◎ Sugi Atlas

Atlas / Disease / Lupus nephritis

Lupus nephritis

disease
On this page

Also known as Glomerulonephritides, lupusglomerulonephritis, lupuslupus Glomerulonephritideslupus glomerulonephritislupus NephritidesNephritides, lupusnephritis, lupusSLE nephritis

Summary

Lupus nephritis (MONDO:0005556) is a disease with 24 cohort genes (25 GWAS associations across 6 studies) and 275 clinical trials. Top therapeutic interventions include tacrolimus anhydrous, azathioprine, and cyclophosphamide anhydrous.

At a glance

  • Cohort genes: 24
  • GWAS associations: 25
  • Clinical trials: 275

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namelupus nephritis
Mondo IDMONDO:0005556
EFOEFO:0005761
MeSHD008181
DOIDDOID:0080162
ICD-111815692673
NCITC34789
SNOMED CT68815009
UMLSC0024143
MedGen6147
GARD0010747
Is cancer (heuristic)no

Also known as: Glomerulonephritides, lupus · glomerulonephritis, lupus · lupus Glomerulonephritides · lupus glomerulonephritis · lupus Nephritides · lupus nephritis · Nephritides, lupus · nephritis, lupus · SLE nephritis

Data availability: 25 GWAS associations (6 studies).

Disease family

Classification path: disease › human disease › disease by body system or component › urinary system disorder › kidney disorder › nephritis › glomerulonephritis › lupus nephritis

Related subtypes (19): acute poststreptococcal glomerulonephritis, membranoproliferative glomerulonephritis, exudative glomerulonephritis, proliferative glomerulonephritis, focal embolic glomerulonephritis, anti-basement membrane glomerulonephritis, diffuse glomerulonephritis, subacute glomerulonephritis, mesangial proliferative glomerulonephritis, immune-complex glomerulonephritis, IgA glomerulonephritis, membranous glomerulonephritis, minimal change disease, granulomatosis with polyangiitis, rapidly progressive glomerulonephritis, primary membranoproliferative glomerulonephritis, Pauci-immune glomerulonephritis, immunotactoid glomerulopathy, autoimmune glomerulonephritis

Genetics & variants

GWAS landscape

25 GWAS associations across 6 studies. Top hits map to 19 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs46992592e-07BANK1A0.66
rs10251292e-07HGF - CACNA2D1C3.06
rs26470123e-07HLA-DQB1 - MTCO3P1?1.52
rs80122833e-07NING1.64
rs802821093e-07BACH2T2.61
rs2740685e-07SLC5A11C2.85
rs13649895e-07GSX2 - RPL22P13T3.41
rs1345455e-07TTC28C2.75
rs77734567e-07LNC-LBCS?1.75
rs6011621e-06LINGO2 - ME2P1A3.11
rs78347651e-06SNTB1-AS1 - RPL35AP19T3.15
rs5161191e-06LINC00354 - SOX1-OTG0.38
rs65386782e-06CCDC38, SNRPFA1.57
rs92679722e-06NOTCH4 - TSBP1-AS1A1.85
rs49018472e-06ARMH4T1.48
rs9676162e-06RNU6ATAC13P - LINC02431?1.45
rs7520102e-06HIVEP3?1.75
rs12940282e-06SPSB1?0.29
rs100419353e-06LINC02225 - LINC02101C2.5
rs24781185e-06PRPF18T1.61
rs22361785e-06KIZ, KIZ-AS1?1.47
rs27861115e-06CRB1C2.26
rs170790295e-06RAET1G, RAET1E-AS1, RAET1E-AS1?2.45
rs92638719e-06HCG27G1.7
rs126061169e-06LINC00470 - AIDAP3T0.67

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90244184Song K20225920Genome-wide association study of SNP- and gene-based approaches to identify susceptibility candidates for lupus nephritis in the Han Chinese population.
GCST002479Chung SA20145881,412Lupus nephritis susceptibility loci in women with systemic lupus erythematosus.
GCST012003Bolin K20213770Variants in BANK1 are associated with lupus nephritis of European ancestry.
GCST90728615Chen HY2025740Novel variants in ARID1B, SPSB1, and RAET1-AS shape genetic susceptibility and protection in systemic lupus erythematosus and lupus nephritis.
GCST90705050Lee JC20256327,529Identification of genetic variants associated with lupus nephritis in a Taiwanese cohort through systematic genetic screening.
GCST90705052Lee JC2025630Identification of genetic variants associated with lupus nephritis in a Taiwanese cohort through systematic genetic screening.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding2
Tier 2: splice/UTR0
Tier 3: regulatory0
Tier 4: intronic/intergenic23

MAF distribution

BucketVariants
common (>=0.05)25
low_freq (0.01-0.05)0
rare (<0.01)0
unknown0

Functional consequences

ConsequenceCount
intron_variant15
intergenic_variant7
missense_variant2
non_coding_transcript_exon_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs46992594101801236C>A0.3intron_variantBANK12e-07Tier 4: intronic/intergenic
rs1025129781805617T>C0.05intergenic_variantHGF - CACNA2D12e-07Tier 4: intronic/intergenic
rs2647012632696681T>A,C,G0.05intergenic_variantHLA-DQB1 - MTCO3P13e-07Tier 4: intronic/intergenic
rs80122831450767442A>C,G0.05intron_variantNIN3e-07Tier 4: intronic/intergenic
rs80282109689981124C>A,T0.05intron_variantBACH23e-07Tier 4: intronic/intergenic
rs2740681624887651C>A,G0.05intron_variantSLC5A115e-07Tier 4: intronic/intergenic
rs1364989454145602T>A,C,G0.05intron_variantGSX2 - RPL22P135e-07Tier 4: intronic/intergenic
rs1345452228403092T>C0.05intron_variantTTC285e-07Tier 4: intronic/intergenic
rs7773456619823007T>G0.05intergenic_variantLNC-LBCS7e-07Tier 4: intronic/intergenic
rs601162929632144A>C,G,T0.05intergenic_variantLINGO2 - ME2P11e-06Tier 4: intronic/intergenic
rs78347658121263666G>T0.05intron_variantSNTB1-AS1 - RPL35AP191e-06Tier 4: intronic/intergenic
rs51611913112014681A>G0.05intron_variantLINC00354 - SOX1-OT1e-06Tier 4: intronic/intergenic
rs65386781295867790A>G0.05intron_variantCCDC38, SNRPF2e-06Tier 4: intronic/intergenic
rs9267972632249455A>C,G,T0.05intergenic_variantNOTCH4 - TSBP1-AS12e-06Tier 4: intronic/intergenic
rs49018471458092523C>G,T0.05intron_variantARMH42e-06Tier 4: intronic/intergenic
rs9676164170967071G>A,C,T0.05intergenic_variantRNU6ATAC13P - LINC024312e-06Tier 4: intronic/intergenic
rs752010141627344C>T0.05intron_variantHIVEP32e-06Tier 4: intronic/intergenic
rs129402819304575A>C,G,T0.3intron_variantSPSB12e-06Tier 4: intronic/intergenic
rs10041935557918990A>C,G0.05intron_variantLINC02225 - LINC021013e-06Tier 4: intronic/intergenic
rs24781181013608032C>T0.05intron_variantPRPF185e-06Tier 4: intronic/intergenic
rs22361782021162172T>A,C0.05missense_variantKIZ, KIZ-AS15e-06Tier 1: coding
rs27861111197336969C>A,G,T0.05intron_variantCRB15e-06Tier 4: intronic/intergenic
rs170790296149918194C>G,T0.4missense_variantRAET1G, RAET1E-AS1, RAET1E-AS15e-06Tier 1: coding
rs9263871631202751A>G,T0.05non_coding_transcript_exon_variantHCG279e-06Tier 4: intronic/intergenic
rs12606116181443316C>A,T0.275intergenic_variantLINC00470 - AIDAP39e-06Tier 4: intronic/intergenic

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 20 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 1

Dual-evidence genes (GWAS + Mendelian — highest-confidence targets)

GeneHGNCEvidence routes
BANK1BANK1GWAS, Orphanet

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
ATL1Orphanet:100984Autosomal dominant spastic paraplegia type 3
ATL1Orphanet:36386Hereditary sensory and autonomic neuropathy type 1
NINOrphanet:319675Microcephalic primordial dwarfism, Dauber type
NINOrphanet:808Seckel syndrome
KIZOrphanet:791Retinitis pigmentosa
BANK1Orphanet:536Systemic lupus erythematosus
ASPMOrphanet:2512Autosomal recessive primary microcephaly
CRB1Orphanet:251295Pigmented paravenous retinochoroidal atrophy
CRB1Orphanet:35612Nanophthalmos
CRB1Orphanet:65Leber congenital amaurosis
CRB1Orphanet:791Retinitis pigmentosa
CFHR5Orphanet:329931C3 glomerulonephritis
GSX2Orphanet:319192Diencephalic-mesencephalic junction dysplasia
F13BOrphanet:331Congenital factor XIII deficiency
PDGFRAOrphanet:168940Chronic eosinophilic leukemia
PDGFRAOrphanet:168947Myeloid/lymphoid neoplasm associated with PDGFRA rearrangement
PDGFRAOrphanet:199306Cleft lip/palate
PDGFRAOrphanet:314950Primary hypereosinophilic syndrome
PDGFRAOrphanet:44890Gastrointestinal stromal tumor
PDGFRAOrphanet:585877B-lymphoblastic leukemia/lymphoma with recurrent genetic abnormality

Cohort genes → proteins

24 cohort genes, 23 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only24

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
ATL1HGNC:11231ENSG00000198513Q8WXF7Atlastin-1gwas
XRN2HGNC:12836ENSG00000088930Q9H0D65’-3’ exoribonuclease 2gwas
HIVEP3HGNC:13561ENSG00000127124Q5T1R4Transcription factor HIVEP3gwas
TSBP1HGNC:13922ENSG00000204296Q5SRN2Testis-expressed basic protein 1gwas
NINHGNC:14906ENSG00000100503Q8N4C6Nineingwas
KIZHGNC:15865ENSG00000088970Q2M2Z5Centrosomal protein kizunagwas
PRPF18HGNC:17351ENSG00000165630Q99633Pre-mRNA-splicing factor 18gwas
SAV1HGNC:17795ENSG00000151748Q9H4B6Protein salvador homolog 1gwas
BANK1HGNC:18233ENSG00000153064Q8NDB2B-cell scaffold protein with ankyrin repeatsgwas
ASPMHGNC:19048ENSG00000066279Q8IZT6Abnormal spindle-like microcephaly-associated proteingwas
ARMH4HGNC:19846ENSG00000139971Q86TY3Armadillo-like helical domain-containing protein 4gwas
SLC5A11HGNC:23091ENSG00000158865Q8WWX8Sodium/myo-inositol cotransporter 2gwas
CRB1HGNC:2343ENSG00000134376P82279Protein crumbs homolog 1gwas
CFHR5HGNC:24668ENSG00000134389Q9BXR6Complement factor H-related protein 5gwas
ZBTB41HGNC:24819ENSG00000177888Q5SVQ8Zinc finger and BTB domain-containing protein 41gwas
GSX2HGNC:24959ENSG00000180613Q9BZM3GS homeobox 2gwas
CCDC38HGNC:26843ENSG00000165972Q502W7Coiled-coil domain-containing protein 38gwas
HCG27HGNC:27366ENSG00000206344HLA complex group 27gwas
F13BHGNC:3534ENSG00000143278P05160Coagulation factor XIII B chaingwas
MAP4K5HGNC:6867ENSG00000012983Q9Y4K4Mitogen-activated protein kinase kinase kinase kinase 5gwas
NKX2-2HGNC:7835ENSG00000125820O95096Homeobox protein Nkx-2.2gwas
NKX2-4HGNC:7837ENSG00000125816Q9H2Z4Homeobox protein Nkx-2.4gwas
NOTCH4HGNC:7884ENSG00000204301Q99466Neurogenic locus notch homolog protein 4gwas
PDGFRAHGNC:8803ENSG00000134853P16234Platelet-derived growth factor receptor alphagwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
ATL1Atlastin-1Atlastin-1 (ATL1) is a membrane-anchored GTPase that mediates the GTP-dependent fusion of endoplasmic reticulum (ER) membranes, maintaining the continuous ER network.
XRN25’-3’ exoribonuclease 2Possesses 5’->3’ exoribonuclease activity.
HIVEP3Transcription factor HIVEP3Plays a role of transcription factor; binds to recognition signal sequences (Rss heptamer) for somatic recombination of immunoglobulin and T-cell receptor gene segments; Also binds to the kappa-B motif of gene such as S100A4, involved in c…
NINNineinCentrosomal protein required in the positioning and anchorage of the microtubule minus-end in epithelial cells.
KIZCentrosomal protein kizunaCentrosomal protein required for establishing a robust mitotic centrosome architecture that can endure the forces that converge on the centrosomes during spindle formation.
PRPF18Pre-mRNA-splicing factor 18Participates in the second step of pre-mRNA splicing.
SAV1Protein salvador homolog 1Regulator of STK3/MST2 and STK4/MST1 in the Hippo signaling pathway which plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis.
BANK1B-cell scaffold protein with ankyrin repeatsInvolved in B-cell receptor (BCR)-induced Ca(2+) mobilization from intracellular stores.
ASPMAbnormal spindle-like microcephaly-associated proteinInvolved in mitotic spindle regulation and coordination of mitotic processes.
ARMH4Armadillo-like helical domain-containing protein 4May modulate immune response and may play a role in inflammation.
SLC5A11Sodium/myo-inositol cotransporter 2Involved in the sodium-dependent cotransport of myo-inositol (MI) with a Na(+):MI stoichiometry of 2:1.
CRB1Protein crumbs homolog 1Plays a role in photoreceptor morphogenesis in the retina.
CFHR5Complement factor H-related protein 5Involved in complement regulation.
ZBTB41Zinc finger and BTB domain-containing protein 41May be involved in transcriptional regulation.
GSX2GS homeobox 2Transcription factor that binds 5’-CNAATTAG-3’ DNA sequence and regulates the expression of numerous genes including genes important for brain development.
CCDC38Coiled-coil domain-containing protein 38Essential for male fertility.
F13BCoagulation factor XIII B chainThe B chain of factor XIII is not catalytically active, but is thought to stabilize the A subunits and regulate the rate of transglutaminase formation by thrombin.
MAP4K5Mitogen-activated protein kinase kinase kinase kinase 5May play a role in the response to environmental stress.
NKX2-2Homeobox protein Nkx-2.2Transcriptional activator involved in the development of insulin-producting beta cells in the endocrine pancreas.
NKX2-4Homeobox protein Nkx-2.4Probable transcription factor.
NOTCH4Neurogenic locus notch homolog protein 4Functions as a receptor for membrane-bound ligands Jagged1, Jagged2 and Delta1 to regulate cell-fate determination.
PDGFRAPlatelet-derived growth factor receptor alphaTyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis.

Protein-family classification

Druggable: 6 · Difficult: 8 · Unknown: 10 · Druggable fraction: 0.25

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Complement222.3×0.025
Scaffold/PPI32.2×0.371
Transcription factor51.7×0.371
Kinase22.3×0.375
Antibody/Immunoglobulin11.2×0.794
Other/Unknown100.8×0.945
Enzyme (other)10.5×0.945

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
ATL1Other/UnknownnoGuanylate-bd_N, P-loop_NTPase, G_GB1_RHD3_dom
XRN2Enzyme (other)yes3.1.13.1Xrn1_N, Xrn2/3/4, 5_3_exoribonuclease
HIVEP3Transcription factornoZnf_C2H2_type, Znf_CCHC_HIVEP, Znf_C2H2_sf
TSBP1Other/UnknownnoTSBP1
NINOther/UnknownnoEF_hand_dom, EF-hand-dom_pair
KIZOther/UnknownnoCentrosomal_kizuma
PRPF18Other/UnknownnoPrp18, PRP4-like, PRP4-like_sf
SAV1Scaffold/PPInoWW_dom, SARAH_dom, Sav
BANK1Scaffold/PPInoTIR_dom, DBB_domain, Toll_tir_struct_dom_sf
ASPMAntibody/ImmunoglobulinyesIQ_motif_EF-hand-BS, CH_dom, ARM-like
ARMH4Other/UnknownnoARMH4
SLC5A11Other/UnknownnoNa/solute_symporter, Na/Glc_symporter_sf
CRB1Other/UnknownnoEGF-type_Asp/Asn_hydroxyl_site, EGF, Laminin_G
CFHR5ComplementyesSushi_SCR_CCP_dom, Sushi/SCR/CCP_sf, ComplSys_Reg/VirEntry_Med
ZBTB41Transcription factornoBTB/POZ_dom, SKP1/BTB/POZ_sf, Znf_C2H2_type
GSX2Transcription factornoHD, Homeodomain-like_sf, Homeobox_CS
CCDC38Other/UnknownnoDUF4200, CFAP_domain-containing
HCG27Other/Unknownno
F13BComplementyesSushi_SCR_CCP_dom, Sushi/SCR/CCP_sf, ComplSys_Reg/VirEntry_Med
MAP4K5KinaseyesProt_kinase_dom, CNH_dom, Kinase-like_dom_sf
NKX2-2Transcription factornoHD, Homeodomain-like_sf, Homeobox_CS
NKX2-4Transcription factornoHD, Homeodomain-like_sf, Homeobox_CS
NOTCH4Scaffold/PPInoEGF-type_Asp/Asn_hydroxyl_site, EGF, Notch_dom
PDGFRAKinaseyes2.7.10.1Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, Tyr_kinase_rcpt_3_CS

Expression context

Cohort genes with no expression data: 0.

21 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)2
broad (>20)22
unknown0

Top tissues across cohort

TissueCohort genes
endothelial cell4
Brodmann (1909) area 233
right testis3
calcaneal tendon3
corpus callosum3
secondary oocyte3
male germ line stem cell (sensu Vertebrata) in testis3
ganglionic eminence2
buccal mucosa cell2
left testis2
testis2
sural nerve2
oocyte2
spleen2
ventricular zone2
liver2
right lobe of liver2
middle temporal gyrus1
leukocyte1
monocyte1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
ATL1241ubiquitousmarkermiddle temporal gyrus, Brodmann (1909) area 23, endothelial cell
XRN2248ubiquitousmarkermonocyte, leukocyte, ganglionic eminence
HIVEP3234ubiquitousmarkerbuccal mucosa cell, endothelial cell, Brodmann (1909) area 23
TSBP158tissue_specificyesleft testis, testis, right testis
NIN253ubiquitousmarkeroviduct epithelium, buccal mucosa cell, cardiac muscle of right atrium
KIZ284ubiquitousmarkersperm, germinal epithelium of ovary, male germ cell
PRPF18134ubiquitousmarkercalcaneal tendon, corpus callosum, sural nerve
SAV1278ubiquitousmarkeroocyte, mucosa of paranasal sinus, secondary oocyte
BANK1205broadmarkerlymph node, spleen, vermiform appendix
ASPM176ubiquitousmarkeroocyte, ventricular zone, secondary oocyte
ARMH4198ubiquitousmarkercortical plate, calcaneal tendon, adrenal tissue
SLC5A11125tissue_specificmarkerC1 segment of cervical spinal cord, corpus callosum, substantia nigra
CRB1163broadmarkerganglionic eminence, ventricular zone, endothelial cell
CFHR515tissue_specificmarkerright lobe of liver, liver, male germ line stem cell (sensu Vertebrata) in testis
ZBTB41242ubiquitousmarkerendothelial cell, Brodmann (1909) area 23, epithelial cell of pancreas
GSX258tissue_specificmarkersecondary oocyte, amygdala, superficial temporal artery
CCDC38157tissue_specificmarkerleft testis, right testis, testis
HCG27134broadyesblood, spleen, cerebellar hemisphere
F13B36tissue_specificmarkerright lobe of liver, liver, male germ line stem cell (sensu Vertebrata) in testis
MAP4K5296ubiquitousmarkercorpus callosum, sural nerve, calcaneal tendon
NKX2-2100tissue_specificmarkerinferior vagus X ganglion, subthalamic nucleus, medulla oblongata
NKX2-412tissue_specificyesprimordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis, right testis
NOTCH4132broadmarkerapex of heart, right lung, omental fat pad
PDGFRA289ubiquitousmarkertibia, decidua, synovial joint

Protein interactions among cohort

Intra-cohort edges: 7.

Hub genes (top 10 by interactor count)

SymbolInteractor count
PDGFRA5,186
XRN23,779
ASPM2,949
NOTCH42,670
NIN2,525
NKX2-21,670
HIVEP31,464
SAV11,414
PRPF181,340
ATL11,206

Intra-cohort edges

ABSources
ASPMCRB1string_interaction
CFHR5ZBTB41string_interaction
KIZNKX2-4string_interaction
KIZXRN2string_interaction
NKX2-2NKX2-4string_interaction
NKX2-4XRN2string_interaction
NOTCH4TSBP1string_interaction

Structural data

PDB: 7 · AlphaFold-only: 16 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PDGFRAP1623415
ATL1Q8WXF714
NOTCH4Q994663
F13BP051602
PRPF18Q996331
SAV1Q9H4B61
CRB1P822791

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
CFHR5Q9BXR683.76
SLC5A11Q8WWX882.19
XRN2Q9H0D678.15
MAP4K5Q9Y4K474.15
CCDC38Q502W773.84
NKX2-2O9509664.62
NINQ8N4C664.47
ZBTB41Q5SVQ861.91
BANK1Q8NDB261.25
GSX2Q9BZM361.18
NKX2-4Q9H2Z459.61
KIZQ2M2Z554.82
TSBP1Q5SRN245.58
ARMH4Q86TY343.94
HIVEP3Q5T1R437.25
ASPMQ8IZT6

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 37. Enrichment computed across 24 evidence-associated genes (10 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 10 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Imatinib-resistant PDGFR mutants11142.0×0.006PDGFRA
Sunitinib-resistant PDGFR mutants11142.0×0.006PDGFRA
Regorafenib-resistant PDGFR mutants11142.0×0.006PDGFRA
Sorafenib-resistant PDGFR mutants11142.0×0.006PDGFRA
PDGFR mutants bind TKIs11142.0×0.006PDGFRA
Inositol transporters1380.7×0.016SLC5A11
Regulation of gene expression in endocrine-committed (NEUROG3+) progenitor cells1228.4×0.020NKX2-2
Defective LFNG causes SCDO31228.4×0.020NOTCH4
Pre-NOTCH Processing in the Endoplasmic Reticulum1190.3×0.022NOTCH4
NOTCH4 Activation and Transmission of Signal to the Nucleus1103.8×0.032NOTCH4
Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants187.8×0.032PDGFRA
Signaling by PDGFRA extracellular domain mutants187.8×0.032PDGFRA
Fibrin formation187.8×0.032F13B
Pre-NOTCH Processing in Golgi163.4×0.041NOTCH4
NOTCH4 Intracellular Domain Regulates Transcription157.1×0.042NOTCH4
Signaling by Hippo154.4×0.042SAV1
Regulation of gene expression in beta cells151.9×0.042NKX2-2
Notch-HLH transcription pathway140.8×0.050NOTCH4
Downstream signal transduction138.1×0.051PDGFRA
Nuclear RNA decay130.9×0.059XRN2
Association of TriC/CCT with target proteins during biosynthesis129.3×0.059XRN2
Signaling by PDGF125.4×0.065PDGFRA
Negative regulation of NOTCH4 signaling123.8×0.065NOTCH4
Regulation of Complement cascade123.3×0.065CFHR5
R-HSA-425366118.1×0.077SLC5A11
Regulation of RUNX2 expression and activity118.1×0.077HIVEP3
Constitutive Signaling by Aberrant PI3K in Cancer112.7×0.104PDGFRA
Pre-NOTCH Transcription and Translation112.3×0.104NOTCH4
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling19.7×0.126PDGFRA
mRNA Polyadenylation18.8×0.133XRN2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 22 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
type B pancreatic cell fate commitment1766.0×0.029NKX2-2
negative regulation of asymmetric cell division1766.0×0.029ASPM
ventral spinal cord interneuron fate determination1766.0×0.029NKX2-2
camera-type eye photoreceptor cell development1766.0×0.029CRB1
keratinocyte apoptotic process1766.0×0.029SAV1
regulation of TORC2 signaling1766.0×0.029ARMH4
spindle organization290.1×0.029KIZ, ASPM
neuron fate specification263.8×0.029GSX2, NKX2-2
positive regulation of oligodendrocyte differentiation261.3×0.029GSX2, NKX2-2
generation of catalytic spliceosome for second transesterification step1383.0×0.031PRPF18
pancreatic A cell fate commitment1383.0×0.031NKX2-2
pancreatic PP cell fate commitment1383.0×0.031NKX2-2
forebrain neuroblast division1383.0×0.031ASPM
platelet-derived growth factor receptor-alpha signaling pathway1383.0×0.031PDGFRA
post-embryonic retina morphogenesis in camera-type eye1383.0×0.031CRB1
subpallium neuron fate commitment1383.0×0.031GSX2
centrosome-templated microtubule nucleation1383.0×0.031NIN
negative regulation of neuron differentiation224.7×0.033ASPM, NKX2-2
spinal cord oligodendrocyte cell fate specification1255.3×0.034NKX2-2
positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway1255.3×0.034PDGFRA
establishment of bipolar cell polarity involved in cell morphogenesis1255.3×0.034CRB1
metanephric glomerular capillary formation1255.3×0.034PDGFRA
meiotic spindle assembly1255.3×0.034ASPM
myo-inositol transport1191.5×0.038SLC5A11
hindbrain morphogenesis1191.5×0.038GSX2
positive regulation of keratinocyte apoptotic process1191.5×0.038SAV1
regulation of mesenchymal stem cell differentiation1191.5×0.038PDGFRA
luteolysis1153.2×0.038NOTCH4
endoplasmic reticulum membrane fusion1153.2×0.038ATL1
olfactory bulb interneuron differentiation1153.2×0.038GSX2

Therapeutics

Drugs indicated for this disease

2 approved, 20 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
BelimumabApproved (phase 4)
VoclosporinApproved (phase 4)
AbataceptPhase 3 (in late-stage trials)
Abetimus SodiumPhase 3 (in late-stage trials)
AcetaminophenPhase 3 (in late-stage trials)
AnifrolumabPhase 3 (in late-stage trials)
AtaciceptPhase 3 (in late-stage trials)
AzathioprinePhase 3 (in late-stage trials)
CyclosporinePhase 3 (in late-stage trials)
DiphenhydraminePhase 3 (in late-stage trials)
IanalumabPhase 3 (in late-stage trials)
LeflunomidePhase 3 (in late-stage trials)
MethylprednisolonePhase 3 (in late-stage trials)
MizoribinePhase 3 (in late-stage trials)
Mycophenolate MofetilPhase 3 (in late-stage trials)
Mycophenolic AcidPhase 3 (in late-stage trials)
ObinutuzumabPhase 3 (in late-stage trials)
PrednisolonePhase 3 (in late-stage trials)
PrednisonePhase 3 (in late-stage trials)
RituximabPhase 3 (in late-stage trials)
SecukinumabPhase 3 (in late-stage trials)
Tacrolimus AnhydrousPhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Curcumin, Daratumumab, Dazodalibep, Efgartigimod Alfa, Etanercept, Guselkumab, Iguratimod, Iptacopan, Laquinimod, Narsoplimab, Nipocalimab, Ruplizumab, Sirolimus, Sirukumab, Sodium Chloride, Tamibarotene, Telitacicept, Vunakizumab, Zanubrutinib.

Drug target analysis

Approved (phase 4): 3 · Phase ≥3: 3 · Phased (≥1): 3 · Undrugged: 21

Druggability breadth: 7 of 24 evidence-associated genes (29%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
SLC5A11DAPAGLIFLOZIN
MAP4K5VEMURAFENIB
PDGFRAPONATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
PDGFRA774
MAP4K5674
SLC5A1114
ATL100
XRN200
HIVEP300
TSBP100
NIN00
KIZ00
PRPF1800

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
DAPAGLIFLOZIN4SLC5A11
VEMURAFENIB4MAP4K5
LENVATINIB4MAP4K5, PDGFRA
AXITINIB4MAP4K5, PDGFRA
SORAFENIB4MAP4K5, PDGFRA
NERATINIB4MAP4K5
PALBOCICLIB4MAP4K5
ENTRECTINIB4MAP4K5
VANDETANIB4MAP4K5, PDGFRA
BOSUTINIB4MAP4K5, PDGFRA
GILTERITINIB4MAP4K5
PAZOPANIB4MAP4K5, PDGFRA
NINTEDANIB4MAP4K5, PDGFRA
SUNITINIB4MAP4K5, PDGFRA
DASATINIB4MAP4K5, PDGFRA
QUIZARTINIB4MAP4K5, PDGFRA
CRIZOTINIB4MAP4K5
MIDOSTAURIN4MAP4K5, PDGFRA
GEFITINIB4MAP4K5
PONATINIB4PDGFRA
FEDRATINIB4PDGFRA
TIVOZANIB4PDGFRA
IMATINIB MESYLATE4PDGFRA
INFIGRATINIB PHOSPHATE4PDGFRA
INFIGRATINIB4PDGFRA
REGORAFENIB4PDGFRA
CERITINIB4PDGFRA
NILOTINIB4PDGFRA
NINTEDANIB ESYLATE4PDGFRA
PEXIDARTINIB4PDGFRA

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
PDGFRA1,172Binding:1160, Functional:8, ADMET:4
MAP4K5262Binding:261, Functional:1
F13B3Binding:3
SLC5A112Binding:1, Functional:1
NOTCH42Binding:2
XRN21Binding:1
SAV11Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
XRN23.1.13.1exoribonuclease II
PDGFRA2.7.10.1receptor protein-tyrosine kinase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
MAP4K5262
PDGFRA1,172

Pharmacogenomics

Cohort genes with a PharmGKB record: 24; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

29 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
VEMURAFENIB4MAP4K5
LENVATINIB4MAP4K5, PDGFRA
AXITINIB4MAP4K5, PDGFRA
SORAFENIB4MAP4K5, PDGFRA
NERATINIB4MAP4K5
PALBOCICLIB4MAP4K5
ENTRECTINIB4MAP4K5
VANDETANIB4MAP4K5, PDGFRA
BOSUTINIB4MAP4K5, PDGFRA
GILTERITINIB4MAP4K5
PAZOPANIB4MAP4K5, PDGFRA
NINTEDANIB4MAP4K5, PDGFRA
SUNITINIB4MAP4K5, PDGFRA
DASATINIB4MAP4K5, PDGFRA
QUIZARTINIB4MAP4K5, PDGFRA
CRIZOTINIB4MAP4K5
MIDOSTAURIN4MAP4K5, PDGFRA
GEFITINIB4MAP4K5
PONATINIB4PDGFRA
FEDRATINIB4PDGFRA
TIVOZANIB4PDGFRA
IMATINIB MESYLATE4PDGFRA
INFIGRATINIB PHOSPHATE4PDGFRA
INFIGRATINIB4PDGFRA
REGORAFENIB4PDGFRA
CERITINIB4PDGFRA
NILOTINIB4PDGFRA
NINTEDANIB ESYLATE4PDGFRA
PEXIDARTINIB4PDGFRA

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3SLC5A11, MAP4K5, PDGFRA
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1F13B
DDruggable family + AlphaFold only, no drug3XRN2, ASPM, CFHR5
EDifficult family or no structure, no drug17ATL1, HIVEP3, TSBP1, NIN, KIZ, PRPF18, SAV1, BANK1, ARMH4, CRB1 (+7 more)

Undrugged target profiles

21 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
ATL10—
XRN21—
HIVEP30—
TSBP10—
NIN0—
KIZ0—
PRPF180—
SAV11—
BANK10—
ASPM0—
ARMH40—
CRB10—
CFHR50—
ZBTB410—
GSX20—
CCDC380—
HCG270—
F13B3—
NKX2-20—
NKX2-40—
NOTCH42—

Clinical trials & evidence

Clinical trials

Clinical trials: 275.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified81
PHASE256
PHASE342
PHASE132
PHASE1/PHASE226
PHASE424
EARLY_PHASE19
PHASE2/PHASE35

Top trials by phase / activity

NCTPhaseStatusTitle
NCT05207358PHASE4RECRUITINGMinimizing Glucocorticoid Administration in Patients With Proliferative Lupus Nephritis
NCT05916781PHASE4RECRUITINGEffectiveness of Mycophenolate Mofetil Combined With Tacrolimus for Steroid Tapering in Systemic Lupus Erythematosus
NCT07035834PHASE4NOT_YET_RECRUITINGSGLT-2 Inhibitors on Albuminuria in Chronic Kidney Disease Patients With Lupus Nephritis and ANCA- Associated Vasculitis
NCT07225387PHASE4RECRUITINGSafety and Efficacy of Combination Belimumab and Voclosporin in the Treatment of Proliferative Forms of Lupus Glomerulopathy: Synergy Trial
NCT07323524PHASE4RECRUITINGDapagliflozin in Active Lupus Nephritis
NCT07611214PHASE4RECRUITINGPRESERVE: LUPKYNIS in Combination With Belimumab, Obinutuzumab or Anifrolumab in Patients With Lupus Nephritis
NCT00125307PHASE4COMPLETEDTacrolimus for the Treatment of Systemic Lupus Erythematosus With Membranous Nephritis
NCT00371319PHASE4COMPLETEDComparing the Efficacy of Tacrolimus and Mycophenolate Mofetil for the Initial Therapy of Active Lupus Nephritis
NCT01169857PHASE4WITHDRAWNVelcade for Proliferative Lupus Nephritis
NCT01203709PHASE4COMPLETEDLow-dose Combination of Mycophenolate Mofetil (MMF) and Tacrolimus (Tac) for Refractory Lupus Nephritis
NCT01206569PHASE4COMPLETEDLong-Acting Tacrolimus for the Treatment of Resistant Lupus Nephritis
NCT01316133PHASE4TERMINATEDA Study to Evaluate the Efficacy and Safety of Tacrolimus With Steroid in Korean Lupus Nephritis Patients
NCT02226341PHASE4TERMINATEDACTHar in the Treatment of Lupus Nephritis
NCT02645565PHASE4COMPLETEDComparison of Low Dose Versus High Dose Cyclophosphamide as Induction Therapy in the Treatment of Lupus Nephritis
NCT03214731PHASE4UNKNOWNEfficacy and Safety of Artesunate Plus Standard of Care in Active Lupus Nephritis
NCT03859570PHASE4WITHDRAWNPentoxifylline in Lupus Nephritis
NCT03920059PHASE4TERMINATEDFixed-dose Versus Concentration-controlled Mycophenolate Mofetil for the Treatment of Active Lupus Nephritis
NCT04145687PHASE4UNKNOWNMetformin In Prevention of Lupus Nephritis
NCT04146220PHASE4COMPLETEDEfficacy of Lower Dose Prednisolone in the Induction of Remission of Lupus Nephritis
NCT04424602PHASE4COMPLETEDComparison between2 Drugs in Lupus Nephritis
NCT05495893PHASE4UNKNOWNMMF Versus CYC in the Induction Therapy of Pediatric Active Proliferative LN
NCT05704088PHASE4COMPLETEDSGLT2 Inhibitors Between Reno Protective Effects and Impact on Bone and Mineral Disease Among Lupus Nephritis Patients
NCT05748925PHASE4COMPLETEDCardio Renal Effects of SGLT2 Inhibitors Among Lupus Nephritis Patients
NCT05933213PHASE4UNKNOWNComparing Mescaline Sodium Enteric-coated Tablets vs Morte-mescaline in the Treatment of Adult Lupus Nephritis
NCT04221477PHASE3ACTIVE_NOT_RECRUITINGA Study to Evaluate the Efficacy and Safety of Obinutuzumab in Participants With ISN/RPS 2003 Class III or IV Lupus Nephritis
NCT04702256PHASE3RECRUITINGInduction Therapy for Lupus Nephritis With no Added Oral Steroids: A Trial Comparing Oral Corticosteroids Plus Mycophenolate Mofetil (MMF) Versus Obinutuzumab and MMF
NCT05126277PHASE3ACTIVE_NOT_RECRUITINGSafety, Efficacy and Tolerability of Ianalumab Versus Placebo, Combination With SoC Therapy, in Participants With Active Lupus Nephritis
NCT05138133PHASE3ACTIVE_NOT_RECRUITINGPhase 3 Study of Anifrolumab in Adult Patients With Active Proliferative Lupus Nephritis
NCT06406205PHASE3RECRUITINGA Study of QLG1074 Combined With Background Therapy in Subjects With Active Lupus Nephritis
NCT06711887PHASE3RECRUITINGPhase III Extension Study of Efficacy and Safety of Ianalumab With or Without Study Treatment Withdrawal in Participants With Lupus Nephritis (SIRIUS-LN Extension)
NCT06904729PHASE3RECRUITINGChimeric Antigen Receptors T Cells for Refractory/Recurrent Lupus Nephritis in Children
NCT07201129PHASE3RECRUITINGA Research Trial to Assess if Cenerimod is Efficacious and Safe to Treat Active Lupus Nephritis on Top of Regular Treatment
NCT00035308PHASE3COMPLETEDSafety and Efficacy Study of LJP 394 (Abetimus Sodium) to Treat Lupus Kidney Disease
NCT00089804PHASE3TERMINATEDStudy of LJP 394 in Lupus Patients With History of Renal Disease
NCT00204022PHASE3COMPLETEDMycophenolate Mofetil Versus Azathioprine for Maintenance Therapy of Lupus Nephritis.
NCT00268567PHASE2/PHASE3COMPLETEDInduction Treatment of Proliferative Lupus Nephritis With Leflunomide Combined With Prednisone
NCT00282347PHASE3COMPLETEDA Study to Evaluate the Efficacy and Safety of Rituximab in Subjects With International Society of Nephrology/Renal Pathology Society (ISN/RPS) 2003 Class III or IV Lupus Nephritis
NCT00368264PHASE2/PHASE3TERMINATEDTNF Blockade With Remicade in Active Lupus Nephritis WHO Class V (TRIAL )
NCT00377637PHASE3COMPLETEDA Study of Mycophenolate Mofetil (CellCept) in Management of Patients With Lupus Nephritis.
NCT00404157PHASE3WITHDRAWNA Study to Evaluate the Safety of Rituximab Retreatment in Subjects With Lupus Nephritis Previously Enrolled in Study U2970g

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
TACROLIMUS ANHYDROUS420
AZATHIOPRINE49
CYCLOPHOSPHAMIDE ANHYDROUS49
MYCOPHENOLATE MOFETIL47
MYCOPHENOLIC ACID47
VOCLOSPORIN47
BELIMUMAB46
DIPHENHYDRAMINE44
ABATACEPT43
DEXCHLORPHENIRAMINE43
OBINUTUZUMAB43
ANIFROLUMAB42
BORTEZOMIB42
DAPAGLIFLOZIN42
ALDESLEUKIN41
ARTESUNATE41
CORTICOTROPIN41
DEUCRAVACITINIB41
ENALAPRIL41
ENALAPRIL MALEATE41
FIBRINOLYSIN, HUMAN41
IPTACOPAN41
LEFLUNOMIDE41
METHYLPREDNISOLONE41
MOSUNETUZUMAB41
OBECABTAGENE AUTOLEUCEL41
OCRELIZUMAB41
PEGCETACOPLAN41
PENTOXIFYLLINE41
PREDNISOLONE41

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 73

This page pulls from 73 datasets indexed by BioBTree:

alphafoldantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetcivic_evidenceclingen_dosageclinical_trialsclinvarctd_gene_interactiondbsnpdepmapdiamond_similaritydoidefoensemblentrezesm2_similarityfantom5_genefantom5_promotergardgenccgenerifgogtopdbgtopdb_interactiongwasgwas_studyhgncicd11intactinterpromedgenmeshmimmondomondochildmondoparentncitorphanetpatentpatent_compoundpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assayreactomerefseqrhearnacentralsctidscxa_expressionscxa_gene_experimentsignorstring_interactiontranscriptufeatureumlsuniprot