eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| lcat deficiency | ||||
| Disease ID | 113 |
|---|---|
| Disease | lcat deficiency |
| Definition | disease characterized by abnormally low levels of plasma lecithin cholesterol acyl transferase; clinical manifestations include corneal opacity, anemia, and proteinuria. |
| Synonym | acyltransferase deficiency, lecithin:cholesterol alpha lcat defic alpha lcat deficiency alpha lecithin cholesterol acyltransferase defic alpha-lcat deficiency alpha-lecithin-cholesterol acyltransferase deficiency alpha-lecithin:cholesterol acyltransferase deficiency deficiency, alpha-lcat deficiency, lcat familial cholesteryl ester deficiency familial lecithin-cholesterol acyltransferase deficiency lcat - lecithin-cholesterol acyltransferase deficiency lcat defic lcata deficiencies lcata deficiency lecithin acyltransferase deficiency lecithin cholesterol acyltransferase defic lecithin cholesterol acyltransferase deficiency lecithin cholesterol acyltransferase deficiency (disorder) lecithin cholesterol acyltransferase deficiency [disease/finding] lecithin:cholesterol acyltransferase deficiency norum disease norum's disease phosphatidylcholine-sterol acyltransferase deficiency phosphatidylcholine-sterol acyltransferase deficiency (disorder) |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C0023195 |
| MeSH | |
| SNOMED-CT | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:6) C0004153 | atherosclerosis | 1 C0027726 | nephrotic syndrome | 1 C0040053 | thrombus | 1 C0033687 | proteinuria | 1 C0020538 | hypertension | 1 C0022658 | kidney disease | 1 |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Inferring Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:7) |
| Locus | (Waiting for update.) |
| Disease ID | 113 |
|---|---|
| Disease | lcat deficiency |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:17) HP:0003233 | Low HDL-cholesterol HP:0002155 | Increased triglycerides HP:0001744 | Splenomegaly HP:0002716 | Lymphadenopathy HP:0007957 | Corneal opacity HP:0001878 | Haemolytic anaemia HP:0002621 | Atherosclerosis HP:0000822 | Hypertension HP:0001895 | Normochromic anemia HP:0007759 | Cloudy cornea HP:0002155 | Hypertriglyceridemia HP:0000790 | Hematuria HP:0000572 | Visual loss HP:0002240 | Hepatomegaly HP:0000093 | Proteinuria HP:0001878 | Hemolytic anemia HP:0000083 | Renal insufficiency |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:5) HP:0003233 | Low HDL-cholesterol | 1 HP:0000822 | Hypertension | 1 HP:0000093 | Proteinuria | 1 HP:0000100 | Nephrosis | 1 HP:0002621 | Atherosclerosis | 1 |
| Disease ID | 113 |
|---|---|
| Disease | lcat deficiency |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:5) |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:2) |
Manually Genotype(Total Text Mining Genotypes:0) |
|---|
| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:16) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs121908048 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67940276 | C | T |
| rs121908049 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67940471 | G | T |
| rs121908054 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67940400 | A | T |
| rs121908055 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67942967 | G | T |
| rs267607211 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67942686 | A | G |
| rs28940886 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67942939 | C | T |
| rs28940886 | 8318557 | 3931 | LCAT | umls:C0023195 | UNIPROT | We have recreated and expressed two known natural mutations within the LCAT gene which were reported on both alleles in a single case of familial LCAT deficiency. | 0.572420313 | 1993 | LCAT | 16 | 67942939 | C | T |
| rs28940887 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67942719 | G | A |
| rs28940887 | 8432868 | 3931 | LCAT | umls:C0023195 | UNIPROT | The presence of lecithin:cholesterol acyltransferase (LCAT) deficiency in six probands from five families originating from four different countries was confirmed by the absence or near absence of LCAT activity. | 0.572420313 | 1993 | LCAT | 16 | 67942719 | G | A |
| rs28940888 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67940193 | G | A |
| rs28940888 | 12957688 | 3931 | LCAT | umls:C0023195 | UNIPROT | A novel LCAT mutation (Phe382-->Val) in a kindred with familial LCAT deficiency and defective apolipoprotein B-100. | 0.572420313 | 2003 | LCAT | 16 | 67940193 | G | A |
| rs28942087 | 8432868 | 3931 | LCAT | umls:C0023195 | UNIPROT | The presence of lecithin:cholesterol acyltransferase (LCAT) deficiency in six probands from five families originating from four different countries was confirmed by the absence or near absence of LCAT activity. | 0.572420313 | 1993 | LCAT | 16 | 67942413 | A | G |
| rs28942087 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67942413 | A | G |
| rs387906300 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67942567 | G | A |
| rs794726662 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67942701 | - | GCC |
| rs794726663 | NA | 3931 | LCAT | umls:C0023195 | CLINVAR | NA | 0.572420313 | NA | LCAT | 16 | 67940029 | - | T |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:6) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0001895 | Normochromic anemia | MP:0001585 | hemolytic anemia | deficiency of red cells resulting from an increased rate of erythrocyte destruction |
| HP:0007759 | Opacification of the corneal stroma | MP:0012129 | failure of blastocyst formation | inability to form a blastocyst from a solid ball of cells known as a morula |
| HP:0000083 | Renal insufficiency | MP:0003335 | exocrine pancreatic insufficiency | inadequate synthesis and/or secretion of digestive enzymes by the exocrine portion of the pancreas, usually due to loss of acinar tissue from idiopathic atrophy or acute or chronic inflammation, causing maldigestion and malabsorption of nutrients |
| HP:0007957 | Corneal opacity | MP:0009859 | eye opacity | changes in the eye grossly observed as a milky or cloudy appearance that may be progressive and persistent throughout life |
| HP:0001878 | Hemolytic anemia | MP:0008388 | hypochromic microcytic anemia | hemoglobin deficiency resulting from a reduction in the concentration of hemoglobin in red cells, where the erythrocyte corpuscular volume is smaller than normal |
| HP:0000572 | Visual loss | MP:0011352 | proximal convoluted tubule brush border loss | attenuation or degeneration of the microvillus brush border normally present on the luminal surface of epithelial cells of the proximal convoluted tubule; may be associated with renal tubular injury and/or cystic changes |
Mapped by homologous gene(Total Items:15) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000790 | Hematuria | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0002621 | Atherosclerosis | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000572 | Visual loss | MP:0020194 | abnormal glycosphingolipid level | any anomaly in the concentrations of glycosphingolipids, a subtype of glycolipids containing the amino alcohol sphingosine, in the body |
| HP:0003233 | Hypoalphalipoproteinemia | MP:0020215 | impaired blood coagulation | impaired ability of the blood to clot |
| HP:0000093 | Proteinuria | MP:0020216 | decreased circulating complement protein level | less than normal levels of the serum proteins that act sequentially to allow for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes |
| HP:0000083 | Renal insufficiency | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0007957 | Corneal opacity | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002716 | Lymphadenopathy | MP:0020215 | impaired blood coagulation | impaired ability of the blood to clot |
| HP:0002155 | Hypertriglyceridemia | MP:0020234 | decreased basal metabolism | decrease in heat production of an organism at the lowest level of cell chemistry in an inactive, awake, and fasting state |
| HP:0001878 | Hemolytic anemia | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0007759 | Opacification of the corneal stroma | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0002240 | Hepatomegaly | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000822 | Hypertension | MP:0020216 | decreased circulating complement protein level | less than normal levels of the serum proteins that act sequentially to allow for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes |
| HP:0001744 | Splenomegaly | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001895 | Normochromic anemia | MP:0020039 | increased bone ossification | increase in the formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance |
| Disease ID | 113 |
|---|---|
| Disease | lcat deficiency |
| Case | (Waiting for update.) |