell adhesion mediator activity (GO:0098632), protein binding (GO:0005515)

GO Cellular Component (8): obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), membrane (GO:0016020), Schaffer collateral - CA1 synapse (GO:0098685), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), synapse (GO:0045202), postsynaptic membrane (GO:0045211)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell-cell adhesion2
synapse2
axonogenesis1
regulation of neuron projection development1
regulation of anatomical structure morphogenesis1
chemical synaptic transmission1
regulation of trans-synaptic signaling1
synapse organization1
protein binding1
cell adhesion mediator activity1
binding1
membrane1
cell periphery1
cellular anatomical structure1
postsynaptic density1
postsynaptic membrane1
postsynaptic specialization membrane1
cell junction1
synaptic membrane1
postsynapse1

Protein interactions and networks

STRING

1572 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LRRC4CNTNG2Q96CW9999
LRRC4CNTNG1Q9Y2I2999
LRRC4CWHRNQ9P202898
LRRC4CDLG4P78352897
LRRC4CMYO15AQ9UKN7709
LRRC4CADGRV1Q8WXG9671
LRRC4CMPP1Q00013649
LRRC4CUSH1GQ495M9649
LRRC4CPTPRSQ13332631
LRRC4CNLGN1Q8N2Q7618
LRRC4CNRXN1Q9ULB1618
LRRC4CCDKL5O76039608
LRRC4CUSH2AO75445574
LRRC4CNTN1O95631524
LRRC4CLRRTM1Q86UE6488

IntAct

89 interactions, top by confidence:

ABTypeScore
LRRC4CDOLKpsi-mi:“MI:0915”(physical association)0.740
NTNG1LRRC4Cpsi-mi:“MI:0407”(direct interaction)0.620
LRRC4CNTNG1psi-mi:“MI:0407”(direct interaction)0.620
BRICD5LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
CMTM5LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
SNAP47LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
GJB2LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
CLDN19LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
SMIM1LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
SERTM1LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
CLEC1ALRRC4Cpsi-mi:“MI:0915”(physical association)0.560
LHFPL5LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
TWSG1LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
BMP10LRRC4Cpsi-mi:“MI:0915”(physical association)0.560
MIPLRRC4Cpsi-mi:“MI:0915”(physical association)0.560
AGTRAPLRRC4Cpsi-mi:“MI:0915”(physical association)0.560

BioGRID (98): LRRC4B (Affinity Capture-MS), LRRC4 (Affinity Capture-MS), VLDLR (Affinity Capture-MS), SULF1 (Affinity Capture-MS), SULF2 (Affinity Capture-MS), DVL2 (Affinity Capture-MS), SBF1 (Affinity Capture-MS), UBE2S (Affinity Capture-MS), NCOA5 (Affinity Capture-MS), DOLK (Affinity Capture-MS), NOB1 (Affinity Capture-MS), FSTL1 (Affinity Capture-MS), SLC39A11 (Affinity Capture-MS), BTBD1 (Affinity Capture-MS), MTMR1 (Affinity Capture-MS)

ESM2 similar proteins: C0STK7, C3YZ59, O00206, O15455, O42235, O60938, O62702, O93233, P58727, Q0PV50, Q2V898, Q45R42, Q58A48, Q5BK65, Q5M7S9, Q5TJ59, Q62192, Q65YW8, Q65Z91, Q68Y56, Q6AXL3, Q6DF55, Q6R5N8, Q6R5P0, Q7Z2Q7, Q80X72, Q8BMT4, Q8BZT5, Q8C031, Q8N6Y2, Q8R5M3, Q8SPE8, Q8SPE9, Q965M2, Q99467, Q99MB1, Q99PH1, Q9CQ76, Q9CXD9, Q9DE66

Diamond homologs: A0N0X6, A1KZ92, A2A8L5, A3KNN3, A4IFW2, A4IGL7, A4IIW9, A6H793, A7MBJ4, A8WGA3, B0BNK7, B0V2N1, B3MH43, B3NS99, B4GBH0, B4HNW4, B4KPU0, B4MR28, B4P5Q9, B4QC63, D2HFT7, D3YXG0, D4A1J9, D4ABX8, E9Q7T7, F1MLX5, F1NWE3, F1NY98, O55005, O60469, O75325, O89026, O94779, O95428, P0C6S8, P0C7J6, P10586, P16621, P59034, P59035

SIGNOR signaling

3 interactions.

AEffectBMechanism
CDKL5unknownLRRC4Cphosphorylation
NTNG1“up-regulates activity”LRRC4Cbinding
LRRC4C“up-regulates activity”DLG4binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance62
Likely benign5
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

5533 predictions. Top by Δscore:

VariantEffectΔscore
11:40116331:CAGT:Cacceptor_gain1.0000
11:40286238:A:ACdonor_gain1.0000
11:40286239:C:CCdonor_gain1.0000
11:40319623:CTTA:Cdonor_loss1.0000
11:40319624:TTA:Tdonor_loss1.0000
11:40319625:TA:Tdonor_loss1.0000
11:40319626:A:ACdonor_gain1.0000
11:40319626:ACCTT:Adonor_loss1.0000
11:40319627:C:Adonor_loss1.0000
11:40319627:C:CCdonor_gain1.0000
11:40319627:CCTTA:Cdonor_gain1.0000
11:40319717:TATAC:Tacceptor_gain1.0000
11:40319719:TAC:Tacceptor_gain1.0000
11:40319720:AC:Aacceptor_gain1.0000
11:40319720:ACCT:Aacceptor_loss1.0000
11:40319721:CC:Cacceptor_gain1.0000
11:40319722:C:CCacceptor_gain1.0000
11:40319722:C:CGacceptor_loss1.0000
11:40319723:T:Cacceptor_loss1.0000
11:40325957:AAAG:Adonor_gain1.0000
11:40648137:CTTA:Cdonor_loss1.0000
11:40648139:TA:Tdonor_loss1.0000
11:40648140:A:ACdonor_gain1.0000
11:40648140:A:ATdonor_loss1.0000
11:40648141:C:CCdonor_gain1.0000
11:40648141:CCTG:Cdonor_gain1.0000
11:40648274:AACTC:Aacceptor_gain1.0000
11:40648275:ACTC:Aacceptor_gain1.0000
11:40648276:CTC:Cacceptor_gain1.0000
11:40648276:CTCC:Cacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000000042 (11:40527643 T>G), RS1000003613 (11:41182926 G>A), RS1000004912 (11:40508162 G>A), RS1000007690 (11:41389294 G>A,T), RS1000010453 (11:40591202 C>A,T), RS1000010723 (11:40935413 G>A), RS1000011794 (11:40295677 T>C), RS1000012628 (11:40178710 C>A,T), RS1000017249 (11:40932007 G>A), RS1000018791 (11:40667301 A>G), RS1000019555 (11:41320737 G>A), RS1000033720 (11:40214681 A>G), RS1000034971 (11:40457717 C>T), RS1000036259 (11:41022203 T>C), RS1000036443 (11:40389303 G>T)

Disease associations

OMIM: gene MIM:608817 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

26 associations (top):

StudyTraitp-value
GCST000698_1Osteoporosis-related phenotypes9.000000e-07
GCST001419_10Temperament (bipolar disorder)6.000000e-06
GCST003229_1Survival in colorectal cancer3.000000e-06
GCST003262_382Post bronchodilator FEV11.000000e-06
GCST003264_1612Post bronchodilator FEV1/FVC ratio1.000000e-06
GCST003997_48Myopia9.000000e-66
GCST004863_27Mosquito bite size6.000000e-06
GCST005714_5Cerebrospinal fluid beta-site APP cleaving enzyme levels9.000000e-06
GCST006291_130Spherical equivalent or myopia (age of diagnosis)2.000000e-44
GCST006585_2583Blood protein levels2.000000e-08
GCST007008_5Cerebrospinal fluid p-tau levels9.000000e-07
GCST007323_33Risk-taking tendency (4-domain principal component model)2.000000e-08
GCST007325_79General risk tolerance (MTAG)7.000000e-10
GCST007327_126Smoking status (ever vs never smokers)3.000000e-09
GCST007743_25Iris color (L* coordinate)4.000000e-06
GCST008477_21Emphysema annual change measurement in smokers (adjusted lung density)9.000000e-06
GCST009203_9Cerebellum cortex volume6.000000e-06
GCST009646_4Diastolic blood pressure response to thiazide and thiazide-like diuretics in hypertension5.000000e-08
GCST009962_14High myopia1.000000e-14
GCST010002_235Refractive error1.000000e-175
GCST011831_1Pediatric central nervous system tumors (early onset)(pleiotropy)8.000000e-07
GCST012017_3Mastocytosis (KIT D816V positive)1.000000e-06
GCST012400_11Low myopia vs hyperopia6.000000e-10
GCST012402_33Low myopia3.000000e-10
GCST012490_178Femur bone mineral density x serum urate levels interaction3.000000e-08
GCST013216_1Order dimension in obsessive compulsive disorder6.000000e-06

EFO canonical traits (15, from GWAS)

EFO IDTrait name
EFO:0004365personality trait
EFO:0000714survival time
EFO:0004314forced expiratory volume
EFO:0004713FEV/FVC ratio
EFO:0008378mosquito bite reaction size measurement
EFO:0009179beta-secretase 1 measurement
EFO:0004847age at onset
EFO:0004763p-tau measurement
EFO:0008579risk-taking behaviour
EFO:0004318smoking behavior
EFO:0009764eye colour measurement
EFO:0007626emphysema imaging measurement
EFO:0006945diastolic blood pressure change measurement
EFO:0004531urate measurement
EFO:0007802obsessive-compulsive symptom measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, decreases expression4
trichostatin Aincreases expression, affects cotreatment3
Vorinostataffects cotreatment, increases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Silicon Dioxidedecreases expression, increases expression2
aristolochic acid Idecreases expression1
bisphenol Adecreases methylation1
decabromobiphenyl etherincreases expression1
ethyl-p-hydroxybenzoatedecreases expression1
sodium arseniteincreases expression1
tetrabromobisphenol Aincreases expression1
aflatoxin B2increases methylation1
tetrachlorodianincreases expression1
mesotrioneaffects methylation, increases abundance1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinonedecreases expression1
Allergensdecreases expression1
Benzo(a)pyreneaffects methylation1
Carbamazepineaffects expression1
Formaldehydedecreases expression1
Herbicidesaffects methylation, increases abundance1
Triclosanincreases expression1
Aflatoxin B1affects methylation, decreases methylation1
Particulate Matterincreases expression1

Clinical trials (associated diseases)

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