eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| tangier disease | ||||
| Disease ID | 231 |
|---|---|
| Disease | tangier disease |
| Definition | An autosomal recessively inherited disorder caused by mutation of ATP-BINDING CASSETTE TRANSPORTERS involved in cellular cholesterol removal (reverse-cholesterol transport). It is characterized by near absence of ALPHA-LIPOPROTEINS (high-density lipoproteins) in blood. The massive tissue deposition of cholesterol esters results in HEPATOMEGALY; SPLENOMEGALY; RETINITIS PIGMENTOSA; large orange tonsils; and often sensory POLYNEUROPATHY. The disorder was first found among inhabitants of Tangier Island in the Chesapeake Bay, MD. |
| Synonym | alpha high density lipoprotein deficiency disease alpha lipoprotein deficiency analphalipoproteinaemia analphalipoproteinemia analphalipoproteinemias analphaliproteinaemia analphaliproteinemia cholesterol thesaurismoses cholesterol thesaurismosis disease tangiers diseases tangiers hdldt1 high density lipoprotein deficiency, tangier type high density lipoprotein deficiency, type 1 high density lipoprotein deficiency, type i high-density lipoprotein deficiency, tangier type high-density lipoprotein deficiency, type i tangier dis tangier disease [disease/finding] tgd thesaurismoses, cholesterol thesaurismosis, cholesterol |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C0039292 |
| MeSH | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:3) |
| 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:36) 19 | ABCA1 | 7.466 | DISEASES 154664 | ABCA13 | 2.592 | DISEASES 20 | ABCA2 | 1.971 | DISEASES 24 | ABCA4 | 3.458 | DISEASES 340273 | ABCB5 | 3.868 | DISEASES 4363 | ABCC1 | 1.465 | DISEASES 6833 | ABCC8 | 1.143 | DISEASES 9619 | ABCG1 | 3.588 | DISEASES 27329 | ANGPTL3 | 2.45 | DISEASES 336 | APOA2 | 5.32 | DISEASES 337 | APOA4 | 1.087 | DISEASES 344 | APOC2 | 2.598 | DISEASES 347 | APOD | 2.092 | DISEASES 319 | APOF | 2.67 | DISEASES 9557 | CHD1L | 2.291 | DISEASES 285440 | CYP4V2 | 1.198 | DISEASES 122786 | FRMD6 | 1.751 | DISEASES 3141 | HLCS | 1.651 | DISEASES 3476 | IGBP1 | 1.473 | DISEASES 3638 | INSIG1 | 1.361 | DISEASES 3949 | LDLR | 1.894 | DISEASES 4018 | LPA | 6.216 | DISEASES 4675 | NAP1L3 | 3.184 | DISEASES 25934 | NIPSNAP3A | 3.541 | DISEASES 55335 | NIPSNAP3B | 3.228 | DISEASES 10062 | NR1H3 | 2.237 | DISEASES 9159 | PCSK7 | 1.453 | DISEASES 5360 | PLTP | 3.53 | DISEASES 5406 | PNLIP | 1.42 | DISEASES 391 | RHOG | 1.986 | DISEASES 11005 | SPINK5 | 2.012 | DISEASES 10011 | SRA1 | 1.196 | DISEASES 6720 | SREBF1 | 1.466 | DISEASES 6721 | SREBF2 | 1.713 | DISEASES 29914 | UBIAD1 | 1.832 | DISEASES 7753 | ZNF202 | 2.681 | DISEASES |
| Locus | Symbol | Locus(Total Locus:1) ABCA1 | 9q31.1 |
| Disease ID | 231 |
|---|---|
| Disease | tangier disease |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:22) HP:0008404 | Nail dystrophy HP:0003477 | Peripheral axonal neuropathy HP:0002027 | Abdominal pain HP:0001349 | Facial diplegia HP:0001433 | Hepatosplenomegaly HP:0001873 | Thrombocytopenia HP:0003396 | Syringomyelia HP:0002155 | Hypertriglyceridemia HP:0005145 | Coronary artery stenosis HP:0007133 | Progressive peripheral neuropathy HP:0001903 | Anemia HP:0006901 | Impaired thermal sensitivity HP:0007957 | Corneal opacity HP:0000656 | Ectropion HP:0001712 | Left ventricular hypertrophy HP:0100546 | Carotid artery stenosis HP:0003146 | Hypocholesterolemia HP:0002730 | Chronic noninfectious lymphadenopathy HP:0030814 | Orange discoloured tonsils HP:0000958 | Dry skin HP:0002460 | Distal muscle weakness HP:0004943 | Accelerated atherosclerosis |
| Text Mined Phenotype | (Waiting for update.) |
| Disease ID | 231 |
|---|---|
| Disease | tangier disease |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:5) |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:1) |
Manually Genotype(Total Manually Genotypes:1) | |||
|---|---|---|---|
| Gene | Mutation | DOI | Article Title |
| ABCA1 | NM_005502.3: c.5383-1dupTT | doi:10.1038/gim.2016.153 | A comprehensive strategy for exome-based preconception carrier screening |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:24) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs137854494 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104806276 | A | G |
| rs137854495 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104822514 | G | A |
| rs137854496 | 24220029 | 335 | APOA1 | umls:C0039292 | BeFree | Depletion of sphingomyelin in stably transfected HEK293 cells expressing the Tangier disease W590S mutant ABCA1 isoform rescued the defect in PS exposure and restored cholesterol efflux to apoAI. | 0.006795978 | 2014 | ABCA1 | 9 | 104831048 | C | G,A |
| rs137854496 | 24220029 | 19 | ABCA1 | umls:C0039292 | BeFree | Depletion of sphingomyelin in stably transfected HEK293 cells expressing the Tangier disease W590S mutant ABCA1 isoform rescued the defect in PS exposure and restored cholesterol efflux to apoAI. | 0.598779969 | 2014 | ABCA1 | 9 | 104831048 | C | G,A |
| rs137854496 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104831048 | C | G,A |
| rs137854497 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104804668 | G | A |
| rs137854498 | 12111371 | 19 | ABCA1 | umls:C0039292 | UNIPROT | Clinical variant of Tangier disease in Japan: mutation of the ABCA1 gene in hypoalphalipoproteinemia with corneal lipidosis. | 0.598779969 | 2002 | ABCA1 | 9 | 104798504 | G | T,A |
| rs137854500 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104814154 | C | T |
| rs137854501 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104786940 | G | A |
| rs137854502 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104831098 | G | T |
| rs141021096 | 10938021 | 19 | ABCA1 | umls:C0039292 | BeFree | With these new sequencing primers, we found 3 novel ABCA1 mutations: a frameshift mutation (4570insA, A1484S-->X1492), a missense mutation (A986D) in a TD family, and a missense mutation (R170C) in aboriginal subjects with FHA. | 0.598779969 | 2000 | ABCA1 | 9 | 104819690 | G | T |
| rs2853574 | 11257260 | 19 | ABCA1 | umls:C0039292 | UNIPROT | A point mutation in ABC1 gene in a patient with severe premature coronary heart disease and mild clinical phenotype of Tangier disease. | 0.598779969 | 2001 | ABCA1 | 9 | 104831058 | G | A |
| rs2853578 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104831027 | T | C |
| rs2853578 | 10431236 | 19 | ABCA1 | umls:C0039292 | UNIPROT | Mutations in ABC1 in Tangier disease and familial high-density lipoprotein deficiency. | 0.598779969 | 1999 | ABCA1 | 9 | 104831027 | T | C |
| rs2853578 | 18343215 | 19 | ABCA1 | umls:C0039292 | BeFree | Previously, we showed that an ABCA1 Q597R mutant (QR) identified in TD is retained in the endoplasmic reticulum. | 0.598779969 | 2008 | ABCA1 | 9 | 104831027 | T | C |
| rs28937313 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104822520 | T | C |
| rs28937313 | 10431237 | 19 | ABCA1 | umls:C0039292 | UNIPROT | The gene encoding ATP-binding cassette transporter 1 is mutated in Tangier disease. | 0.598779969 | 1999 | ABCA1 | 9 | 104822520 | T | C |
| rs28937314 | 12111381 | 19 | ABCA1 | umls:C0039292 | UNIPROT | Double deletions and missense mutations in the first nucleotide-binding fold of the ATP-binding cassette transporter A1 ( ABCA1) gene in Japanese patients with Tangier disease. | 0.598779969 | 2002 | ABCA1 | 9 | 104822521 | T | G |
| rs28937314 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104822521 | T | G |
| rs374404992 | 19765707 | 19 | ABCA1 | umls:C0039292 | BeFree | Compound heterozygosity for the nonsense mutation R282X and the missense mutation Y1532C in the ABCA1 gene causes Tangier disease. | 0.598779969 | 2010 | ABCA1 | 9 | 104840489 | G | A |
| rs387906413 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104830993 | C | - |
| rs387906414 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104818781 | GA | - |
| rs564764153 | 15019541 | 19 | ABCA1 | umls:C0039292 | UNIPROT | This survey underlines the allelic heterogeneity of ABCA1 mutations and suggests that: (i) TD subjects, if asymptomatic, may be overlooked and (ii) there may be a selection bias in genotyping towards carriers of ABCA1 mutations who have pCAD possibly related to a combination of genetic and environmental cardiovascular risk factors. | 0.598779969 | 2004 | ABCA1 | 9 | 104785453 | C | G |
| rs796051872 | NA | 19 | ABCA1 | umls:C0039292 | CLINVAR | NA | 0.598779969 | NA | ABCA1 | 9 | 104816142 | C | G |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:5) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000958 | Dry skin | MP:0010678 | abnormal skin adnexa morphology | any structural anomaly of the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails |
| HP:0001712 | Left ventricular hypertrophy | MP:0010402 | ventricular septal defect | abnormal communications between the two lower chambers of the heart, including such defects in the perimembranous, inlet, outlet (infundibular), central muscular, marginal muscular, or apical muscular regions |
| HP:0002460 | Distal muscle weakness | MP:0000748 | progressive muscle weakness | increasing loss of muscle strength over time |
| HP:0003477 | Peripheral axonal neuropathy | MP:0004768 | abnormal axonal transport | any functional anomaly of the directed movement of organelles or vesicles along microtubules in nerve cell axons |
| 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 |
Mapped by homologous gene(Total Items:20) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0008404 | Nail dystrophy | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001349 | Facial diplegia | MP:0014185 | cerebellum atrophy | acquired diminution of the size of the cerebellum associated with wasting as from death and reabsorption of cells, diminished cellular proliferation, decreased cellular volume, pressure, ischemia, malnutrition, reduced function or malfunction, or hormonal |
| HP:0001433 | Hepatosplenomegaly | MP:0020215 | impaired blood coagulation | impaired ability of the blood to clot |
| HP:0004943 | Accelerated atherosclerosis | 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 |
| HP:0006901 | Impaired thermal sensitivity | MP:0012504 | increased forebrain apoptosis | increase in the number of cells of the forebrain undergoing programmed cell death |
| HP:0001903 | Anemia | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0002730 | Chronic noninfectious lymphadenopathy | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0000958 | Dry skin | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0002027 | Abdominal pain | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0003146 | Hypocholesterolemia | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| 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: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:0007133 | Progressive peripheral neuropathy | MP:0011967 | increased or absent threshold for auditory brainstem response | increase in the value at which one or more sound frequencies or broadband clicks first elicits a recordable response generated by electrical activity of neurons in the ascending auditory system, or complete lack of a recordable response at any frequency o |
| HP:0005145 | Coronary artery stenosis | MP:0012676 | dilated brain ventricles | the luminal space of one or more of the four communicating cavities within the brain that are continuous with the central canal of the spinal cord is increased in volume or area, usually with an increase in contained fluid |
| HP:0001712 | Left ventricular hypertrophy | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001873 | Thrombocytopenia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0003477 | Peripheral axonal neuropathy | MP:0013696 | increased granulocyte monocyte progenitor cell number | increase in the number of a hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages; these cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1 |
| HP:0002460 | Distal muscle weakness | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0000656 | Ectropion | MP:0013787 | photophobia | abnormal aversion or avoidance behavior in response to light; photophobia is symptom of abnormal intolerance to visual perception of light; as a medical symptom, photophobia is not a morbid fear or phobia, but an experience of discomfort or pain to the e |
| HP:0003396 | Syringomyelia | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| Disease ID | 231 |
|---|---|
| Disease | tangier disease |
| Case | (Waiting for update.) |