eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| x-linked agammaglobulinemia | ||||
| Disease ID | 88 |
|---|---|
| Disease | x-linked agammaglobulinemia |
| Definition | X-linked agammaglobulinemia. An immunodeficiency state characterized (usually) by profoundly low concentrations of serum immunoglobulins of all classes, although occasionally significant amounts of one or more isotypes can be found. The fundamental defect in XLA affects early lineage B cells. |
| Synonym | agammaglobulinemia x-linked agammaglobulinemia, bruton tyrosine kinase agammaglobulinemia, btk agammaglobulinemia, congenital agammaglobulinemia, sex-linked agammaglobulinemia, x-linked agammaglobulinemia, x-linked infantile agammaglobulinemia, x-linked, type 1 agammaglobulinemia, x-linked, type i agmx1 bruton disease bruton type agammaglobulinemia bruton's agammaglobulinaemia bruton's agammaglobulinemia bruton's hypogammaglobulinaemia bruton's hypogammaglobulinemia bruton's sex-linked agammaglobulinemia bruton's type agammaglobulinaemia bruton's type agammaglobulinemia bruton's x-linked agammaglobulinemia bruton-type (congenital x-linked) agammaglobulinemia bruton-type agammaglobulinemia congenital agammaglobulinaemia congenital agammaglobulinemia congenital agammaglobulinemia (disorder) imd1 immunodeficiency 1 sex-linked agammaglobulinemia x linked agammaglobulinaemia x linked agammaglobulinemia x-linked agammaglobulinaemia x-linked agammaglobulinemia (disorder) xla xla - x-linked agammaglobulinaemia xla - x-linked agammaglobulinemia |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C0221026 |
| SNOMED-CT | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:16) C0553662 | juvenile idiopathic arthritis | 2 C0003864 | arthritis | 2 C0023448 | lymphoblastic leukemia | 1 C0008924 | cleft lip | 1 C0085652 | pyoderma gangrenosum | 1 C0023449 | acute lymphoblastic leukemia | 1 C0034212 | pyoderma | 1 C0024291 | hemophagocytic syndrome | 1 C0002726 | amyloidosis | 1 C0013338 | growth hormone deficiency | 1 C0024299 | lymphoma | 1 C0002986 | fabry's disease | 1 C0079774 | peripheral t-cell lymphoma | 1 C0013421 | dystonia | 1 C0001768 | agammaglobulinemia | 1 C0014038 | encephalitis | 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:17) 930 | CD19 | 1.5 | DISEASES 9308 | CD83 | 1.504 | DISEASES 355 | FAS | 1.141 | DISEASES 2213 | FCGR2B | 1.712 | DISEASES 2308 | FOXO1 | 1.198 | DISEASES 2533 | FYB | 2.8 | DISEASES 388585 | HES5 | 2.693 | DISEASES 3702 | ITK | 2.125 | DISEASES 4067 | LYN | 3.561 | DISEASES 4615 | MYD88 | 1.102 | DISEASES 5336 | PLCG2 | 3.268 | DISEASES 2185 | PTK2B | 2.046 | DISEASES 6714 | SRC | 1.37 | DISEASES 51284 | TLR7 | 1.381 | DISEASES 54106 | TLR9 | 1.222 | DISEASES 7124 | TNF | 1.183 | DISEASES 7454 | WAS | 1.664 | DISEASES |
| Locus | Symbol | Locus(Total Locus:1) BTK | Xq22.1 |
| Disease ID | 88 |
|---|---|
| Disease | x-linked agammaglobulinemia |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:35) HP:0012378 | Fatigue HP:0004322 | Short stature HP:0000246 | Sinusitis HP:0002960 | Autoimmunity HP:0001824 | Weight loss HP:0001287 | Meningitis HP:0006532 | Recurrent pneumonia HP:0100806 | Sepsis HP:0004432 | Agammaglobulinemia HP:0001873 | Thrombocytopenia HP:0001053 | Hypopigmented skin patches HP:0002028 | Chronic diarrhea HP:0200042 | Skin ulcer HP:0000407 | Sensorineural hearing impairment HP:0001903 | Anemia HP:0002024 | Malabsorption HP:0002088 | Abnormality of lung morphology HP:0002754 | Osteomyelitis HP:0002664 | Neoplasm HP:0002901 | Hypocalcemia HP:0100838 | Recurrent cutaneous abscess formation HP:0000162 | Glossoptosis HP:0000389 | Chronic otitis media HP:0001945 | Fever HP:0001508 | Failure to thrive HP:0100763 | Abnormality of the lymphatic system HP:0001875 | Neutropenia HP:0000988 | Skin rash HP:0100658 | Cellulitis HP:0001596 | Alopecia HP:0002721 | Immunodeficiency HP:0001369 | Arthritis HP:0100765 | Abnormality of the tonsils HP:0000509 | Conjunctivitis HP:0012115 | Hepatitis |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:17) HP:0001369 | Arthritis | 2 HP:0005681 | Juvenile idiopathic arthritis | 2 HP:0000365 | Hearing impairment | 2 HP:0012190 | T cell lymphoma | 1 HP:0000824 | Growth hormone deficiency | 1 HP:0011034 | Amyloid disease | 1 HP:0002665 | Lymphoma | 1 HP:0001300 | Parkinsonism | 1 HP:0005764 | Polyarticular arthritis | 1 HP:0002383 | Encephalitis | 1 HP:0002721 | Immunodeficiency | 1 HP:0006721 | Acute lymphocytic leukemia | 1 HP:0000999 | Pyoderma | 1 HP:0001332 | Dystonia | 1 HP:0004432 | Agammaglobulinaemia | 1 HP:0002960 | Autoimmune condition | 1 HP:0001917 | Renal amyloidosis | 1 |
| Disease ID | 88 |
|---|---|
| Disease | x-linked agammaglobulinemia |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:27) C2364133 | infection C2186532 | liver disease C2029884 | hearing loss C1963211 | pericarditis C1963178 | myelitis C1963165 | malabsorption C1963101 | encephalopathy C1839611 | n syndrome C1096582 | campylobacter jejuni infection C0684249 | lung cancer C0423319 | iris atrophy C0338401 | enteroviral encephalitis C0085435 | reactive arthritis C0085113 | von recklinghausen disease C0034012 | delayed puberty C0027947 | neutropenia C0027121 | myositis C0026986 | myelodysplastic syndrome C0026936 | mycoplasma infections C0025309 | meningoencephalitis C0023524 | progressive multifocal leukoencephalopathy C0017662 | membranoproliferative glomerulonephritis C0014038 | encephalitis C0009404 | colorectal neoplasms C0004610 | bacteremia C0003872 | psoriatic arthritis C0003864 | arthritis |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:3) |
Manually Genotype(Total Manually Genotypes:1) | |||
|---|---|---|---|
| Gene | Mutation | DOI | Article Title |
| BTK | - | doi:10.1038/gim.2015.51 | Clinical performance of the CytoScan Dx Assay in diagnosing developmental delay/intellectual disability |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:40) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs104894770 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353935 | C | G |
| rs128620183 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101354687 | C | T |
| rs128620184 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356845 | T | C |
| rs128620185 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101375202 | C | T |
| rs128620186 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101375283 | A | G |
| rs128620187 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101375248 | G | A |
| rs128620188 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101375242 | G | A |
| rs128620189 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101375188 | T | G |
| rs128621190 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101370051 | A | T |
| rs128621191 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101360626 | C | A |
| rs128621192 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101360589 | C | T |
| rs128621193 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101360581 | G | A |
| rs128621194 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101359325 | G | A |
| rs128621195 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101358672 | T | C |
| rs128621196 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101358411 | T | G |
| rs128621198 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356910 | A | G |
| rs128621199 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356858 | G | T,A |
| rs128621200 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356102 | A | G |
| rs128621201 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356060 | G | A |
| rs128621202 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356059 | C | T |
| rs128621204 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353936 | G | A |
| rs128621205 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353879 | A | G |
| rs128621206 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353336 | T | C |
| rs128621207 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353329 | G | T |
| rs128621208 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353282 | G | T |
| rs128621209 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353264 | C | T |
| rs128621210 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353213 | A | T |
| rs128622211 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353196 | C | A |
| rs128622212 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK;TIMM8A | X | 101349910 | A | G |
| rs193922124 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356163 | G | T |
| rs193922125 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356107 | T | A |
| rs193922126 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101353940 | TGGAAATT | - |
| rs193922128 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101362606 | CTGT | - |
| rs193922129 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101360152 | T | C |
| rs193922131 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101359348 | C | T |
| rs193922132 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101358698 | T | C |
| rs193922133 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101358414 | T | C |
| rs28935176 | 10678660 | 695 | BTK | umls:C0221026 | UNIPROT | Twin carriers of X-linked agammaglobulinemia (XLA) due to germline mutation in the Btk gene. | 0.590130048 | 2000 | NA | NA | NA | NA | NA |
| rs28935478 | 7849697 | 695 | BTK | umls:C0221026 | UNIPROT | These studies document the considerable variability in the Btk mutations causing XLA and they demonstrate an approach that will be useful for carrier detection as well as mutation identification. | 0.590130048 | 1994 | BTK | X | 101358330 | T | C |
| rs41310709 | NA | 695 | BTK | umls:C0221026 | CLINVAR | NA | 0.590130048 | NA | BTK | X | 101356112 | G | A,T |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:9) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0100765 | Abnormality of the tonsils | MP:0008158 | increased diameter of femur | increased width of the cross-sectional distance that extends from one lateral edge of the femur, through its center and to the opposite lateral edge |
| 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:0001053 | Hypopigmented skin patches | MP:0004947 | skin inflammation | local accumulation of fluid, plasma proteins, and leukocytes in the skin |
| 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:0006532 | Recurrent pneumonia | MP:0001862 | interstitial pneumonia | any of a group of inflammatory and fibrotic disorders of the lower respiratory tract, primarily affecting the supporting framework of the lung, including the alveolar wall, but may also involve the small airways and blood vessels of the lung parenchyma |
| HP:0002028 | Chronic diarrhea | MP:0005036 | diarrhea | abnormally frequent discharge of semi-solid or fluid fecal matter from the bowel |
| HP:0001824 | Weight loss | MP:0005114 | premature hair loss | release of fur at an earlier than expected time |
Mapped by homologous gene(Total Items:34) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0002754 | Osteomyelitis | MP:0020080 | increased bone mineralization | increase in the rate at which minerals are deposited into bone |
| 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:0002664 | Neoplasm | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0000509 | Conjunctivitis | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0001369 | Arthritis | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| 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:0001903 | Anemia | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0002024 | Malabsorption | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| 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: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:0002721 | Immunodeficiency | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| 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:0001287 | Meningitis | MP:0020215 | impaired blood coagulation | impaired ability of the blood to clot |
| HP:0004432 | Agammaglobulinemia | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0002901 | Hypocalcemia | MP:0014169 | decreased brown adipose tissue mass | decreased physical bulk or volume of brown adipose tissue |
| HP:0001873 | Thrombocytopenia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0012378 | Fatigue | MP:0013659 | abnormal erythroid lineage cell morphology | any structural anomaly of an immature or mature cell in the lineage leading to and including erythrocytes |
| HP:0006532 | Recurrent pneumonia | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| 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:0001824 | Weight loss | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0001053 | Hypopigmented skin patches | MP:0014164 | abnormal ciliary process morphology | any structural anomaly of any of the pigmented processes that radiate from the ciliary muscle and give attachments to ligaments supporting the lens of the eye; these processes increase in thickness as they advance from the orbiculus ciliaris to the exter |
| HP:0100838 | Recurrent cutaneous abscess formation | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000162 | Glossoptosis | MP:0013292 | embryonic lethality prior to organogenesis | death prior to the completion of embryo turning (Mus: E9-9.5) |
| HP:0200042 | Skin ulcer | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000246 | Sinusitis | MP:0020186 | altered susceptibility to bacterial infection | a change in the likelihood that an organism will develop ill effects from a bacterial infection or from components of or toxins produced by bacteria |
| HP:0001875 | Neutropenia | MP:0020215 | impaired blood coagulation | impaired ability of the blood to clot |
| HP:0100658 | Cellulitis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0100765 | Abnormality of the tonsils | 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: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:0012115 | Hepatitis | MP:0013716 | hypolactation | partial failure, or reduced ability to produce or secrete milk from the mammary gland |
| 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 | 88 |
|---|---|
| Disease | x-linked agammaglobulinemia |
| Case | (Waiting for update.) |