Gene Gene information from NCBI Gene database.
Entrez ID 3949
Gene name Low density lipoprotein receptor
Gene symbol LDLR
Synonyms (NCBI Gene)
FHFHCFHCL1LDLCQ2
Chromosome 19
Chromosome location 19p13.2
Summary The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins involved in receptor-mediated endocytosis of specific ligands. Low density lipoprotein (LDL) is normally bound at the cell membrane and taken into the cell ending up
SNPs SNP information provided by dbSNP.
1033
SNP ID Visualize variation Clinical significance Consequence
rs5926 C>G,T Conflicting-interpretations-of-pathogenicity, benign Synonymous variant, non coding transcript variant, coding sequence variant, missense variant
rs2228671 C>A,G,T Benign-likely-benign, pathogenic, benign Synonymous variant, coding sequence variant, stop gained, missense variant, non coding transcript variant
rs2569548 C>A,T Likely-pathogenic, pathogenic-likely-pathogenic Missense variant, intron variant, coding sequence variant, non coding transcript variant
rs11547917 C>A,G,T Likely-pathogenic, pathogenic Stop gained, non coding transcript variant, coding sequence variant, missense variant
rs13306512 C>A,G,T Uncertain-significance, likely-pathogenic, pathogenic Synonymous variant, coding sequence variant, stop gained, missense variant, non coding transcript variant
miRNA miRNA information provided by mirtarbase database.
1763
miRTarBase ID miRNA Experiments Reference
MIRT007140 hsa-miR-130a-3p qRT-PCR 23418453
MIRT017122 hsa-miR-335-5p Microarray 18185580
MIRT020235 hsa-miR-130b-3p Sequencing 20371350
MIRT021895 hsa-miR-128-3p Microarray 17612493
MIRT022254 hsa-miR-124-3p Microarray 18668037
Transcription factors Transcription factors information provided by TRRUST V2 database.
10
Transcription factor Regulation Reference
ATF3 Repression 21294679
EGR1 Activation 12235180
EGR1 Unknown 12947119
HNF4A Activation 21123766
KLF13 Repression 16303770
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
136
GO ID Ontology Definition Evidence Reference
GO:0001523 Process Retinoid metabolic process IEA
GO:0001540 Function Amyloid-beta binding IEA
GO:0001540 Function Amyloid-beta binding ISS
GO:0001618 Function Virus receptor activity IEA
GO:0001920 Process Negative regulation of receptor recycling IDA 17452316
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
606945 6547 ENSG00000130164
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P01130
Protein name Low-density lipoprotein receptor (LDL receptor)
Protein function Binds low density lipoprotein /LDL, the major cholesterol-carrying lipoprotein of plasma, and transports it into cells by endocytosis. In order to be internalized, the receptor-ligand complexes must first cluster into clathrin-coated pits. Forms
PDB 1AJJ , 1D2J , 1F5Y , 1F8Z , 1HJ7 , 1HZ8 , 1I0U , 1IJQ , 1LDL , 1LDR , 1N7D , 1XFE , 2FCW , 2KRI , 2LGP , 2M7P , 2MG9 , 2W2M , 2W2N , 2W2O , 2W2P , 2W2Q , 3BPS , 3GCW , 3GCX , 3M0C , 3P5B , 3P5C , 3SO6 , 4NE9 , 5OY9 , 5OYL , 9BD8 , 9BDE , 9BDT , 9COO
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00057 Ldl_recept_a 25 63 Low-density lipoprotein receptor domain class A Repeat
PF00057 Ldl_recept_a 66 104 Low-density lipoprotein receptor domain class A Repeat
PF00057 Ldl_recept_a 107 143 Low-density lipoprotein receptor domain class A Repeat
PF00057 Ldl_recept_a 146 184 Low-density lipoprotein receptor domain class A Repeat
PF00057 Ldl_recept_a 195 231 Low-density lipoprotein receptor domain class A Repeat
PF00057 Ldl_recept_a 234 270 Low-density lipoprotein receptor domain class A Repeat
PF00057 Ldl_recept_a 274 313 Low-density lipoprotein receptor domain class A Repeat
PF12662 cEGF 335 357 Complement Clr-like EGF-like Domain
PF00058 Ldl_recept_b 439 483 Low-density lipoprotein receptor repeat class B Repeat
PF00058 Ldl_recept_b 486 526 Low-density lipoprotein receptor repeat class B Repeat
PF00058 Ldl_recept_b 529 570 Low-density lipoprotein receptor repeat class B Repeat
PF00058 Ldl_recept_b 573 615 Low-density lipoprotein receptor repeat class B Repeat
PF00058 Ldl_recept_b 616 656 Low-density lipoprotein receptor repeat class B Repeat
PF14670 FXa_inhibition 671 711 Domain
Sequence
MGPWGWKLRWTVALLLAAAGTAVGDRCERNEFQCQDGKCISYKWVCDGSAECQDGSDESQ
ETC
LSVTCKSGDFSCGGRVNRCIPQFWRCDGQVDCDNGSDEQGCPPKTCSQDEFRCHDGK
CISRQFVCDSDRDCLDGSDEASC
PVLTCGPASFQCNSSTCIPQLWACDNDPDCEDGSDEW
PQRC
RGLYVFQGDSSPCSAFEFHCLSGECIHSSWRCDGGPDCKDKSDEENCAVATCRPDE
FQCSDGNCIHGSRQCDREYDCKDMSDEVGC
VNVTLCEGPNKFKCHSGECITLDKVCNMAR
DCRDWSDEPIKEC
GTNECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQD
PDTCSQLCVNLEGGYKCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYT
SLIPNLRNVVALDTEVASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLA
VDW
IHSNIYWTDSVLGTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPA
KIKKGGLNGVDIYSLVTENIQWPNGITLDL
LSGRLYWVDSKLHSISSIDVNGGNRKTILE
DEKRLAHPFSLAVFE
DKVFWTDIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHNLTQ
PRGVNWCERTTLSNGGCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEAEAAVA
TQETSTVRLKVSSTAVRTQHTTTRPVPDTSRLPGATPGLTTVEIVTMSHQALGDVAGRGN
EKKPSSVRALSIVLPIVLLVFLCLGVFLLWKNWRLKNINSINFDNPVYQKTTEDEVHICH
NQDGYSYPSRQMVSLEDDVA
Sequence length 860
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Virion - Hepatitis viruses
Endocytosis
Ovarian steroidogenesis
Aldosterone synthesis and secretion
Cortisol synthesis and secretion
Cushing syndrome
Bile secretion
Cholesterol metabolism
Toxoplasmosis
Hepatitis C
Lipid and atherosclerosis
  Cargo recognition for clathrin-mediated endocytosis
Clathrin-mediated endocytosis
Chylomicron clearance
LDL clearance
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
7592
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Abnormal circulating lipid concentration Pathogenic; Likely pathogenic rs2516004430, rs2516004016 RCV002283589
RCV002283590
Cardiovascular phenotype Likely pathogenic; Pathogenic rs779913921, rs879254694, rs2077282376, rs879254851, rs2147241680, rs879254915, rs1057519655, rs2077057318, rs2147223179, rs879255134, rs1372739823, rs779732323, rs377271627, rs144172724, rs139043155
View all (402 more)
RCV004302312
RCV002413905
RCV004995735
RCV002377745
RCV004995927
RCV002388665
RCV002352683
RCV005660273
RCV006352509
RCV005350841
RCV002407117
RCV002386926
RCV002433638
RCV002433637
RCV002408658
RCV002371991
RCV002345455
RCV002362782
RCV002390310
RCV002390311
RCV004019779
RCV002390312
RCV002399517
RCV002399519
RCV002444605
RCV002381462
RCV002336345
RCV002390373
RCV002323293
RCV002328193
RCV002326588
RCV002333842
RCV002357847
RCV002326125
RCV002333236
RCV002356208
RCV002366854
RCV002444668
RCV002453561
RCV002336377
RCV002345556
RCV002354407
RCV002362854
RCV002362855
RCV002444669
RCV002399588
RCV002381528
RCV002378150
RCV003162682
RCV002390392
RCV004992041
RCV002390395
RCV004639156
RCV002415706
RCV002416922
RCV002369394
RCV002385138
RCV002414422
RCV002367202
RCV002375991
RCV002383474
RCV002398548
RCV002410161
RCV002414737
RCV002415206
RCV002380907
RCV002400934
RCV002406193
RCV002401885
RCV002455623
RCV002421603
RCV002430773
RCV002410906
RCV002457688
RCV002423768
RCV002423856
RCV002423959
RCV002424147
RCV002446457
RCV002455811
RCV002435968
RCV002321678
RCV002381238
RCV002426484
RCV002345224
RCV002399308
RCV002415393
RCV002362555
RCV002362556
RCV002371758
RCV002381240
RCV002399309
RCV002390088
RCV002415394
RCV002415395
RCV002426485
RCV002362557
RCV002336075
RCV002345225
RCV002362558
RCV002362559
RCV002321469
RCV002362560
RCV002345227
RCV002408448
RCV002381241
RCV002426486
RCV002354146
RCV002362561
RCV005363004
RCV005655199
RCV002336450
RCV002354478
RCV002372113
RCV002399654
RCV002408795
RCV002415774
RCV002390558
RCV002408910
RCV002408912
RCV005365144
RCV002426986
RCV002363055
RCV002426989
RCV002408913
RCV002426990
RCV005361231
RCV002426991
RCV002444846
RCV002321828
RCV002444847
RCV002453756
RCV002372212
RCV002327075
RCV004992087
RCV002363056
RCV002363057
RCV002372213
RCV002363058
RCV002363059
RCV005589792
RCV002372214
RCV002372215
RCV002372216
RCV002381726
RCV002390566
RCV002399775
RCV002399776
RCV002408914
RCV002415886
RCV002433922
RCV002336589
RCV002354591
RCV004020584
RCV002399780
RCV002408916
RCV002408917
RCV002399782
RCV004020585
RCV002408918
RCV002415887
RCV002415888
RCV002415889
RCV002444848
RCV002444849
RCV002426992
RCV004020586
RCV002453757
RCV002354607
RCV002390577
RCV003188051
RCV003188052
RCV003188053
RCV003188054
RCV005589795
RCV005589796
RCV002450672
RCV002401929
RCV002379055
RCV002379056
RCV002418050
RCV006342194
RCV002347934
RCV002436068
RCV002327169
RCV002365236
RCV002365237
RCV002429161
RCV002446470
RCV002436069
RCV002411079
RCV004020946
RCV004020947
RCV002411080
RCV002418051
RCV005659874
RCV002429163
RCV002429164
RCV002429165
RCV002429167
RCV002450742
RCV004992112
RCV002429168
RCV002436070
RCV002436071
RCV002436073
RCV002321912
RCV002321913
RCV002321914
RCV004020948
RCV002450743
RCV002450744
RCV002347935
RCV002356328
RCV002327170
RCV002327171
RCV002327172
RCV002327173
RCV005652345
RCV002327174
RCV004020949
RCV002338778
RCV002327175
RCV002338779
RCV002327176
RCV002338780
RCV002338782
RCV003372663
RCV002338783
RCV002338784
RCV002338785
RCV002338786
RCV004020950
RCV002338787
RCV004020951
RCV002338788
RCV003165665
RCV002347936
RCV002347937
RCV002347938
RCV004639189
RCV002356329
RCV002356330
RCV002356331
RCV002356332
RCV002365238
RCV002365239
RCV004020952
RCV002365240
RCV002356333
RCV002356334
RCV002365241
RCV005365206
RCV002374395
RCV002365242
RCV002365243
RCV002374396
RCV002374397
RCV003165666
RCV004639190
RCV002392740
RCV002418052
RCV002418053
RCV002429169
RCV002429170
RCV002429171
RCV002429172
RCV002446473
RCV002446474
RCV002374398
RCV004020954
RCV004020955
RCV002374401
RCV002446475
RCV005365208
RCV004992114
RCV004992115
RCV004992116
RCV005589799
RCV003165667
RCV002379057
RCV002379058
RCV004992117
RCV002365244
RCV002374404
RCV002365245
RCV004992118
RCV002379060
RCV002411081
RCV002401933
RCV002401932
RCV002411082
RCV004639192
RCV002401934
RCV003380529
RCV004020958
RCV002411084
RCV004020959
RCV002446476
RCV004020960
RCV005659875
RCV002429173
RCV002429174
RCV004992119
RCV002436075
RCV002436076
RCV002321916
RCV002321917
RCV004992120
RCV002321918
RCV004992121
RCV002347939
RCV004992122
RCV002365246
RCV005659876
RCV004020962
RCV005659877
RCV002418055
RCV002446477
RCV002446478
RCV006342197
RCV003372664
RCV002379061
RCV003298315
RCV002379063
RCV002379064
RCV002379065
RCV004639193
RCV004629172
RCV002392744
RCV002392745
RCV004020967
RCV002401937
RCV004020968
RCV004020969
RCV002401939
RCV003165669
RCV002411085
RCV002401941
RCV002401943
RCV002411086
RCV005589801
RCV002411087
RCV002401945
RCV002411090
RCV004992125
RCV004639194
RCV002411094
RCV002411095
RCV003165671
RCV002411097
RCV002411098
RCV004020970
RCV002411099
RCV006342198
RCV002411102
RCV004020971
RCV004992126
RCV002411104
RCV004992127
RCV002418060
RCV004629173
RCV002418061
RCV002418062
RCV002418064
RCV002418065
RCV002418067
RCV002418068
RCV002418069
RCV005589802
RCV004020973
RCV002429175
RCV002429176
RCV003165672
RCV003298318
RCV002418073
RCV003298319
RCV002446479
RCV004992130
RCV002429177
RCV004639197
RCV002450746
RCV002450749
RCV002446480
RCV002450750
RCV004639198
RCV002450751
RCV002450752
RCV002446481
RCV002450753
RCV005589805
RCV004280081
RCV004291380
RCV003283510
RCV003283511
RCV003283512
RCV005356447
RCV004369053
RCV004412640
RCV004412641
RCV004518662
RCV004518663
RCV004518666
RCV004518676
RCV004518678
RCV004629206
RCV002436228
RCV003168585
RCV002348123
RCV002365444
RCV002411269
RCV004022129
RCV004639228
RCV002429335
RCV002411271
RCV002411270
RCV003372695
RCV002402107
RCV004992200
RCV002411282
RCV002418242
RCV002365580
RCV002365581
RCV002429465
RCV002367651
RCV003302731
RCV002446966
RCV005348139
RCV005589844
RCV005652382
RCV002323869
RCV002404318
RCV004639256
RCV002383986
RCV002431468
RCV002323874
RCV002455981
RCV002367700
RCV003352899
RCV002448553
RCV002341198
RCV003302747
RCV002408481
RCV002362601
RCV002381272
RCV002453273
RCV005367444
RCV002413665
RCV004024879
RCV002413687
RCV003303184
RCV005589904
RCV002427031
RCV004994012
RCV002422777
RCV003169526
RCV002362695
RCV002415518
RCV002409335
RCV002379508
RCV002379587
RCV005589954
RCV004033034
RCV002379706
RCV005652542
RCV005589989
RCV003380891
RCV004994333
RCV002356967
RCV002411863
RCV002366084
RCV002379959
RCV002411918
RCV002436986
RCV002411922
RCV003284137
RCV004035599
Cervical cancer Pathogenic rs112029328 RCV005887273
Dyslipidemia Likely pathogenic; Pathogenic rs2147241957, rs144172724, rs146200173, rs139624145, rs370777955, rs373646964, rs137929307, rs557344672, rs544453230, rs570942190, rs201102492, rs121908025, rs28942082, rs28942083, rs121908028
View all (54 more)
RCV005405876
RCV005403768
RCV005403769
RCV005403772
RCV005400703
RCV005403773
RCV005403770
RCV005628233
RCV005404298
RCV005404299
RCV005400712
RCV005400687
RCV005403713
RCV005400688
RCV005403714
RCV005400689
RCV005628226
RCV005403715
RCV005400690
RCV005400691
RCV005403716
RCV005403717
RCV005628237
RCV005404348
RCV005404394
RCV005404399
RCV005404400
RCV005404401
RCV005404402
RCV005404403
RCV005404404
RCV005404405
RCV005400715
RCV005404406
RCV005404407
RCV005404408
RCV005404409
RCV005404430
RCV005628245
RCV005628246
RCV005404432
RCV005404433
RCV005404434
RCV005400717
RCV005404435
RCV005404437
RCV005404438
RCV005400718
RCV005404439
RCV005404442
RCV005404443
RCV005404444
RCV005400719
RCV005404447
RCV005404448
RCV005404449
RCV005404450
RCV005404452
RCV005404453
RCV005400724
RCV005400725
RCV005404546
RCV005404584
RCV005404618
RCV005403724
RCV005403726
RCV005404764
RCV005405489
RCV005405560
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
- no classification for the single variant rs879254357, rs879254358 -
Acute myeloid leukemia Benign rs72658867, rs13306513 RCV005888732
RCV005900101
Adrenocortical carcinoma, hereditary Benign rs2228671, rs72658867 RCV005890973
RCV005888735
Autosomal dominant familial hypercholesterolemia Likely benign rs13306498 RCV001272182
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
Acute Coronary Syndrome Associate 33003376, 35879787, 40257950
Adrenocortical Carcinoma Associate 10215860
Alzheimer Disease Associate 15689450, 18065781, 20232416, 22414021, 36901902
Angina Pectoris Associate 8429261
Antiphospholipid Syndrome Associate 26820623
Aortic Aneurysm Abdominal Associate 25198969, 32039711
Aortic Valve Calcification of Associate 26700830, 30592719
Aortic Valve Disease Associate 32757650
Aortic Valve Stenosis Associate 27152866
Aphakia congenital primary Associate 26204136