eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| severe combined immunodeficiency | ||||
| Disease ID | 125 |
|---|---|
| Disease | severe combined immunodeficiency |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:54) C2707258 | infections C2364133 | infection C2363741 | hiv-1 infection C1962971 | myocarditis C1961102 | acute lymphoblastic leukemias C1855471 | lymphokine deficiency C1839611 | n syndrome C1609516 | necrotizing retinitis C1512411 | hepatocellular carcinoma C1458155 | breast tumors C1336745 | thymic lymphoma C1264606 | persistent infection C0869523 | carditis C0860040 | bcg infection C0856825 | acute gvhd C0796561 | melanoma C0717360 | lyme disease C0684249 | lung cancer C0677886 | ovarian carcinoma C0424755 | fever C0267375 | chronic colitis C0220754 | biotinidase deficiency C0206061 | interstitial pneumonia C0085669 | acute leukemias C0085669 | acute leukemia C0079731 | b-cell lymphomas C0079731 | b-cell lymphoma C0078048 | varicella C0042769 | virus infection C0042721 | virus hepatitis C0039538 | teratomas C0032305 | pneumocystis carinii pneumonia C0032285 | pneumonitis C0029443 | osteomyelitis C0026987 | myelofibrosis C0026916 | mycobacterium avium infection C0026896 | myasthenia gravis C0025202 | melanomas C0024312 | lymphocytopenia C0024299 | lymphoma C0024198 | lyme borreliosis C0023418 | leukemia C0021841 | intestinal tumors C0019158 | hepatitis C0018133 | graft-versus-host disease C0018133 | graft versus host disease C0017638 | glioma C0017168 | gastroesophageal reflux C0014733 | erysipelas C0011616 | contact sensitivity C0010823 | cytomegalovirus infection C0008513 | chorioretinitis C0006413 | burkitt's lymphoma C0005940 | bone disease |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:13) C0039538 | teratomas | 4 C0009450 | infection | 4 C0023418 | leukemia | 3 C0042769 | virus infection | 2 C0860040 | bcg infection | 1 C0021311 | infections | 1 C0024299 | lymphoma | 1 C0079731 | b-cell lymphoma | 1 C0024312 | lymphocytopenia | 1 C0010823 | cytomegalovirus infection | 1 C1839611 | n syndrome | 1 C0018133 | graft-versus-host disease | 1 C0011847 | diabetes | 1 |
Manually Genotype(Total Manually Genotypes:1) | |||
|---|---|---|---|
| Gene | Mutation | DOI | Article Title |
| DCLRE1C | Hom del exon 1–3 | doi:10.1038/gim.2011.65 | Exon-level array CGH in a large clinical cohort demonstrates increased sensitivity of diagnostic testing for Mendelian disorders |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:30) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs104894287 | 18592361 | 5896 | RAG1 | umls:C0085110 | BeFree | These presentations are consistent with atypical severe combined immunodeficiency (SCID)/Omenn Syndrome and the diagnosis was confirmed by demonstration of homozygosity for the R841W mutation in the catalytic core of RAG1. | 0.145684746 | 2008 | RAG1 | 11 | 36575825 | C | T |
| rs104894421 | 20133615 | 3981 | LIG4 | umls:C0085110 | BeFree | Homozygous DNA ligase IV R278H mutation in mice leads to leaky SCID and represents a model for human LIG4 syndrome. | 0.009172942 | 2010 | LIG4 | 13 | 108210436 | C | T |
| rs112431538 | 24077944 | 7157 | TP53 | umls:C0085110 | BeFree | Sequencing of OANC1 DNA identified homozygous TP53 missense (c.856G[A, p.E286K)and SMAD4 nonsense (c.1333C[T, p.R445X) mutations.OANC1 are tumorigenic when injected sub-cutaneously into SCID mice and xenografts were positive for columnar, glandular and intestinal epithelial markers commonly expressed in EAC. | 0.002171535 | 2013 | TP53 | 17 | 7673767 | C | T |
| rs112431538 | 24077944 | 4089 | SMAD4 | umls:C0085110 | BeFree | Sequencing of OANC1 DNA identified homozygous TP53 missense (c.856G[A, p.E286K)and SMAD4 nonsense (c.1333C[T, p.R445X) mutations.OANC1 are tumorigenic when injected sub-cutaneously into SCID mice and xenografts were positive for columnar, glandular and intestinal epithelial markers commonly expressed in EAC. | 0.000271442 | 2013 | TP53 | 17 | 7673767 | C | T |
| rs121908721 | NA | 100 | ADA | umls:C0085110 | CLINVAR | NA | 0.151954196 | NA | ADA | 20 | 44621121 | G | C,A |
| rs121908725 | 7599635 | 100 | ADA | umls:C0085110 | BeFree | Three new missense mutations (H15D, A83D, and A179D) and a new splicing defect (573 + IG-->A) in the 5' splice site of intron 5 were among six mutant adenosine deaminase (ADA) alleles found in three unrelated patients with severe combined immunodeficiency disease, the most common phenotype associated with ADA deficiency. | 0.151954196 | 1995 | ADA | 20 | 44636279 | G | C |
| rs121908726 | 7599635 | 100 | ADA | umls:C0085110 | BeFree | Three new missense mutations (H15D, A83D, and A179D) and a new splicing defect (573 + IG-->A) in the 5' splice site of intron 5 were among six mutant adenosine deaminase (ADA) alleles found in three unrelated patients with severe combined immunodeficiency disease, the most common phenotype associated with ADA deficiency. | 0.151954196 | 1995 | ADA | 20 | 44626570 | G | T |
| rs121908727 | 7599635 | 100 | ADA | umls:C0085110 | BeFree | Three new missense mutations (H15D, A83D, and A179D) and a new splicing defect (573 + IG-->A) in the 5' splice site of intron 5 were among six mutant adenosine deaminase (ADA) alleles found in three unrelated patients with severe combined immunodeficiency disease, the most common phenotype associated with ADA deficiency. | 0.151954196 | 1995 | ADA | 20 | 44624272 | G | T |
| rs121917894 | 17476358 | 5897 | RAG2 | umls:C0085110 | BeFree | In order to better define the molecular and cellular pathophysiology of OS, we generated a knockin murine model carrying the Rag2 R229Q mutation previously described in several patients with OS and leaky forms of SCID. | 0.138607394 | 2007 | RAG2;C11orf74 | 11 | 36593483 | C | T,A |
| rs137852624 | 10075926 | 3718 | JAK3 | umls:C0085110 | BeFree | Here we describe a naturally occurring Jak3 mutation from a patient with autosomal severe combined immunodeficiency (SCID), where a single amino acid substitution, Y100C, in Janus homology domain 7 (JH7) prevents kinase-receptor interaction. | 0.141583323 | 1999 | JAK3 | 19 | 17843786 | T | C |
| rs148001159 | NA | 3575 | IL7R | umls:C0085110 | CLINVAR | NA | 0.125895776 | NA | IL7R | 5 | 35860983 | G | C |
| rs148508754 | NA | 5897 | RAG2 | umls:C0085110 | CLINVAR | NA | 0.138607394 | NA | RAG2;C11orf74 | 11 | 36594065 | C | G |
| rs193922361 | NA | 3718 | JAK3 | umls:C0085110 | CLINVAR | NA | 0.141583323 | NA | JAK3 | 19 | 17837171 | G | A |
| rs193922362 | NA | 3718 | JAK3 | umls:C0085110 | CLINVAR | NA | 0.141583323 | NA | JAK3 | 19 | 17837148 | G | A |
| rs193922364 | NA | 3718 | JAK3 | umls:C0085110 | CLINVAR | NA | 0.141583323 | NA | JAK3 | 19 | 17842498 | AG | - |
| rs193922462 | NA | 5896 | RAG1 | umls:C0085110 | CLINVAR | NA | 0.145684746 | NA | RAG1 | 11 | 36575907 | C | T |
| rs193922464 | NA | 5896 | RAG1 | umls:C0085110 | CLINVAR | NA | 0.145684746 | NA | RAG1 | 11 | 36573626 | C | G,T |
| rs193922573 | NA | 5897 | RAG2 | umls:C0085110 | CLINVAR | NA | 0.138607394 | NA | RAG2;C11orf74 | 11 | 36592860 | C | T |
| rs193922574 | NA | 5897 | RAG2 | umls:C0085110 | CLINVAR | NA | 0.138607394 | NA | RAG2;C11orf74 | 11 | 36593952 | G | A |
| rs193922575 | NA | 5897 | RAG2 | umls:C0085110 | CLINVAR | NA | 0.138607394 | NA | RAG2;C11orf74 | 11 | 36593841 | T | G,C |
| rs193922640 | NA | 3575 | IL7R | umls:C0085110 | CLINVAR | NA | 0.125895776 | NA | IL7R | 5 | 35867364 | - | ATATATTTCA |
| rs193922641 | NA | 3575 | IL7R | umls:C0085110 | CLINVAR | NA | 0.125895776 | NA | IL7R | 5 | 35867437 | G | A |
| rs193922642 | NA | 3575 | IL7R | umls:C0085110 | CLINVAR | NA | 0.125895776 | NA | IL7R | 5 | 35873481 | A | C |
| rs193922643 | NA | 3575 | IL7R | umls:C0085110 | CLINVAR | NA | 0.125895776 | NA | NA | NA | NA | NA | NA |
| rs193922644 | NA | 3575 | IL7R | umls:C0085110 | CLINVAR | NA | 0.125895776 | NA | IL7R | 5 | 35873559 | G | A,T |
| rs193922645 | NA | 3575 | IL7R | umls:C0085110 | CLINVAR | NA | 0.125895776 | NA | IL7R | 5 | 35873586 | G | T |
| rs193922647 | NA | 3575 | IL7R | umls:C0085110 | CLINVAR | NA | 0.125895776 | NA | IL7R | 5 | 35875988 | A | C |
| rs377767360 | 24077944 | 4089 | SMAD4 | umls:C0085110 | BeFree | Sequencing of OANC1 DNA identified homozygous TP53 missense (c.856G[A, p.E286K)and SMAD4 nonsense (c.1333C[T, p.R445X) mutations.OANC1 are tumorigenic when injected sub-cutaneously into SCID mice and xenografts were positive for columnar, glandular and intestinal epithelial markers commonly expressed in EAC. | 0.000271442 | 2013 | SMAD4 | 18 | 51076662 | C | T |
| rs377767360 | 24077944 | 7157 | TP53 | umls:C0085110 | BeFree | Sequencing of OANC1 DNA identified homozygous TP53 missense (c.856G[A, p.E286K)and SMAD4 nonsense (c.1333C[T, p.R445X) mutations.OANC1 are tumorigenic when injected sub-cutaneously into SCID mice and xenografts were positive for columnar, glandular and intestinal epithelial markers commonly expressed in EAC. | 0.002171535 | 2013 | SMAD4 | 18 | 51076662 | C | T |
| rs41297018 | NA | 64421 | DCLRE1C | umls:C0085110 | CLINVAR | NA | 0.132072926 | NA | DCLRE1C | 10 | 14935470 | C | T,A |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:8) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0000389 | Chronic otitis media | MP:0001850 | increased susceptibility to otitis media | greater likelihood of middle ear inflammation, with an accumulation of a thick, mucous-like fluid; usually associated with a viral or bacterial respiratory infection |
| HP:0000407 | Sensorineural hearing impairment | MP:0006330 | syndromic hearing impairment | hearing impairment that is usually associated with malformations of the external ear and other inherited signs and symptoms |
| 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:0100763 | Abnormality of the lymphatic system | MP:0004502 | decreased incidence of tumors by chemical induction | lower than normal frequency of tumor incidence induced by one or more chemical carcinogens or mutagens |
| HP:0000164 | Abnormality of the teeth | MP:0010382 | abnormal dosage compensation, by inactivation of X chromosome | anomaly in the process of compensating for the two-fold variation in X-chromosome:autosome ratios between sexes by a global inactivation of all, or most of, the genes on one of the X-chromosomes in the XX sex |
| HP:0000010 | Recurrent urinary tract infections | MP:0014044 | absent cardiac outflow tract | absence of or complete failure to form the common arterial trunk that normally forms the aorta and pulmonary artery and the ventricular outflow regions |
| HP:0002028 | Chronic diarrhea | MP:0005036 | diarrhea | abnormally frequent discharge of semi-solid or fluid fecal matter from the bowel |
| HP:0002205 | Recurrent respiratory infections | MP:0014182 | decreased respiratory epithelial sodium ion transmembrane transport | decrease in the directed movement of sodium ions from one side of the respiratory epithelial cell membrane to the other |
Mapped by homologous gene(Total Items:18) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0100763 | Abnormality of the lymphatic system | MP:0012431 | increased lymphoma incidence | greater than the expected number of neoplasms characterized by a proliferation of malignant lymphocytes in lymphoid tissue in a specific population in a given time period |
| HP:0100806 | Sepsis | MP:0011708 | decreased fibroblast cell migration | reduced frequency of or less rapid fibroblast cell migration that is accomplished by extension and retraction of a fibroblast pseudopodium |
| HP:0002028 | Chronic diarrhea | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0001945 | Fever | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001888 | Lymphopenia | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002721 | Immunodeficiency | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0000407 | Sensorineural hearing impairment | 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:0004430 | Severe combined immunodeficiency | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| 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:0000164 | Abnormality of the teeth | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000389 | Chronic otitis media | 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:0000010 | Recurrent urinary tract infections | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0002205 | Recurrent respiratory infections | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0000252 | Microcephaly | 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:0001744 | Splenomegaly | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001596 | Alopecia | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0000988 | Skin rash | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| Disease ID | 125 |
|---|---|
| Disease | severe combined immunodeficiency |
| Case | (Waiting for update.) |