LDLRAD4

gene
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Summary

LDLRAD4 (low density lipoprotein receptor class A domain containing 4, HGNC:1224) is a protein-coding gene on chromosome 18p11.21, encoding Low-density lipoprotein receptor class A domain-containing protein 4 (O15165). Functions as a negative regulator of TGF-beta signaling and thereby probably plays a role in cell proliferation, differentiation, apoptosis, motility, extracellular matrix production and immunosuppression.

Enables R-SMAD binding activity. Involved in negative regulation of cell migration; negative regulation of epithelial to mesenchymal transition; and negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway. Located in early endosome membrane.

Source: NCBI Gene 753 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 61 total
  • MANE Select transcript: NM_001378100

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:1224
Approved symbolLDLRAD4
Namelow density lipoprotein receptor class A domain containing 4
Location18p11.21
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000168675
Ensembl biotypeprotein_coding
OMIM606571
Entrez753

Gene structure

Transcript identifiers

Ensembl transcripts: 61 — 40 protein_coding, 15 protein_coding_CDS_not_defined, 3 retained_intron, 3 nonsense_mediated_decay

ENST00000359446, ENST00000361303, ENST00000399848, ENST00000435606, ENST00000585931, ENST00000586207, ENST00000586222, ENST00000586765, ENST00000587344, ENST00000587440, ENST00000587600, ENST00000587757, ENST00000587905, ENST00000590115, ENST00000590308, ENST00000590371, ENST00000592657, ENST00000592812, ENST00000592991, ENST00000593236, ENST00000610087, ENST00000676672, ENST00000676773, ENST00000676815, ENST00000676891, ENST00000677055, ENST00000677304, ENST00000677387, ENST00000677744, ENST00000677867, ENST00000677910, ENST00000678223, ENST00000678309, ENST00000678400, ENST00000678459, ENST00000678556, ENST00000679091, ENST00000679167, ENST00000679177, ENST00000679303, ENST00000896326, ENST00000896327, ENST00000896328, ENST00000896329, ENST00000896330, ENST00000896331, ENST00000896332, ENST00000896333, ENST00000896334, ENST00000896335, ENST00000896336, ENST00000896337, ENST00000896338, ENST00000896339, ENST00000896340, ENST00000943635, ENST00000943636, ENST00000943637, ENST00000943638, ENST00000943639, ENST00000943640

RefSeq mRNA: 16 — MANE Select: NM_001378100 NM_001003674, NM_001003675, NM_001276249, NM_001276251, NM_001378098, NM_001378099, NM_001378100, NM_001378101, NM_001394662, NM_001394663, NM_001394664, NM_001394665, NM_001394666, NM_001394667, NM_181481, NM_181482

CCDS: CCDS32793, CCDS32794, CCDS32795, CCDS42415, CCDS62392, CCDS92439

Canonical transcript exons

ENST00000359446 — 7 exons

ExonStartEnd
ENSE000012694761343824413438384
ENSE000013542971338734113387762
ENSE000014069541327810513278188
ENSE000028216961321876013218988
ENSE000035097271364335913643412
ENSE000035537771362111713621271
ENSE000035840511364512713652751

Expression profiles

Bgee: expression breadth ubiquitous, 272 present calls, max score 97.09.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.9159 / max 594.0381, expressed in 1064 samples.

FANTOM5 promoters (40 alternative TSS)

Promoter IDTPM avgSamples expressed
1695764.0260289
1695262.2763669
1695551.6841395
1695481.0237177
1695300.9266304
1695560.7451298
1695700.7068245
1695680.5946171
1695290.5286197
1695750.4900178

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011597.09gold quality
C1 segment of cervical spinal cordUBERON:000646995.24gold quality
calcaneal tendonUBERON:000370193.67gold quality
spinal cordUBERON:000224093.18gold quality
colonic epitheliumUBERON:000039792.62gold quality
putamenUBERON:000187492.45gold quality
choroid plexus epitheliumUBERON:000391191.93gold quality
primary visual cortexUBERON:000243691.62gold quality
caudate nucleusUBERON:000187391.42gold quality
Brodmann (1909) area 23UBERON:001355490.62gold quality
sural nerveUBERON:001548890.54gold quality
tendonUBERON:000004390.38gold quality
corpus callosumUBERON:000233690.37gold quality
substantia nigraUBERON:000203889.66gold quality
tibiaUBERON:000097989.61gold quality
right atrium auricular regionUBERON:000663189.61gold quality
Brodmann (1909) area 10UBERON:001354188.80gold quality
prostate glandUBERON:000236788.61gold quality
blood vessel layerUBERON:000479788.47gold quality
midbrainUBERON:000189188.34gold quality
body of uterusUBERON:000985388.31gold quality
occipital lobeUBERON:000202188.11gold quality
prefrontal cortexUBERON:000045188.05gold quality
descending thoracic aortaUBERON:000234588.00gold quality
ganglionic eminenceUBERON:000402387.47gold quality
thoracic aortaUBERON:000151587.37gold quality
ascending aortaUBERON:000149687.33gold quality
nucleus accumbensUBERON:000188287.10gold quality
amygdalaUBERON:000187686.90gold quality
thymusUBERON:000237086.88gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-HCAD-30yes1618.13
E-HCAD-4yes56.77
E-HCAD-35yes42.24
E-CURD-119yes31.71
E-HCAD-25yes18.17
E-CURD-122yes15.58
E-CURD-46yes11.67
E-ANND-3yes6.88
E-ANND-2no975.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

197 targeting LDLRAD4, 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-1277-5P100.0073.955056
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-366299.9973.825684
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-607799.9968.042299
HSA-MIR-806899.9873.852376
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-60799.9773.625593
HSA-MIR-493-5P99.9672.472382
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-426799.9666.532368
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-548J-3P99.9472.614881

Literature-anchored findings (GeneRIF, showing 3)

  • Data suggest that C18ORF1 acts as a gatekeeper that abrogates excessive TGF-beta signaling. (PMID:24627487)
  • Depletion of LDLRAD4 in HepG2 liver cancer cells inhibited tumorigenesis in nude mice. These results reveal an oncogenic role of LDLRAD4 in tumorigenesis through its association with Nedd4. (PMID:28888937)
  • Identification of low-density lipoprotein receptor class A domain containing 4 (LDLRAD4) as a prognostic indicator in primary gastrointestinal stromal tumors. (PMID:32507364)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioldlrad4bENSDARG00000054941
danio_rerioldlrad4aENSDARG00000070555
mus_musculusLdlrad4ENSMUSG00000024544
rattus_norvegicusLdlrad4ENSRNOG00000016879
drosophila_melanogasterCG5151FBGN0036576

Paralogs (1): PMEPA1 (ENSG00000124225)

Protein

Protein identifiers

Low-density lipoprotein receptor class A domain-containing protein 4O15165 (reviewed: O15165)

All UniProt accessions (10): O15165, A0A7I2V2E6, A0A7I2V2Z9, A0A7I2V3Q9, A0A7I2V3W1, A0A7I2V3Z2, A0A7I2V575, A0A7I2YQI3, K7EJM9, K7EMG1

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a negative regulator of TGF-beta signaling and thereby probably plays a role in cell proliferation, differentiation, apoptosis, motility, extracellular matrix production and immunosuppression. In the canonical TGF-beta pathway, ZFYVE9/SARA recruits the intracellular signal transducer and transcriptional modulators SMAD2 and SMAD3 to the TGF-beta receptor. Phosphorylated by the receptor, SMAD2 and SMAD3 then form a heteromeric complex with SMAD4 that translocates to the nucleus to regulate transcription. Through interaction with SMAD2 and SMAD3, LDLRAD4 may compete with ZFYVE9 and SMAD4 and prevent propagation of the intracellular signal.

Subunit / interactions. Interacts with PMEPA1. Interacts (via the SMAD interaction motif) with SMAD2 and SMAD3.

Subcellular location. Early endosome membrane.

Tissue specificity. Expressed in lymphocytes.

Domain organisation. The SMAD interaction motif is required for interaction with SMAD2 and SMAD3 and the negative regulation of TGF-beta signaling.

Similarity. Belongs to the PMEPA1 family.

Isoforms (8)

UniProt IDNamesCanonical?
O15165-1Alpha-1yes
O15165-2Alpha-2
O15165-3Beta-1
O15165-4Beta-2
O15165-55
O15165-66
O15165-77
O15165-88

RefSeq proteins (15): NP_001003674, NP_001003675, NP_001263178, NP_001365027, NP_001365028, NP_001365029, NP_001365030, NP_001381591, NP_001381592, NP_001381593, NP_001381594, NP_001381595, NP_001381596, NP_852146, NP_852147 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002172LDrepeatLR_classA_rptRepeat
IPR023415LDLR_class-A_CSConserved_site
IPR036055LDL_receptor-like_sfHomologous_superfamily
IPR043445TMEPAI/LRAD4Family

Pfam: PF00057

UniProt features (20 total): splice variant 5, sequence conflict 3, short sequence motif 3, topological domain 2, disulfide bond 2, chain 1, transmembrane region 1, domain 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O15165-F158.440.06

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (2): 19–38, 32–47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 270 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GOBP_SMAD_PROTEIN_SIGNAL_TRANSDUCTION, VERHAAK_AML_WITH_NPM1_MUTATED_DN, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, WANG_CLIM2_TARGETS_UP, TATTATA_MIR374, GOBP_NEGATIVE_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION, CAGCTG_AP4_Q5, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN, MAHAJAN_RESPONSE_TO_IL1A_DN, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, ONKEN_UVEAL_MELANOMA_UP, GOBP_MESENCHYMAL_CELL_DIFFERENTIATION, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5

GO Biological Process (5): negative regulation of epithelial to mesenchymal transition (GO:0010719), negative regulation of cell migration (GO:0030336), negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512), negative regulation of SMAD protein signal transduction (GO:0060392), negative regulation of signal transduction (GO:0009968)

GO Molecular Function (2): R-SMAD binding (GO:0070412), protein binding (GO:0005515)

GO Cellular Component (4): Golgi membrane (GO:0000139), membrane (GO:0016020), early endosome membrane (GO:0031901), endosome (GO:0005768)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway2
epithelial to mesenchymal transition1
regulation of epithelial to mesenchymal transition1
negative regulation of cell differentiation1
negative regulation of multicellular organismal process1
cell migration1
regulation of cell migration1
negative regulation of cell motility1
transforming growth factor beta receptor signaling pathway1
regulation of transforming growth factor beta receptor signaling pathway1
regulation of SMAD protein signal transduction1
SMAD protein signal transduction1
negative regulation of intracellular signal transduction1
signal transduction1
regulation of signal transduction1
negative regulation of cell communication1
negative regulation of signaling1
negative regulation of response to stimulus1
SMAD binding1
binding1
Golgi apparatus1
bounding membrane of organelle1
cellular anatomical structure1
early endosome1
endosome membrane1
endomembrane system1
cytoplasmic vesicle1

Protein interactions and networks

STRING

1848 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LDLRAD4TSC22D1Q15714720
LDLRAD4TPT1P13693535
LDLRAD4ARP10275525
LDLRAD4TSC22D3Q99576366
LDLRAD4MC5RP33032333
LDLRAD4ISM1B1AKI9324
LDLRAD4ARMC12Q5T9G4306
LDLRAD4TMEM158Q8WZ71304
LDLRAD4MIMS1Q96ND0303
LDLRAD4KANK4Q5T7N3302
LDLRAD4ZFYVE9O95405300
LDLRAD4CCDC144AA2RUR9287
LDLRAD4HEPACAMQ14CZ8277
LDLRAD4LMNTD2Q8IXW0270
LDLRAD4MC2RQ01718268

IntAct

8 interactions, top by confidence:

ABTypeScore
NEDD4LDLRAD4psi-mi:“MI:0407”(direct interaction)0.690
LDLRAD4NEDD4psi-mi:“MI:0914”(association)0.690
LDLRAD4WWP2psi-mi:“MI:0914”(association)0.530
TFAP2CLDLRAD4psi-mi:“MI:0915”(physical association)0.370
KATNA1LDLRAD4psi-mi:“MI:0914”(association)0.350

BioGRID (131): RTFDC1 (Affinity Capture-MS), HECW2 (Affinity Capture-MS), HECW1 (Affinity Capture-MS), WWP2 (Affinity Capture-MS), NEDD4 (Affinity Capture-MS), ITCH (Affinity Capture-MS), NEDD4L (Affinity Capture-MS), WWP1 (Affinity Capture-MS), TAX1BP1 (Affinity Capture-MS), WWC2 (Affinity Capture-MS), KIDINS220 (Affinity Capture-MS), NCAPD3 (Affinity Capture-MS), UBR3 (Affinity Capture-MS), ARFGEF2 (Affinity Capture-MS), UBR1 (Affinity Capture-MS)

ESM2 similar proteins: A2AR95, A4IHY6, B7ZWI3, D3ZF92, O15165, O43278, O75509, O88204, P98153, P98154, Q0VBF2, Q1L8G6, Q29RU0, Q4KMG9, Q566M8, Q5DTZ6, Q5HZW5, Q5R662, Q5R8E0, Q5RD34, Q5RF74, Q5VUB5, Q61003, Q68FU0, Q6AXS2, Q6NRX0, Q6UWW9, Q6ZPS6, Q6ZUJ8, Q7TQH7, Q86YD5, Q8BGN6, Q8BLD6, Q8BUJ9, Q8R182, Q8TEB7, Q8WUU8, Q91ZV2, Q91ZV3, Q96PD2

Diamond homologs: D2KUZ7, O15165, Q8BWJ4, Q969W9, Q9D7R2, E9Q6D8, P13671, P61134, P61135, Q29RU4, Q811M5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance49
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

6078 predictions. Top by Δscore:

VariantEffectΔscore
18:13438292:T:Aacceptor_gain1.0000
18:13438381:AACT:Adonor_gain1.0000
18:13438382:ACT:Adonor_gain1.0000
18:13438383:CT:Cdonor_gain1.0000
18:13438383:CTGTA:Cdonor_loss1.0000
18:13438384:TGTAA:Tdonor_loss1.0000
18:13438385:G:GAdonor_loss1.0000
18:13438385:G:GGdonor_gain1.0000
18:13438386:TA:Tdonor_loss1.0000
18:13438387:AA:Adonor_loss1.0000
18:13621110:A:AGacceptor_gain1.0000
18:13621110:AT:Aacceptor_gain1.0000
18:13621111:T:Aacceptor_gain1.0000
18:13621111:T:Gacceptor_gain1.0000
18:13621112:G:Aacceptor_gain1.0000
18:13621112:GGCA:Gacceptor_loss1.0000
18:13621113:GCAG:Gacceptor_loss1.0000
18:13621114:CAGC:Cacceptor_loss1.0000
18:13621115:A:AGacceptor_gain1.0000
18:13621115:AGC:Aacceptor_gain1.0000
18:13621115:AGCG:Aacceptor_gain1.0000
18:13621116:G:GAacceptor_gain1.0000
18:13621116:GC:Gacceptor_gain1.0000
18:13621116:GCG:Gacceptor_gain1.0000
18:13621116:GCGG:Gacceptor_gain1.0000
18:13621116:GCGGA:Gacceptor_gain1.0000
18:13621268:GCAG:Gdonor_gain1.0000
18:13621270:AGGT:Adonor_loss1.0000
18:13621272:G:GGdonor_gain1.0000
18:13621272:GTG:Gdonor_loss1.0000

AlphaMissense

2038 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:13438297:T:AC32S0.999
18:13438298:G:CC32S0.999
18:13438315:T:AC38S0.999
18:13438316:G:AC38Y0.999
18:13438316:G:CC38S0.999
18:13645251:T:AI172N0.999
18:13645366:C:AN210K0.999
18:13645366:C:GN210K0.999
18:13438259:G:AC19Y0.998
18:13438260:C:GC19W0.998
18:13438297:T:CC32R0.998
18:13438298:G:AC32Y0.998
18:13438315:T:CC38R0.998
18:13438317:T:GC38W0.998
18:13645251:T:CI172T0.998
18:13645251:T:GI172S0.998
18:13645335:T:CL200P0.998
18:13645359:C:AP208Q0.998
18:13645368:G:CR211P0.998
18:13438252:T:CF17L0.997
18:13438254:C:AF17L0.997
18:13438254:C:GF17L0.997
18:13438258:T:AC19S0.997
18:13438258:T:CC19R0.997
18:13438259:G:CC19S0.997
18:13438299:T:GC32W0.997
18:13438316:G:TC38F0.997
18:13438330:G:CD43H0.997
18:13438330:G:TD43Y0.997
18:13438344:T:GC47W0.997

dbSNP variants (sampled 300 via entrez): RS1000015134 (18:13582372 G>A,T), RS1000025389 (18:13241094 A>G), RS1000029530 (18:13423911 G>A), RS1000038400 (18:13481640 G>A), RS1000049350 (18:13541228 A>G), RS1000049929 (18:13503988 A>G), RS1000051040 (18:13619618 G>A), RS1000056073 (18:13624511 T>A), RS1000056407 (18:13326926 A>G), RS1000059264 (18:13406207 C>G,T), RS1000064020 (18:13273269 G>A), RS1000065067 (18:13554544 C>G,T), RS1000067122 (18:13319307 T>G), RS1000074955 (18:13437387 A>G), RS1000076650 (18:13400219 A>G)

Disease associations

OMIM: gene MIM:606571 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

StudyTraitp-value
GCST001749_1Pancreatic cancer6.000000e-07
GCST003059_20Parkinson’s disease1.000000e-06
GCST003854_35Gut microbiota (functional units)3.000000e-08
GCST004485_60Survival in pancreatic cancer2.000000e-07
GCST006444_11Bone mineral density (hip)3.000000e-06
GCST006976_137Macular thickness4.000000e-08
GCST007666_3Depressive symptom improvement7.000000e-07
GCST009028_18Adverse response to drug9.000000e-09
GCST009028_58Adverse response to drug2.000000e-08
GCST012490_571Femur bone mineral density x serum urate levels interaction3.000000e-11
GCST90002400_238Plateletcrit4.000000e-10
GCST90011900_154Serum alkaline phosphatase levels1.000000e-08

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0007874gut microbiome measurement
EFO:0000638overall survival
EFO:0007702hip bone mineral density
EFO:0007006depressive symptom measurement
EFO:0009658adverse effect
EFO:0004531urate measurement
EFO:0007985platelet crit
EFO:0004533alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects expression, affects methylation, decreases expression, increases methylation7
Valproic Acidaffects expression, decreases expression, increases expression5
Tetrachlorodibenzodioxinaffects cotreatment, increases expression, decreases expression3
Aflatoxin B1affects expression, affects methylation, decreases methylation3
Estradiolaffects cotreatment, increases expression, decreases expression2
Seleniumdecreases reaction, increases expression2
Tamoxifenaffects expression, affects cotreatment, increases expression2
Cyclosporinedecreases expression, increases methylation2
aristolochic acid Iincreases expression1
GSK-J4decreases expression1
sotorasibincreases expression, affects cotreatment1
biochanin Adecreases expression1
methyleugenoldecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
sodium arseniteaffects methylation1
benzo(e)pyreneincreases methylation1
aflatoxin B2affects methylation1
pentanalincreases expression1
abrinedecreases expression1
licochalcone Bincreases expression1
trametinibaffects cotreatment, increases expression1
NVP-BKM120affects cotreatment, increases expression1
Rosiglitazoneincreases expression1
Sunitinibdecreases expression1
Leflunomideincreases expression1
Acetaminophendecreases expression1
Amphotericin Bincreases expression1
Cadmiumincreases expression, decreases reaction1

Clinical trials (associated diseases)

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