eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| omenn syndrome | ||||
| Disease ID | 680 |
|---|---|
| Disease | omenn syndrome |
| Definition | An autosomal recessive combined immunodeficiency syndrome caused by mutations in the RAG-1 and RAG-2 genes. It is characterized by the presence of alopecia, erythroderma, desquamation, lymphadenopathy, and chronic diarrhea. |
| Synonym | familial reticuloendothelioses familial reticuloendotheliosis omenn's syndrome omenns syndrome reticuloendothelioses, familial reticuloendotheliosis, familial syndrome, omenn syndrome, omenn's |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C2700553 |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:3) |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:9) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:25) 100 | ADA | 1.17 | DISEASES 84433 | CARD11 | 1.967 | DISEASES 64170 | CARD9 | 3.063 | DISEASES 10803 | CCR9 | 1.881 | DISEASES 959 | CD40LG | 1.279 | DISEASES 55636 | CHD7 | 1.521 | DISEASES 1503 | CTPS1 | 2.516 | DISEASES 64421 | DCLRE1C | 5.076 | DISEASES 81704 | DOCK8 | 3.02 | DISEASES 1946 | EFNA5 | 3.991 | DISEASES 2214 | FCGR3A | 1.299 | DISEASES 50943 | FOXP3 | 2.929 | DISEASES 23765 | IL17RA | 1.646 | DISEASES 3561 | IL2RG | 3.827 | DISEASES 3836 | KPNA1 | 2.281 | DISEASES 3841 | KPNA5 | 3.246 | DISEASES 3981 | LIG4 | 2.022 | DISEASES 5238 | PGM3 | 3.354 | DISEASES 4860 | PNP | 1.509 | DISEASES 639 | PRDM1 | 1.452 | DISEASES 6023 | RMRP | 3.167 | DISEASES 58528 | RRAGD | 3.711 | DISEASES 6772 | STAT1 | 1.415 | DISEASES 7062 | TCHH | 1.672 | DISEASES 10673 | TNFSF13B | 2.205 | DISEASES |
| Locus | Symbol | Locus(Total Locus:9) |
| Disease ID | 680 |
|---|---|
| Disease | omenn syndrome |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:28) HP:0004332 | Abnormality of lymphocytes HP:0002960 | Autoimmunity HP:0100806 | Sepsis HP:0002716 | Lymphadenopathy HP:0100646 | Thyroiditis HP:0002028 | Chronic diarrhea HP:0004430 | Severe combined immunodeficiency HP:0100840 | Aplasia/Hypoplasia of the eyebrow HP:0001903 | Anemia HP:0001831 | Short toe HP:0002665 | Lymphoma HP:0001019 | Erythroderma HP:0001945 | Fever HP:0001508 | Failure to thrive HP:0002240 | Hepatomegaly HP:0007549 | Desquamation of skin soon after birth HP:0001744 | Splenomegaly HP:0001974 | Leukocytosis HP:0001596 | Alopecia HP:0000958 | Dry skin HP:0000100 | Nephrotic syndrome HP:0001072 | Thickened skin HP:0000989 | Pruritus HP:0002090 | Pneumonia HP:0000821 | Hypothyroidism HP:0000944 | Abnormality of the metaphyses HP:0001880 | Eosinophilia HP:0000969 | Edema |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:4) |
| Disease ID | 680 |
|---|---|
| Disease | omenn syndrome |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:1) C0302148 | thrombus |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Text Mining Genotypes:0) |
|---|
| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:25) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs104894284 | 9630231 | 5896 | RAG1 | umls:C2700553 | UNIPROT | We report here that patients with Omenn syndrome, a severe immunodeficiency characterized by the presence of activated, anergic, oligoclonal T cells, hypereosinophilia, and high IgE levels, bear missense mutations in either the Rag-1 or Rag-2 genes that result in partial activity of the two proteins. | 0.24 | 1998 | RAG1 | 11 | 36574986 | G | A |
| rs104894285 | 9630231 | 5896 | RAG1 | umls:C2700553 | UNIPROT | We report here that patients with Omenn syndrome, a severe immunodeficiency characterized by the presence of activated, anergic, oligoclonal T cells, hypereosinophilia, and high IgE levels, bear missense mutations in either the Rag-1 or Rag-2 genes that result in partial activity of the two proteins. | 0.24 | 1998 | RAG1 | 11 | 36574985 | C | T |
| rs104894286 | 18463379 | 5896 | RAG1 | umls:C2700553 | UNIPROT | An immunodeficiency disease with RAG mutations and granulomas. | 0.24 | 2008 | RAG1 | 11 | 36575514 | G | A |
| rs104894289 | 10606976 | 5896 | RAG1 | umls:C2700553 | UNIPROT | Omenn syndrome was recently found to be caused by missense mutations in RAG1 or RAG2 gene that result in partial V(D)J recombination activity. | 0.24 | 2000 | RAG1 | 11 | 36574490 | C | T |
| rs104894290 | 9630231 | 5896 | RAG1 | umls:C2700553 | UNIPROT | We report here that patients with Omenn syndrome, a severe immunodeficiency characterized by the presence of activated, anergic, oligoclonal T cells, hypereosinophilia, and high IgE levels, bear missense mutations in either the Rag-1 or Rag-2 genes that result in partial activity of the two proteins. | 0.24 | 1998 | RAG1 | 11 | 36576039 | A | G |
| rs104894291 | 19912631 | 5896 | RAG1 | umls:C2700553 | UNIPROT | Omenn syndrome (OS) shares the genetic aetiology of T-B-NK+ SCID, with mutations in RAG1, RAG2, or DCLRE1C. | 0.24 | 2009 | RAG1 | 11 | 36574491 | G | A,T |
| rs104894291 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574491 | G | A,T |
| rs104894292 | 9630231 | 5896 | RAG1 | umls:C2700553 | UNIPROT | We report here that patients with Omenn syndrome, a severe immunodeficiency characterized by the presence of activated, anergic, oligoclonal T cells, hypereosinophilia, and high IgE levels, bear missense mutations in either the Rag-1 or Rag-2 genes that result in partial activity of the two proteins. | 0.24 | 1998 | RAG1 | 11 | 36574590 | A | G |
| rs104894298 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574823 | C | T |
| rs121918571 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574287 | G | A |
| rs141524540 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574607 | A | G |
| rs150739647 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36576228 | G | A,C |
| rs193922461 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574870 | G | T |
| rs199474676 | 21771083 | 5896 | RAG1 | umls:C2700553 | UNIPROT | Clinical characteristics and molecular analysis of three Chinese children with Omenn syndrome. | 0.24 | 2011 | RAG1 | 11 | 36575399 | C | T |
| rs199474677 | 21624848 | 5896 | RAG1 | umls:C2700553 | UNIPROT | Novel mutations in RAG1/2 and ADA genes in Israeli patients presenting with T-B-SCID or Omenn syndrome. | 0.24 | 2011 | RAG1 | 11 | 36574665 | T | A |
| rs199474679 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574601 | G | A |
| rs199474681 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574981 | G | T |
| rs199474682 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574505 | T | C |
| rs199474684 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574533 | G | A |
| rs199474685 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574635 | C | T |
| rs199474686 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36574725 | G | A |
| rs199474687 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36575562 | A | G,T |
| rs199474688 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36575174 | C | T |
| rs199474689 | 11133745 | 5896 | RAG1 | umls:C2700553 | UNIPROT | V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. | 0.24 | 2001 | RAG1 | 11 | 36575310 | A | G |
| rs199474691 | 10606976 | 5896 | RAG1 | umls:C2700553 | UNIPROT | Omenn syndrome was recently found to be caused by missense mutations in RAG1 or RAG2 gene that result in partial V(D)J recombination activity. | 0.24 | 2000 | RAG1 | 11 | 36575958 | T | 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:7) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0001072 | Thickened skin | MP:0009932 | skin fibrosis | invasion of fibrous connective tissue into the skin, often resulting from inflammation or injury |
| HP:0100840 | Aplasia/Hypoplasia of the eyebrow | MP:0012167 | abnormal epigenetic regulation of gene expression | any anomaly in the process that modulates the frequency, rate or extent of gene expression, in which the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA |
| 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:0000944 | Abnormality of the metaphyses | MP:0013621 | decreased internal diameter of femur | reduced cross-sectional distance that extends from one lateral edge of the femur long bone marrow cavity, through its center and to the opposite lateral edge of the bone marrow cavity through the mid point of the femur |
| HP:0007549 | Desquamation of skin soon after birth | MP:0009674 | decreased birth weight | reduction in average weight at birth compared to controls |
| 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:0002028 | Chronic diarrhea | MP:0005036 | diarrhea | abnormally frequent discharge of semi-solid or fluid fecal matter from the bowel |
Mapped by homologous gene(Total Items:27) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| 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: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:0001072 | Thickened skin | 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:0001903 | Anemia | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0001744 | Splenomegaly | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001880 | Eosinophilia | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002960 | Autoimmunity | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| 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:0001019 | Erythroderma | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0100646 | Thyroiditis | MP:0014171 | increased fatty acid oxidation | increased rate or incidence of the process of removal of one or more electrons from a fatty acid, with or without the concomitant removal of a proton or protons, by reaction with an electron-accepting substance, by addition of oxygen or by removal of hydr |
| HP:0000821 | Hypothyroidism | MP:0020169 | increased thyroid gland weight | higher than average weight of the thyroid gland |
| HP:0007549 | Desquamation of skin soon after birth | MP:0011100 | preweaning lethality, complete penetrance | death of all organisms of a given genotype in a population between fertilization and weaning age (Mus: approximately 3-4 weeks of age) |
| 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:0000969 | Edema | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0001831 | Short toe | 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:0002090 | Pneumonia | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002665 | Lymphoma | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0000100 | Nephrotic syndrome | 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:0000958 | Dry skin | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000989 | Pruritus | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0100840 | Aplasia/Hypoplasia of the eyebrow | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0001974 | Leukocytosis | 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:0000944 | Abnormality of the metaphyses | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001596 | Alopecia | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| Disease ID | 680 |
|---|---|
| Disease | omenn syndrome |
| Case | (Waiting for update.) |