eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| lig4 syndrome | ||||
| Disease ID | 1351 |
|---|---|
| Disease | lig4 syndrome |
| Definition | A very rare genetic disorder caused by mutation in the LIG4 gene. It is characterized by unusual facial features, microcephaly, growth and developmental delay, severe immunodeficiency, and skin abnormalities. |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C1847827 |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | (Waiting for update.) |
| Locus | Symbol | Locus(Total Locus:2) |
| Disease ID | 1351 |
|---|---|
| Disease | lig4 syndrome |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:35) HP:0000028 | Cryptorchidism HP:0001263 | Global developmental delay HP:0100585 | Telangiectasia of the skin HP:0000248 | Brachycephaly HP:0000233 | Thin vermilion border HP:0008736 | Hypoplasia of penis HP:0010783 | Erythema HP:0002716 | Lymphadenopathy HP:0000582 | Upslanted palpebral fissure HP:0000347 | Micrognathia HP:0000506 | Telecanthus HP:0004430 | Severe combined immunodeficiency HP:0003220 | Abnormality of chromosome stability HP:0002024 | Malabsorption HP:0001510 | Growth delay HP:0000924 | Abnormality of the skeletal system HP:0001876 | Pancytopenia HP:0005978 | Type II diabetes mellitus HP:0000286 | Epicanthus HP:0002665 | Lymphoma HP:0000294 | Low anterior hairline HP:0000252 | Microcephaly HP:0002240 | Hepatomegaly HP:0004209 | Clinodactyly of the 5th finger HP:0000431 | Wide nasal bridge HP:0001249 | Intellectual disability HP:0001974 | Leukocytosis HP:0003683 | Large beaked nose HP:0002721 | Immunodeficiency HP:0005561 | Abnormality of bone marrow cell morphology HP:0000992 | Cutaneous photosensitivity HP:0002488 | Acute leukemia HP:0004422 | Biparietal narrowing HP:0000320 | Bird-like facies HP:0000821 | Hypothyroidism |
| Text Mined Phenotype | (Waiting for update.) |
| Disease ID | 1351 |
|---|---|
| Disease | lig4 syndrome |
| Manually Symptom | (Waiting for update.) |
| 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:9) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs104894418 | 15333585 | 3981 | LIG4 | umls:C1847827 | BeFree | Analysis of additional mutational changes in LIG4 syndrome (R580X, R814X and G469E) have led to the identification of a nuclear localization signal in DNA ligase IV and sites impacting upon DNA ligase IV adenylation. | 0.562171535 | 2004 | LIG4 | 13 | 108209531 | G | C,A |
| rs104894418 | NA | 3981 | LIG4 | umls:C1847827 | CLINVAR | NA | 0.562171535 | NA | LIG4 | 13 | 108209531 | G | C,A |
| rs104894419 | 15333585 | 3981 | LIG4 | umls:C1847827 | BeFree | Analysis of additional mutational changes in LIG4 syndrome (R580X, R814X and G469E) have led to the identification of a nuclear localization signal in DNA ligase IV and sites impacting upon DNA ligase IV adenylation. | 0.562171535 | 2004 | LIG4 | 13 | 108208829 | G | A |
| rs104894419 | NA | 3981 | LIG4 | umls:C1847827 | CLINVAR | NA | 0.562171535 | NA | LIG4 | 13 | 108208829 | G | A |
| rs104894420 | NA | 3981 | LIG4 | umls:C1847827 | CLINVAR | NA | 0.562171535 | NA | LIG4 | 13 | 108209863 | C | T |
| rs104894420 | 15333585 | 3981 | LIG4 | umls:C1847827 | BeFree | Analysis of additional mutational changes in LIG4 syndrome (R580X, R814X and G469E) have led to the identification of a nuclear localization signal in DNA ligase IV and sites impacting upon DNA ligase IV adenylation. | 0.562171535 | 2004 | LIG4 | 13 | 108209863 | C | T |
| rs104894421 | 20133615 | 3981 | LIG4 | umls:C1847827 | BeFree | Homozygous DNA ligase IV R278H mutation in mice leads to leaky SCID and represents a model for human LIG4 syndrome. | 0.562171535 | 2010 | LIG4 | 13 | 108210436 | C | T |
| rs104894421 | NA | 3981 | LIG4 | umls:C1847827 | CLINVAR | NA | 0.562171535 | NA | LIG4 | 13 | 108210436 | C | T |
| rs587776663 | NA | 3981 | LIG4 | umls:C1847827 | CLINVAR | NA | 0.562171535 | NA | LIG4 | 13 | 108209969 | GTT | - |
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:0003220 | Abnormality of chromosome stability | MP:0006241 | abnormal placement of pupils | abnormal location of the pupil so that it is not in the center of the iris |
| HP:0000431 | Wide nasal bridge | MP:0006292 | abnormal nasal placode morphology | any structural anomaly in the paired ectodermal placodes that come to lie in the bottom of the olfactory pits as the pits are deepened by the growth of the surrounding medial and lateral nasal processes; the nasal placode gives rise to the olfactory epith |
| HP:0003683 | Large beaked nose | MP:0002233 | abnormal nose morphology | any structural anomaly of the organ that is specialized for smell and is part of the respiratory system |
| HP:0000992 | Cutaneous photosensitivity | MP:0001202 | skin photosensitivity | abnormally heightened reactivity of the skin to sunlight |
| HP:0002488 | Acute leukemia | MP:0005481 | increased chronic myelocytic leukemia incidence | higher than normal incidence of a heterogeneous group of myeloproliferative disorders that may evolve into acute leukemia in late stages |
| HP:0004209 | Clinodactyly of the 5th finger | MP:0011665 | d-loop transposition of the great arteries | complete transposition of the great arteries; the d- refers to the dextroposition of the bulboventricular loop (ie, the position of the right ventricle, which is on the right side); in addition, the aorta also tends to be on the right and anterior, and th |
| HP:0001263 | Global developmental delay | MP:0002084 | abnormal developmental patterning | abnormal systematic arrangement of the developing body along an axis |
| HP:0000294 | Low anterior hairline | MP:0004784 | abnormal anterior cardinal vein morphology | any structural anomaly of the two paired veins draining the cephalic part of the body |
| HP:0000582 | Upslanted palpebral fissure | MP:0012535 | abnormal optic fissure closure | failure to initiate and/or complete closure of the transient gap in the ventral margin of the developing optic cup; fusion of the optic fissure begins with apposition of the inferior lips of the ventral-most optic cup and continues anteriorly toward its r |
| HP:0005561 | Abnormality of bone marrow cell morphology | MP:0013283 | failure of ventral body wall closure | failure of the lateral body wall folds (a combination of mesoderm and ectoderm arising on each side of the embryo) to progress ventrally and meet in the midline and/or fuse to close the ventral body wall; normally, this closure is aided by growth of the h |
| HP:0000924 | Abnormality of the skeletal system | MP:0013283 | failure of ventral body wall closure | failure of the lateral body wall folds (a combination of mesoderm and ectoderm arising on each side of the embryo) to progress ventrally and meet in the midline and/or fuse to close the ventral body wall; normally, this closure is aided by growth of the h |
| HP:0100585 | Telangiectasia of the skin | MP:0011022 | abnormal circadian regulation of systemic arterial blood pressure | any anomaly in the process in which an organism modulates its blood pressure at different values with a regularity of approximately 24 hours |
| HP:0008736 | Hypoplasia of penis | MP:0013283 | failure of ventral body wall closure | failure of the lateral body wall folds (a combination of mesoderm and ectoderm arising on each side of the embryo) to progress ventrally and meet in the midline and/or fuse to close the ventral body wall; normally, this closure is aided by growth of the h |
| HP:0005978 | Type II diabetes mellitus | MP:0004803 | increased susceptibility to autoimmune diabetes | greater likelihood that an organism will develop inflammatory pancreatic disease resulting from the body attacking and destroying the insulin-producing beta islet cells of the pancreas |
Mapped by homologous gene(Total Items:35) | ||||
|---|---|---|---|---|
| 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: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:0000320 | Bird-like facies | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0010783 | Erythema | MP:0013781 | abnormal mammary gland luminal epithelium morphology | any structural anomaly of the inner cell layer of the mammary epithelium bilayer that lines the luminal surface of mammary gland ducts and alveoli; luminal cells have only limited contact with the underlying basement membrane and surrounding connective ti |
| HP:0002240 | Hepatomegaly | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000506 | Telecanthus | 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:0002024 | Malabsorption | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0000347 | Micrognathia | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0002488 | Acute leukemia | MP:0013886 | increased CD4-negative, CD25-positive NK T cell number | increase in the number of CD4-negative NK T cells expressing the activation marker CD25 |
| 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:0000992 | Cutaneous photosensitivity | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001510 | Growth delay | MP:0020169 | increased thyroid gland weight | higher than average weight of the thyroid gland |
| HP:0000028 | Cryptorchidism | 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:0000248 | Brachycephaly | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000821 | Hypothyroidism | MP:0020169 | increased thyroid gland weight | higher than average weight of the thyroid gland |
| HP:0005978 | Type II diabetes mellitus | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000582 | Upslanted palpebral fissure | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| 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:0001249 | Intellectual disability | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0003220 | Abnormality of chromosome stability | 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:0002665 | Lymphoma | MP:0020154 | impaired humoral immune response | impaired response of the immune system that mediates secreted antibodies produced in B cells |
| HP:0000924 | Abnormality of the skeletal system | MP:0014071 | increased cardiac muscle glycogen level | greater than the normal concentration of a readily converted carbohydrate reserve in heart muscle |
| HP:0003683 | Large beaked nose | 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:0000233 | Thin vermilion border | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000294 | Low anterior hairline | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000286 | Epicanthus | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0004422 | Biparietal narrowing | 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:0005561 | Abnormality of bone marrow cell morphology | MP:0014071 | increased cardiac muscle glycogen level | greater than the normal concentration of a readily converted carbohydrate reserve in heart muscle |
| HP:0004209 | Clinodactyly of the 5th finger | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| HP:0008736 | Hypoplasia of penis | 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:0100585 | Telangiectasia of the skin | MP:0014127 | increased thymoma incidence | greater than the expected number of a malignant neoplasm originating from the epithelial cells of the thymus, occurring in a specific population in a given time period; thymoma is an uncommon tumor linked with myasthenia gravis and other autoimmune diseas |
| 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: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:0000431 | Wide nasal bridge | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| Disease ID | 1351 |
|---|---|
| Disease | lig4 syndrome |
| Case | (Waiting for update.) |