eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| syndactyly type 2 | ||||
| Disease ID | 1454 |
|---|---|
| Disease | syndactyly type 2 |
| Definition | A rare genetic disorder characterized by malformations in the hands and feet. The abnormalities include increased number of fingers and toes and fusion of digits into one large digit. |
| Synonym | sdty2 spd1 syndactyly type 2 (disorder) syndactyly, type 2 syndactyly, type ii synpolydactyly synpolydactyly 1 synpolydactyly-1 |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C2699746 |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:1) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:20) 78987 | CRELD1 | 1.901 | DISEASES 1745 | DLX1 | 2.964 | DISEASES 1812 | DRD1 | 3.021 | DISEASES 2045 | EPHA7 | 3.57 | DISEASES 2192 | FBLN1 | 3.415 | DISEASES 8200 | GDF5 | 2.159 | DISEASES 2737 | GLI3 | 1.396 | DISEASES 9464 | HAND2 | 1.76 | DISEASES 3205 | HOXA9 | 1.652 | DISEASES 3231 | HOXD1 | 4.388 | DISEASES 3238 | HOXD12 | 4.428 | DISEASES 3239 | HOXD13 | 7.688 | DISEASES 10660 | LBX1 | 2.445 | DISEASES 144165 | PRICKLE1 | 3.068 | DISEASES 860 | RUNX2 | 2.394 | DISEASES 89874 | SLC25A21 | 3.926 | DISEASES 6658 | SOX3 | 2.442 | DISEASES 55553 | SOX6 | 2.528 | DISEASES 3195 | TLX1 | 2.256 | DISEASES 25844 | YIPF3 | 3.28 | DISEASES |
| Locus | (Waiting for update.) |
| Disease ID | 1454 |
|---|---|
| Disease | syndactyly type 2 |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:12) HP:0001830 | Postaxial foot polydactyly HP:0001841 | Preaxial foot polydactyly HP:0004691 | 2-3 toe syndactyly HP:0001163 | Abnormality of the metacarpal bones HP:0009773 | Symphalangism affecting the phalanges of the hand HP:0001852 | Sandal gap HP:0100490 | Camptodactyly of finger HP:0004279 | Short palm HP:0004209 | Clinodactyly of the 5th finger HP:0006097 | 3-4 finger syndactyly HP:0001773 | Short foot HP:0100260 | Mesoaxial polydactyly |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:1) |
| Disease ID | 1454 |
|---|---|
| Disease | syndactyly type 2 |
| 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:4) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs121912541 | NA | 3239 | HOXD13 | umls:C1861367 | CLINVAR | NA | 0.560542884 | NA | HOXD13 | 2 | 176093573 | G | T |
| rs193922939 | NA | 3239 | HOXD13 | umls:C1861367 | CLINVAR | NA | 0.560542884 | NA | NA | NA | NA | NA | NA |
| rs28933082 | 12414828 | 3239 | HOXD13 | umls:C1861367 | UNIPROT | Severe digital abnormalities in a patient heterozygous for both a novel missense mutation in HOXD13 and a polyalanine tract expansion in HOXA13. | 0.560542884 | 2002 | HOXD13 | 2 | 176094614 | C | T |
| rs28933082 | NA | 3239 | HOXD13 | umls:C1861367 | CLINVAR | NA | 0.560542884 | NA | HOXD13 | 2 | 176094614 | C | T |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:10) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0006097 | 3-4 finger syndactyly | MP:0000564 | syndactyly | any degree of webbing or fusion of the digits, may involve only soft tissues or also can include bone |
| HP:0001773 | Short foot | MP:0008138 | absent podocyte foot process | absence of the footlike extension of podocytes that interdigitate with one another to form the walls of the glomerular capillaries |
| HP:0100490 | Camptodactyly of finger | 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: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:0100260 | Mesoaxial polydactyly | MP:0009743 | preaxial polydactyly | duplication of all or part of the first ray on one or more of the autopods |
| HP:0009773 | Symphalangism affecting the phalanges of the hand | MP:0010728 | fusion of atlas and occipital bones | union of elements of the atlas and the bone at the lower, posterior part of the skull into one structure |
| HP:0004691 | 2-3 toe syndactyly | MP:0000564 | syndactyly | any degree of webbing or fusion of the digits, may involve only soft tissues or also can include bone |
| HP:0001830 | Postaxial foot polydactyly | MP:0009744 | postaxial polydactyly | duplication of all or part of any of the rays except the first ray on one or more of the autopods |
| HP:0001841 | Preaxial foot polydactyly | MP:0009743 | preaxial polydactyly | duplication of all or part of the first ray on one or more of the autopods |
| HP:0001163 | Abnormality of the metacarpal bones | MP:0012069 | abnormal horizontal basal cell of olfactory epithelium morphology | any structural anomaly of the flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells, that lie in contact with the bas |
Mapped by homologous gene(Total Items:12) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| 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:0006097 | 3-4 finger syndactyly | MP:0013901 | absent female preputial gland | absence of the paired, lobulated, modified sebaceous glands located on the side of the clitoris in female rodents; in contrast to the preputial glands in male rodents, clitoral glands are a minor source of olfactory stimuli contributing to sexual attracti |
| HP:0001773 | Short foot | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| HP:0100260 | Mesoaxial polydactyly | MP:0013279 | increased fasted circulating glucose level | increase in the amount of glucose in the blood at some defined time point after eating compared to controls |
| HP:0004691 | 2-3 toe syndactyly | MP:0014198 | absent pituitary infundibular stalk | absence of the apical portion of the tubular structure extending from the hypothalamus to the posterior lobe of the pituitary gland |
| HP:0001841 | Preaxial foot polydactyly | 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:0001830 | Postaxial foot polydactyly | MP:0013901 | absent female preputial gland | absence of the paired, lobulated, modified sebaceous glands located on the side of the clitoris in female rodents; in contrast to the preputial glands in male rodents, clitoral glands are a minor source of olfactory stimuli contributing to sexual attracti |
| HP:0004279 | Short palm | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001852 | Sandal gap | MP:0020157 | abnormal behavioral response to alcohol | any anomaly in the behavioral response induced by alcohol, such as induced hyperactivity or stereotypic behavior |
| HP:0001163 | Abnormality of the metacarpal bones | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0100490 | Camptodactyly of finger | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0009773 | Symphalangism affecting the phalanges of the hand | MP:0014198 | absent pituitary infundibular stalk | absence of the apical portion of the tubular structure extending from the hypothalamus to the posterior lobe of the pituitary gland |
| Disease ID | 1454 |
|---|---|
| Disease | syndactyly type 2 |
| Case | (Waiting for update.) |