eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| shwachman diamond syndrome | ||||
| Disease ID | 802 |
|---|---|
| Disease | shwachman diamond syndrome |
| Definition | A rare, inherited disorder in which the pancreas and bone marrow do not work the way they should. Symptoms include problems digesting food, a low number of neutrophils (a type of white blood cell), bone problems, and being short. Infants with the disorder get bacterial infections and are at an increased risk of aplastic anemia, myelodysplastic syndrome, and leukemia. |
| Synonym | congenital lipomatosis of pancreas congenital lipomatosis pancreas lipomatosis of pancreas, congenital metaphyseal chondrodysplasia with pancreatic insufficiency and neutropenia metaphyseal chondrodysplasia, shwachman type metaphyseal dysplasia with malabsorption and neutropenia pancreatic insufficiency and bone marrow dysfunction schwachman diamond syndrome schwachman's syndrome schwachman's syndrome (disorder) schwachman-bodian syndrome schwachman-diamond syndrome schwachmann diamond syndrome schwachmann-diamond syndrome schwachmann-diamond syndrome (disorder) shwachman syndrome shwachman syndrome (disorder) shwachman's syndrome shwachman-bodian syndrome shwachman-bodian-diamond syndrome shwachman-diamond syndrome shwachman-diamond-oski syndrome |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C0272170 |
| SNOMED-CT | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:13) C0027947 | neutropenia | 2 C0024299 | lymphoma | 1 C0281361 | pancreatic adenocarcinoma | 1 C0023895 | liver disease | 1 C1368107 | bone marrow aplasia | 1 C0001418 | adenocarcinoma | 1 C0018799 | heart diseases | 1 C0152021 | congenital heart disease | 1 C0742472 | cns lymphoma | 1 C0030312 | pancytopenia | 1 C0018799 | heart disease | 1 C0002871 | anemia | 1 C0011880 | diabetic ketoacidosis | 1 |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:33) 154664 | ABCA13 | 3.029 | DISEASES 51099 | ABHD5 | 1.758 | DISEASES 22852 | ANKRD26 | 2.26 | DISEASES 23365 | ARHGEF12 | 1.658 | DISEASES 885 | CCK | 1.142 | DISEASES 1441 | CSF3R | 2.243 | DISEASES 29119 | CTNNA3 | 1.998 | DISEASES 1736 | DKC1 | 3.049 | DISEASES 3692 | EIF6 | 6.314 | DISEASES 2175 | FANCA | 1.073 | DISEASES 2189 | FANCG | 1.286 | DISEASES 2209 | FCGR1A | 1.755 | DISEASES 2214 | FCGR3A | 1.593 | DISEASES 2624 | GATA2 | 2.054 | DISEASES 2993 | GYPA | 1.111 | DISEASES 10456 | HAX1 | 1.656 | DISEASES 10320 | IKZF1 | 1.003 | DISEASES 26013 | L3MBTL1 | 2.488 | DISEASES 654346 | LGALS9C | 4.26 | DISEASES 4311 | MME | 1.635 | DISEASES 4352 | MPL | 3.33 | DISEASES 9124 | PDLIM1 | 1.523 | DISEASES 256297 | PTF1A | 2.254 | DISEASES 9939 | RBM8A | 1.243 | DISEASES 6122 | RPL3 | 2.824 | DISEASES 6125 | RPL5 | 2.138 | DISEASES 6223 | RPS19 | 2.254 | DISEASES 6229 | RPS24 | 2.124 | DISEASES 51065 | RPS27L | 3.817 | DISEASES 10110 | SGK2 | 3.257 | DISEASES 6731 | SRP72 | 2.558 | DISEASES 7012 | TERC | 2.393 | DISEASES 157680 | VPS13B | 1.644 | DISEASES |
| Locus | (Waiting for update.) |
| Disease ID | 802 |
|---|---|
| Disease | shwachman diamond syndrome |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:34) HP:0002643 | Respiratory distress, neonatal HP:0002240 | Enlarged liver HP:0003300 | Oval vertebral bodies HP:0002863 | Myelodysplastic syndrome HP:0002910 | Elevated transaminases HP:0000920 | Enlarged costochondral junctions HP:0004322 | Stature below 3rd percentile HP:0001876 | Low blood cell count HP:0002719 | infections, recurrent HP:0005871 | Metaphyseal chondrodysplasia HP:0001700 | Myocardial necrosis HP:0001903 | Anemia HP:0003016 | Wide metaphyses HP:0000907 | Anteriorly splayed ribs HP:0001263 | Developmental retardation HP:0008803 | Narrow sacroiliac notch HP:0001518 | Small for gestational age HP:0000121 | Nephrocalcinosis HP:0002750 | Delayed bone maturation HP:0000774 | Low chest circumference HP:0001508 | Weight faltering HP:0004808 | Acute myelogenous leukemia HP:0006598 | Irregular ossification at anterior rib ends HP:0001875 | Neutropenia HP:0001873 | Low platelet count HP:0004979 | Metaphyseal sclerosis HP:0001738 | Exocrine pancreatic insufficiency HP:0002570 | Steatorrhea HP:0002812 | Coxa vara HP:0006461 | Slipped capilal femoral epiphysis HP:0001328 | Specific learning disability HP:0001256 | Mild mental retardation HP:0011904 | Persistence of hemoglobin F HP:0003411 | Proximal femoral metaphyseal irregularity |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:9) HP:0001875 | Neutropenia | 2 HP:0001953 | Diabetic ketosis | 1 HP:0001876 | Low blood cell count | 1 HP:0002665 | Lymphoma | 1 HP:0006725 | Pancreatic adenocarcinoma | 1 HP:0001903 | Anemia | 1 HP:0100543 | Cognitive deficits | 1 HP:0001607 | Subglottic stenosis | 1 HP:0000924 | Abnormality of the skeletal system | 1 |
| Disease ID | 802 |
|---|---|
| Disease | shwachman diamond syndrome |
| Manually Symptom | (Waiting for update.) |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:1) |
Manually Genotype(Total Text Mining Genotypes:0) |
|---|
| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:12) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs113993990 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS;TYW1 | 7 | 66995299 | C | - |
| rs113993991 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | NA | NA | NA | NA | NA |
| rs113993992 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS | 7 | 66994211 | C | G |
| rs113993993 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS | 7 | 66994210 | A | G |
| rs113993994 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS | 7 | 66993376 | TCTT | - |
| rs113993995 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS | 7 | 66993299 | C | G |
| rs113993996 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS | 7 | 66991256 | G | C,A |
| rs113993997 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS | 7 | 66991136 | C | T,G |
| rs113993998 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS | 7 | 66988472 | G | A |
| rs28942099 | NA | 51119 | SBDS | umls:C0272170 | CLINVAR | NA | 0.492757768 | NA | SBDS;TYW1 | 7 | 66995394 | G | T |
| rs28942099 | 12496757 | 51119 | SBDS | umls:C0272170 | UNIPROT | Mutations in SBDS are associated with Shwachman-Diamond syndrome. | 0.492757768 | 2003 | SBDS;TYW1 | 7 | 66995394 | G | T |
| rs79344818 | 12496757 | 51119 | SBDS | umls:C0272170 | UNIPROT | Mutations in SBDS are associated with Shwachman-Diamond syndrome. | 0.492757768 | 2003 | SBDS | 7 | 66988489 | A | G |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:14) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0001328 | Specific learning disability | MP:0002802 | abnormal discrimination learning | anomaly in the ability to exhibit a differential response to different stimuli that is achieved by the reinforcement of the desired response for each particular stimulus |
| HP:0002910 | Elevated hepatic transaminases | MP:0002628 | hepatic steatosis | an accumulation of fat deposits in the liver |
| HP:0001263 | Global developmental delay | MP:0002084 | abnormal developmental patterning | abnormal systematic arrangement of the developing body along an axis |
| HP:0001508 | Failure to thrive | MP:0013294 | prenatal lethality prior to heart atrial septation | death prior to the completion of heart atrial septation (Mus: E14.5-15.5) |
| HP:0000907 | Anterior rib cupping | MP:0000150 | abnormal rib morphology | any structural anomaly of the bones forming the bony wall of the chest |
| HP:0004808 | Acute myeloid leukemia | MP:0013663 | increased myeloid cell number | greater than the expected number of cells of the myeloid lineage |
| HP:0000774 | Narrow chest | MP:0004134 | abnormal chest morphology | any structural anomaly of the part of the body between the neck and the abdomen |
| HP:0000920 | Enlargement of the costochondral junction | MP:0008163 | increased diameter of ulna | increased width of the cross-sectional distance that extends from one lateral edge of the ulna, through its center and to the opposite lateral edge |
| HP:0001738 | Exocrine pancreatic insufficiency | MP:0014117 | increased pancreatic beta cell apoptosis | increase in the number of pancreatic beta cells undergoing programmed cell death |
| HP:0011904 | Persistence of hemoglobin F | MP:0010178 | increased number of Howell-Jolly bodies | abnormal 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:0003300 | Ovoid vertebral bodies | MP:0004704 | short vertebral column | decreased rostral-caudal length 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:0002643 | Neonatal respiratory distress | MP:0011649 | immotile respiratory cilia | failure of the multiple epithelial tiny, motile hair-like projections of the repiratory tract epithelium to beat with a characteristic whip-like pattern in order to promote transport of fluids and other cells across the epithelium of the respiratory tract |
| HP:0001518 | Small for gestational age | 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:0002750 | Delayed skeletal maturation | MP:0003379 | absent sexual maturation | failure to initiate pubertal changes that result in achievement of full sexual capacity |
Mapped by homologous gene(Total Items:34) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0001876 | Pancytopenia | MP:0020080 | increased bone mineralization | increase in the rate at which minerals are deposited into bone |
| HP:0001256 | Intellectual disability, mild | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0000920 | Enlargement of the costochondral junction | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0004979 | Metaphyseal sclerosis | MP:0012114 | absent inner cell mass proliferation | |
| HP:0000774 | Narrow chest | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0002570 | Steatorrhea | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0008803 | Narrow sacroiliac notch | MP:0012114 | absent inner cell mass proliferation | |
| HP:0001518 | Small for gestational age | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0004322 | Short stature | MP:3000003 | abnormal Ebner's gland morphology | any 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:0002240 | Hepatomegaly | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| 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:0001700 | Myocardial necrosis | MP:0012114 | absent inner cell mass proliferation | |
| HP:0005871 | Metaphyseal chondrodysplasia | MP:0020010 | decreased bone mineral density of femur | reduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh |
| HP:0001508 | Failure to thrive | 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:0000121 | Nephrocalcinosis | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0011904 | Persistence of hemoglobin F | 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:0001873 | Thrombocytopenia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0001328 | Specific learning disability | MP:3000003 | abnormal Ebner's gland morphology | any 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:0003300 | Ovoid vertebral bodies | 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:0001263 | Global developmental delay | MP:3000003 | abnormal Ebner's gland morphology | any 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:0002910 | Elevated hepatic transaminases | 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:0001738 | Exocrine pancreatic insufficiency | MP:0014233 | bile duct epithelium hyperplasia | |
| HP:0003411 | Proximal femoral metaphyseal irregularity | MP:0012114 | absent inner cell mass proliferation | |
| HP:0002812 | Coxa vara | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0006461 | Proximal femoral epiphysiolysis | MP:0013006 | abnormal enteric neural crest cell migration | any anomaly in the migratory path or behavior of the neural crest cells (NCCs) that arise predominantly from the vagal (neck) region of the neural tube (vagal neural crest), adjacent to somites 1-7, and migrate rostro-caudally along the gastrointestinal t |
| HP:0001875 | Neutropenia | MP:0020215 | impaired blood coagulation | impaired ability of the blood to clot |
| HP:0002643 | Neonatal respiratory distress | MP:0020010 | decreased bone mineral density of femur | reduction in the quatitative measurment value of mineral content of bone in the long bone of the thigh |
| HP:0006598 | Irregular ossification at anterior rib ends | MP:0012114 | absent inner cell mass proliferation | |
| HP:0002719 | Recurrent infections | 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:0004808 | Acute myeloid leukemia | MP:0014130 | thymus cysts | presence of fluid-filled spaces lined by epithelium within the thymus; thymic cysts are rare mediastinal lesions and are thought to result from the congenital persistence of thymopharyngeal tracts and acquired, progressive cystic degeneration of thymic (H |
| HP:0002750 | Delayed skeletal maturation | MP:0020169 | increased thyroid gland weight | higher than average weight of the thyroid gland |
| HP:0002863 | Myelodysplasia | 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:0000907 | Anterior rib cupping | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0003016 | Metaphyseal widening | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| Disease ID | 802 |
|---|---|
| Disease | shwachman diamond syndrome |
| Case | (Waiting for update.) |