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encyclopedia of Rare Disease Annotation for Precision Medicine



   homocystinuria due to cystathionine beta-synthase deficiency
  

Disease ID 790
Disease homocystinuria due to cystathionine beta-synthase deficiency
Definition
The symptoms associated with homocystinuria due to CBS deficiency are highly variable. Some affected individuals may have only very mild signs of the disorder; others may have many different symptoms including some potentially life-threatening complications. Individuals can be separated into two distinct groups: those who respond to therapy with pyridoxine (vitamin B6) therapy and those who do not. Generally, individuals who respond to pyridoxine therapy have a milder form of the disorder, most likely because of residual activity of the CBS enzyme. In addition, the presence and specific location of blood clots also determines the severity of associated symptoms in each individual.Infants with homocystinuria due to CBS deficiency are normal at birth, but, if left untreated, will slowly develop the various symptoms associated with the disorder. Prompt detection and treatment of homocystinuria due to CBS deficiency is important in preventing or reducing the symptoms associated with the disorder.Homocystinuria due to CBS deficiency can potentially affect many different organ systems of the body. The four organ systems most commonly involved are the eyes, central nervous system, skeleton and the network of vessels that carry blood and other fluids throughout the body (vascular [circulatory] system).In some cases, the abnormalities affecting the eyes may be the first outward sign of homocystinuria due to CBS-deficiency. Many individuals develop displacement of the lenses of the eyes (ectopia lentis) away from the center of the eyeball. Affected individuals also usually develop severe nearsightedness (myopia) and quivering of the colored portion of the eye (iridodonesis). Ectopia lentis and myopia usually develop after the first year of life, often by 10 years of age.Additional abnormalities of the eyes have been reported in individuals with homocystinuria due to CBS deficiency. These abnormalities occur less frequently than ectopia lentis and myopia. Such abnormalities include clouding of the lenses of the eyes (cataracts), degeneration of the nerve (optic nerve) that relays signals from the eye to the brain (optic atrophy), and glaucoma, a condition in which increased pressure within the eye causes characteristic damage to the optic nerve. Some individuals may have separation of the thin layer of nerve cells (retina) that lines the back of the eyes from its underlying support tissue (retinal detachment). The retina normally senses light and converts it into nerve signals, which are then relayed to the brain through the optic nerve. Retinal detachment may cause blurred vision or the appearance of floaters in the field of vision.In some cases, delays in attaining developmental milestones (developmental delays) may be the first noticeable symptom in children with homocystinuria due to CBS deficiency. Affected children may be slow in sitting, standing, walking and speaking or other milestones. Some children have normal intelligence; others develop varying degrees of mental retardation. Approximately 20 percent of children with homocystinuria due to CBS deficiency develop seizures. Some affected children also exhibit psychiatric issues including depression, anxiety, obsessive-compulsive disorder, and other behavioral or personality disorders.Individuals with homocystinuria due to CBS deficiency also develop a variety of skeletal abnormalities. Skeletal abnormalities are usually not present at birth and may not become detectable until later during childhood. Common findings include thinning and lengthening of the long bones (dolichostenomelia), knees that are bent inward so that they touch when the legs are straight (knock knees or genu valgum), a highly arched foot (pes cavus), abnormal sideways curvature of the spine (scoliosis), or an abnormally protruding chest (pectus carinatum) or an abnormally sunken chest (pectus excavatum). Many individuals with homocystinuria due to CBS deficiency are at a greater risk than the general population of developing osteoporosis. Osteoporosis is condition characterized by a general loss of bone density that can lead to an increased risk of fractures.A serious complication associated with homocystinuria due to CBS deficiency is an increased risk of developing clots (thrombi) in blood vessels that can break off and become lodged in another vessel (thromboembolism). Blood clots can occur at any age. Specific symptoms associated with a thromboembolic event depend on the exact site of the clot and the specific blood vessels and organs that are affected. Thromboemboli can cause serious, life-threatening complications.Although less common, several additional findings have been reported in individuals with homocystinuria due to CBS deficiency including extremely fine, fragile skin, discoloration of the skin (hypopigmentation), rashes on the cheeks (malar flushing) and abnormally thin skin. Some individuals may develop fatty changes in the liver, protrusion of part of the intestines through a tear in the abdominal wall (inguinal hernia) or inflammation of the pancreas (pancreatitis), a small organ located behind the stomach that secretes enzymes that travel to the intestines and aid in digestion. Abnormal front-to-back curvature of the spine (kyphosis) and a collapsed lung (spontaneous pneumothorax) have also been reported in individuals with homocystinuria due to CBS deficiency.  - NORD
Reference: NORD
Synonym
cbs deficiencies
cbs deficiency
cystathionine beta synthase defic dis
cystathionine beta synthase deficiency
cystathionine beta synthase deficiency disease
cystathionine beta-synthase deficiency
cystathionine beta-synthase deficiency (disorder)
cystathionine beta-synthase deficiency disease
defic dis cystathionine beta synthase
deficiencies, cbs
deficiency disease, cystathionine beta synthase
deficiency disease, cystathionine beta-synthase
deficiency of beta-thionase
deficiency of cystathionine beta-synthase
deficiency of cystathionine beta-synthase (disorder)
deficiency of methylcysteine synthase
deficiency of serine sulfhydrase
deficiency of serine sulphydrase
deficiency, cbs
homocystinuria with or without response to pyridoxine
Orphanet
OMIM
DOID
UMLS
C0751202
SNOMED-CT
Comorbidity
UMLS | Disease | Sentences' Count(Total Sentences:3)
C0019880  |  homocystinuria  |  16
C0598608  |  hyperhomocysteinemia  |  3
C0027092  |  myopia  |  1
Curated Gene
Entrez_id | Symbol | Resource(Total Genes:1)
875  |  CBS  |  ORPHANET;UNIPROT
Inferring Gene(Waiting for update.)
Text Mined Gene(Waiting for update.)
Locus(Waiting for update.)
Disease ID 790
Disease homocystinuria due to cystathionine beta-synthase deficiency
Integrated Phenotype
HPO | Name(Total Integrated Phenotypes:30)
HP:0002156  |  High urine homocystine levels
HP:0040160  |  Generalized osteoporosis
HP:0000767  |  Funnel chest
HP:0012075  |  Personality disorder
HP:0001166  |  Long, slender fingers
HP:0002299  |  Brittle hair
HP:0001519  |  Dolichostenomelia
HP:0000678  |  Dental crowding
HP:0001083  |  Dislocated lenses
HP:0001010  |  Hypopigmentation of the skin
HP:0001249  |  Mental retardation
HP:0001250  |  Seizures
HP:0002751  |  Kyphoscoliosis
HP:0000965  |  Livedo reticularis
HP:0001658  |  Myocardial infarction
HP:0000545  |  Near sightedness
HP:0001733  |  Pancreatic inflammation
HP:0000218  |  Increased palatal height
HP:0001508  |  Weight faltering
HP:0001397  |  Hepatic steatosis
HP:0001297  |  Cerebral vascular events
HP:0000023  |  Inguinal hernia
HP:0001376  |  Decreased joint mobility
HP:0004586  |  Fish vertebrae
HP:0001907  |  Thromboembolic disease
HP:0001634  |  Mitral valve prolapse
HP:0000098  |  Increased body height
HP:0000716  |  Depression
HP:0000501  |  Glaucoma
HP:0000768  |  Pectus carinatum
Text Mined Phenotype
HPO | Name | Sentences' Count(Total Phenotypes:3)
Disease ID 790
Disease homocystinuria due to cystathionine beta-synthase deficiency
Manually Symptom(Waiting for update.)
Text Mined Symptom
UMLS | Name | Sentences' Count(Total Symptoms:2)
C0019880  |  homocystinuria  |  13
C0598608  |  hyperhomocysteinemia  |  3
Manually Genotype(Total Text Mining Genotypes:0)
(Waiting for update.)
Text Mining Genotype(Total Genotypes:0)
(Waiting for update.)
All Snps(Total Genotypes:9)
snpId pubmedId geneId geneSymbol diseaseId sourceId sentence score Year geneSymbol_dbSNP CHROMOSOME POS REF ALT
rs11700812NA875CBSumls:C0751202UNIPROTNA0.327524428NACBS2143060480CG,T
rs11768768112124992875CBSumls:C0751202UNIPROTWe determined the molecular basis of CBS deficiency in 36 Australian patients from 28 unrelated families, using direct sequencing of the entire coding region of the CBS gene.0.3275244282002CBS2143060481GA
rs1219649688990018875CBSumls:C0751202UNIPROTTwo novel mutations (K384E and L539S) in the C-terminal moiety of the cystathionine beta-synthase protein in two French pyridoxine-responsive homocystinuria patients.0.3275244281997CBS2143053920AG
rs2893427522738154875CBSumls:C0751202UNIPROTEffect of the disease-causing R266K mutation on the heme and PLP environments of human cystathionine β-synthase.0.3275244282012NANANANANA
rs2893489123974653875CBSumls:C0751202UNIPROTOur study experimentally supports a deficient regulation of CBS by SAM as a frequently found mechanism in CBS deficiency, which should be considered not only as a valuable diagnostic tool but also as a potential target for the development of new therapeutic approaches in classical homocystinuria.0.3275244282013CBS2143058862CT
rs2893489212007221875CBSumls:C0751202UNIPROTHigh homocysteine and thrombosis without connective tissue disorders are associated with a novel class of cystathionine beta-synthase (CBS) mutations.0.3275244282002CBS2143058927GA
rs3404014811013450875CBSumls:C0751202UNIPROTHomocystinuria in the Arab population of Israel: identification of two novel mutations using DGGE analysis.0.3275244282000CBS2143068521TG
rs574290523974653875CBSumls:C0751202UNIPROTOur study experimentally supports a deficient regulation of CBS by SAM as a frequently found mechanism in CBS deficiency, which should be considered not only as a valuable diagnostic tool but also as a potential target for the development of new therapeutic approaches in classical homocystinuria.0.3275244282013CBS2143063074AG
rs574290517540596875CBSumls:C0751202BeFreeMissense mutations in the cystathionine beta-synthase (CBS) gene, such as I278T, are responsible for CBS deficiency, the most common inherited disorder in sulfur metabolism.0.3275244282007CBS2143063074AG
GWASdb Annotation(Total Genotypes:5)
Chr Pos SNP_Id RefGene EnsemblGene ENCODE_Factor ENCODE_TFBS Chromosome_interaction GTEx_eQTL SNP_TFBS_affinity_GWAS3D SNP_miRNA_target_affinity_PolymiRTS SNP_splicing_effect_Skippy SNP_splicing_effect_MutPred_Splice SNP_ns_protein_effect_dbNSFP SNP_syn_effect_Silva SNP_phosphorylation_effect_PhosSNP PhastCons_score PhyloP_score GERP++_RS Segway_state Ancestral_allele ESP_AF ESP_AFR ESP_AFR ESP_EUR TG_ASN TG_AMR TG_AFR TG_EUR Type Consequence bStatistic EncH3K27Ac EncH3K4Me1 EncH3K4Me3 EncNucleo OMIM Clinvar
2144475714rs2124459NM_000071,CBSNM_001178008,CBSNM_001178009,CBSENST00000461686,ENSG00000160200ENST00000398158,ENSG00000160200ENST00000398165,ENSG00000160200ENST00000359624,ENSG00000160200ENST00000352178,ENSG00000160200ENST00000398168,ENSG00000160200ENST00000451248,ENSG00000160200ENST00000462349,ENSG00000160200ENST00000491776,ENSG00000160200ENST00000458223,ENSG00000160200ENST00000430013,ENSG00000160200TFP.JUNDTFP.CCNT2TFP.CHD2TFP.TCF12NAchr21,44470001,44480000,chr21,44490001,44500000,34,Hi-Cchr21,44470001,44480000,chr21,44330001,44340000,35,Hi-Cchr21,44470001,44480000,chr2,118780001,118790000,5,Hi-Cchr21,44470001,44480000,chr5,78230001,78240000,6,Hi-Cchr21,44470001,44480000,chr6,137010001,137020000,9,Hi-CNAEcm22-primary,55.2631Mig2-primary,3.1525Mig3-primary,3.4776Oaf1-DBD-primary,93.0188Pbf1-primary,1.332NANANANANA
2144478497rs6586282NM_000071,CBSNM_001178008,CBSNM_001178009,CBSENST00000461686,ENSG00000160200ENST00000398158,ENSG00000160200ENST00000398165,ENSG00000160200ENST00000359624,ENSG00000160200ENST00000352178,ENSG00000160200ENST00000398168,ENSG00000160200ENST00000451248,ENSG00000160200ENST00000462349,ENSG00000160200ENST00000491776,ENSG00000160200ENST00000458223,ENSG00000160200ENST00000430013,ENSG00000160200ENST00000496485,ENSG00000160200TFP.JUNDTFP.CHD2MCV-6NAchr21,44470001,44480000,chr21,44490001,44500000,34,Hi-Cchr21,44470001,44480000,chr21,44330001,44340000,35,Hi-Cchr21,44470001,44480000,chr2,118780001,118790000,5,Hi-Cchr21,44470001,44480000,chr5,78230001,78240000,6,Hi-Cchr21,44470001,44480000,chr6,137010001,137020000,9,Hi-CNALM4,2.8309LM149,3.0947LM202,3.1483Arnt,4.4348Arnt,1.7991NANANANANA
2144486964rs234709NM_000071,CBSNM_001178008,CBSNM_001178009,CBSENST00000461686,ENSG00000160200ENST00000398158,ENSG00000160200ENST00000398165,ENSG00000160200ENST00000359624,ENSG00000160200ENST00000352178,ENSG00000160200ENST00000398168,ENSG00000160200ENST00000441030,ENSG00000160200ENST00000470912,ENSG00000160200MCV-4NANANAEcm22-primary,1.5406Hal9-primary,1.3782Hal9-primary,1.3782Leu3-primary,2.9572Mcm1-primary,9.0579NANANANANANA0.000-0.638-1.6GE2TNANANANA
2144487404rs2851391NM_000071,CBSNM_001178008,CBSNM_001178009,CBSENST00000461686,ENSG00000160200ENST00000398158,ENSG00000160200ENST00000398165,ENSG00000160200ENST00000359624,ENSG00000160200ENST00000352178,ENSG00000160200ENST00000398168,ENSG00000160200ENST00000441030,ENSG00000160200ENST00000470912,ENSG00000160200MCV-1NANANALM130,2.5091NR2F1,2.3865GGGYGTGNY,1.9555RNCTGNYNRNCTGNY,1.4583CTCNANGTGNY,1.7785NANANANANANA0.001-0.169-0.475GE2CNANANANA
2144488033rs234714NM_000071,CBSNM_001178008,CBSNM_001178009,CBSENST00000461686,ENSG00000160200ENST00000398158,ENSG00000160200ENST00000398165,ENSG00000160200ENST00000359624,ENSG00000160200ENST00000352178,ENSG00000160200ENST00000398168,ENSG00000160200ENST00000441030,ENSG00000160200ENST00000470912,ENSG00000160200ENST00000465732,ENSG00000160200ENST00000488526,ENSG00000160200NANANANAAsg1-DBD-primary,1.7312Mig1-primary,3.3888Nkx2-4_3074,4.6457Pho4-primary,10.0022Pho4-primary,15.8125NANANANANANA0.0010.9011.08GE2CNANA
GWASdb Snp Trait(Total Genotypes:0)
(Waiting for update.)
Mapped by lexical matching(Total Items:10)
HP ID HP Name MP ID MP Name Annotation
HP:0001376Limitation of joint mobilityMP:0010732abnormal node of Ranvier morphologyany structural anomaly of the short unmyelinated segments of an axon between myelinated segments, where voltage gated channels accumulate and regenerate an action potential as it is conducted along the axon
HP:0004586Biconcave vertebral bodiesMP:0004703abnormal vertebral column morphologyany structural anomaly of the complete structure forming the rostral-caudal axis of the skeleton formed from the alternating segments of vertebra and intervertebral discs which support the spinal cord
HP:0001010Hypopigmentation of the skinMP:0010178increased number of Howell-Jolly bodiesabnormal presence of basophilic nuclear remnants of condensed DNA (1 to 2 um in diameter) in circulating erythrocytes, typically seen in severe hemolytic anemias or after splenectomy; these inclusions are normally removed by the spleen but will persist in
HP:0000218High palateMP:0011615submucous cleft palatea cleft of the palate with cardinal signs including a bifid uvula, a V-shaped notch at the back of the hard palate, and/or a translucent line in the midline of the soft palate and a short palate
HP:0040160Generalized osteoporosisMP:0000066osteoporosisreduction in bone mass or atrophy of skeletal tissue; may lead to skeletal fragility
HP:0000023Inguinal herniaMP:0010146umbilical herniaan outward bulging (protrusion) of the abdominal lining or part of the abdominal organ(s) through the area around the umbilicus; occurs when the muscle through which blood vessels pass to feed the developing fetus fails to completely close
HP:0001508Failure to thriveMP:0013294prenatal lethality prior to heart atrial septationdeath prior to the completion of heart atrial septation (Mus: E14.5-15.5)
HP:0001083Ectopia lentisMP:0005263ectopia lentiscongenital displacement of the lens due to defective zonule formation
HP:0002299Brittle hairMP:0010685abnormal hair follicle inner root sheath morphologyany structural anomaly of the multilayered tube composed of terminally differentiated hair follicle keratinocytes that is surrounded by the outer root sheath; the layers of the inner root sheath include the companion layer, Henle's layer, Huxley's layer a
HP:0001634Mitral valve prolapseMP:0010617thick mitral valve cuspsan increase in the ratio of the mitral valve cusp wall thickness to the atrioventricular septum thickness
Mapped by homologous gene(Total Items:30)
HP ID HP Name MP ID MP Name Annotation
HP:0001634Mitral valve prolapseMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0001250SeizuresMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0000098Tall statureMP:0020039increased bone ossificationincrease 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:0001376Limitation of joint mobilityMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0000501GlaucomaMP:3000003abnormal Ebner's gland morphologyany structural anomaly of the serous salivary glands which reside adjacent to the moats surrounding the circumvallate and foliate papillae just anterior to the posterior third of the tongue, anterior to the terminal sulcus; these exocrine glands secrete l
HP:0002156HomocystinuriaMP:0014179abnormal blood-retinal barrier functionanomaly in the function of the part of the blood-ocular barrier that consists of cells that are joined tightly together to prevent certain substances from entering the tissue of the retina; the BRB consists of non-fenestrated capillaries of the retinal ci
HP:0001907ThromboembolismMP:0014179abnormal blood-retinal barrier functionanomaly in the function of the part of the blood-ocular barrier that consists of cells that are joined tightly together to prevent certain substances from entering the tissue of the retina; the BRB consists of non-fenestrated capillaries of the retinal ci
HP:0001508Failure to thriveMP:0020234decreased basal metabolismdecrease in heat production of an organism at the lowest level of cell chemistry in an inactive, awake, and fasting state
HP:0001297StrokeMP:0020329decreased capillary densityreduction in the number of capillaries in a given cross-sectional area of a tissue
HP:0000768Pectus carinatumMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0012075Personality disorderMP:0014179abnormal blood-retinal barrier functionanomaly in the function of the part of the blood-ocular barrier that consists of cells that are joined tightly together to prevent certain substances from entering the tissue of the retina; the BRB consists of non-fenestrated capillaries of the retinal ci
HP:0000767Pectus excavatumMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0002751KyphoscoliosisMP:0020309increased creatine kinase activityincreased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+).
HP:0001249Intellectual disabilityMP:0020316decreased vascular endothelial cell proliferationdecrease in the expansion rate of any vascular endothelial cell population by cell division
HP:0040160Generalized osteoporosisMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0002299Brittle hairMP:0014179abnormal blood-retinal barrier functionanomaly in the function of the part of the blood-ocular barrier that consists of cells that are joined tightly together to prevent certain substances from entering the tissue of the retina; the BRB consists of non-fenestrated capillaries of the retinal ci
HP:0004586Biconcave vertebral bodiesMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0000218High palateMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0001166ArachnodactylyMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0001658Myocardial infarctionMP:0020137decreased bone mineralizationdecrease in the rate at which minerals are deposited into bone
HP:0000545MyopiaMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0001733PancreatitisMP:0020134abnormal gallbladder sizean anomaly in the size of the gall bladder compared to average, the organ that serves as a storage reservoir for bile
HP:0001397Hepatic steatosisMP:0020234decreased basal metabolismdecrease in heat production of an organism at the lowest level of cell chemistry in an inactive, awake, and fasting state
HP:0000678Dental crowdingMP:0020309increased creatine kinase activityincreased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+).
HP:0000716DepressionMP:0020329decreased capillary densityreduction in the number of capillaries in a given cross-sectional area of a tissue
HP:0000023Inguinal herniaMP:0020321increased vascular endothelial cell apoptosisincrease in the timing or the number of vascular endothelial cells undergoing programmed cell death
HP:0000965Cutis marmorataMP:0014179abnormal blood-retinal barrier functionanomaly in the function of the part of the blood-ocular barrier that consists of cells that are joined tightly together to prevent certain substances from entering the tissue of the retina; the BRB consists of non-fenestrated capillaries of the retinal ci
HP:0001083Ectopia lentisMP:0020254decreased collagen leveldecreased level of the main structural protein of the various connective tissues in animals
HP:0001519Disproportionate tall statureMP:0014179abnormal blood-retinal barrier functionanomaly in the function of the part of the blood-ocular barrier that consists of cells that are joined tightly together to prevent certain substances from entering the tissue of the retina; the BRB consists of non-fenestrated capillaries of the retinal ci
HP:0001010Hypopigmentation of the skinMP:0020039increased bone ossificationincrease 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 790
Disease homocystinuria due to cystathionine beta-synthase deficiency
Case(Waiting for update.)