Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
3949
Gene name Gene Name - the full gene name approved by the HGNC.
Low density lipoprotein receptor
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
LDLR
Synonyms (NCBI Gene) Gene synonyms aliases
FH, FHC, FHCL1, LDLCQ2
Chromosome Chromosome number
19
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
19p13.2
Summary Summary of gene provided in NCBI Entrez Gene.
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.
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.
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 factor Regulation Reference
ATF3 Repression 21294679
EGR1 Activation 12235180
EGR1 Unknown 12947119
HNF4A Activation 21123766
KLF13 Repression 16303770
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
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 ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
606945 6547 ENSG00000130164
Protein
UniProt ID 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 categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Coronary artery disease Early-onset coronary artery disease rs1555800701 N/A
Hypercholesterolemia Hypercholesterolemia, familial, 1, Familial hypercholesterolemia, hypercholesterolemia rs879254382, rs879254827, rs1131692217, rs375009082, rs757252110, rs879255224, rs139400379, rs730880130, rs1555807388, rs875989929, rs879254794, rs1555808044, rs763998635, rs879255006, rs2077361078
View all (1121 more)
N/A
Mental Retardation, X-Linked Syndromic X-linked intellectual disability Najm type rs137929307 N/A
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Cowden Syndrome Cowden syndrome 1 N/A N/A ClinVar
Homozygous Hypercholesterolemia homozygous familial hypercholesterolemia N/A N/A GenCC
Hyperlipidemia Familial combined hyperlipidemia defined by Brunzell criteria N/A N/A GWAS
Myocardial Infarction Myocardial infarction N/A N/A GWAS
Associations from Text Mining Disease 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