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 (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
79
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Abnormal circulating lipid concentration Pathogenic; Likely pathogenic rs2516004430, rs2516004016 RCV002283589
RCV002283590
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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
View all (472 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Cervical cancer Pathogenic rs112029328 RCV005887273
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
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
View all (64 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMERS DISEASE Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Abetalipoproteinemia Abetalipoproteinemia BEFREE 164482
★☆☆☆☆
Found in Text Mining only
Acute Coronary Syndrome Coronary Syndrome BEFREE 27665855, 28958330, 29974534, 30968218, 31500889
★☆☆☆☆
Found in Text Mining only
Acute lymphocytic leukemia Lymphocytic Leukemia BEFREE 12537975
★☆☆☆☆
Found in Text Mining only
Acute Promyelocytic Leukemia Promyelocytic Leukemia BEFREE 14646600
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 9116058
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of lung (disorder) Lung adenocarcinoma BEFREE 9116058
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of pancreas Pancreatic adenocarcinoma BEFREE 29088295
★☆☆☆☆
Found in Text Mining only
Adenomatous Polyposis Coli Multiple polyposis syndrome BEFREE 21471826
★☆☆☆☆
Found in Text Mining only
Adiponectin Deficiency Adiponectin Deficiency BEFREE 24113220
★☆☆☆☆
Found in Text Mining only
Adrenal Gland Pheochromocytoma Adrenal Gland Pheochromocytoma BEFREE 14708972, 20304625, 25004247, 28332880, 29079178, 30050099
★☆☆☆☆
Found in Text Mining only