eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| brachydactyly type a1 | ||||
| Disease ID | 1068 |
|---|---|
| Disease | brachydactyly type a1 |
| Definition | A congenital malformation with apparent shortness (or absence) of the middle phalanges of all digits and occasional fusion with the terminal phalanges. The proximal phalanges of the thumbs and big toes are short. Tendency to be of short stature in adulthood. Inherited as an autosomal dominant trait. |
| Synonym | brachydactyly farabee type brachydactyly type a1 (disorder) brachydactyly, farabee type brachydactyly, type a1 brachydactyly, type a1 (disorder) farabee-type brachydactyly type a1 brachydactyly |
| Orphanet | |
| OMIM | |
| UMLS | C1862151 |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:2) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | (Waiting for update.) |
| Locus | Symbol | Locus(Total Locus:3) |
| Disease ID | 1068 |
|---|---|
| Disease | brachydactyly type a1 |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:12) HP:0003022 | Hypoplasia of the ulna HP:0010109 | Short hallux HP:0001230 | Broad metacarpals HP:0004322 | Short stature HP:0002650 | Scoliosis HP:0001762 | Talipes equinovarus HP:0005819 | Short middle phalanx of finger HP:0010579 | Cone-shaped epiphysis HP:0004209 | Clinodactyly of the 5th finger HP:0001204 | Distal symphalangism (hands) HP:0001773 | Short foot HP:0009778 | Short thumb |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:1) |
| Disease ID | 1068 |
|---|---|
| Disease | brachydactyly type a1 |
| 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:13) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs121917852 | 19252479 | 3092 | HIP1 | umls:C1862151 | BeFree | Here we show that a BDA1 mutation (E95K) in Ihh impairs the interaction of IHH with PTCH1 and HIP1. | 0.000271442 | 2009 | IHH;MIR3131 | 2 | 219060185 | C | T |
| rs121917852 | NA | 3549 | IHH | umls:C1862151 | CLINVAR | NA | 0.562171535 | NA | IHH;MIR3131 | 2 | 219060185 | C | T |
| rs121917852 | 19252479 | 5727 | PTCH1 | umls:C1862151 | BeFree | Here we show that a BDA1 mutation (E95K) in Ihh impairs the interaction of IHH with PTCH1 and HIP1. | 0.000271442 | 2009 | IHH;MIR3131 | 2 | 219060185 | C | T |
| rs121917852 | 19252479 | 3549 | IHH | umls:C1862151 | BeFree | Here we show that a BDA1 mutation (E95K) in Ihh impairs the interaction of IHH with PTCH1 and HIP1. | 0.562171535 | 2009 | IHH;MIR3131 | 2 | 219060185 | C | T |
| rs121917853 | NA | 3549 | IHH | umls:C1862151 | CLINVAR | NA | 0.562171535 | NA | IHH | 2 | 219057619 | C | T |
| rs121917854 | NA | 3549 | IHH | umls:C1862151 | CLINVAR | NA | 0.562171535 | NA | IHH;MIR3131 | 2 | 219060168 | G | T |
| rs121917855 | NA | 3549 | IHH | umls:C1862151 | CLINVAR | NA | 0.562171535 | NA | IHH;MIR3131 | 2 | 219060170 | C | T |
| rs121917859 | NA | 3549 | IHH | umls:C1862151 | CLINVAR | NA | 0.562171535 | NA | IHH;MIR3131 | 2 | 219060184 | T | C |
| rs121917861 | NA | 3549 | IHH | umls:C1862151 | CLINVAR | NA | 0.562171535 | NA | IHH | 2 | 219057549 | G | A |
| rs267606872 | NA | 3549 | IHH | umls:C1862151 | CLINVAR | NA | 0.562171535 | NA | IHH | 2 | 219057621 | G | T |
| rs267606873 | NA | 3549 | IHH | umls:C1862151 | CLINVAR | NA | 0.562171535 | NA | IHH | 2 | 219057627 | C | T |
| rs28936377 | 12384778 | 3549 | IHH | umls:C1862151 | UNIPROT | A novel mutation in the IHH gene causes brachydactyly type A1: a 95-year-old mystery resolved. | 0.562171535 | 2002 | NA | NA | NA | NA | NA |
| rs397514519 | 24098149 | 8200 | GDF5 | umls:C1862151 | BeFree | Functional studies, including chondrogenesis assays with primary mesenchymal cells, luciferase reporter gene assays and Surface Plasmon Resonance analysis, of the GDF5(W414R) variant in comparison to other GDF5 mutations associated with isolated BDA1 (p.R399C) or SYNS2 (p.E491K) revealed a dual pathomechanism characterized by a gain- and loss-of-function at the same time. | 0.120271442 | 2013 | GDF5 | 20 | 35434220 | G | A |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:5) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| 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:0005819 | Short middle phalanx 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:0003022 | Hypoplasia of the ulna | 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: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:0010109 | Short hallux | MP:0009001 | absent hallux | absence of the first or primary digit of the foot |
Mapped by homologous gene(Total Items:12) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0002650 | Scoliosis | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0001762 | Talipes equinovarus | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| 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: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:0003022 | Hypoplasia of the ulna | 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:0010579 | Cone-shaped epiphysis | 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:0001230 | Broad metacarpals | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0001204 | Distal symphalangism (hands) | 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:0005819 | Short middle phalanx of finger | 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:0009778 | Short thumb | MP:0020040 | decreased bone ossification | decrease 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: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:0010109 | Short hallux | MP:0020040 | decreased bone ossification | decrease 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 |
| Disease ID | 1068 |
|---|---|
| Disease | brachydactyly type a1 |
| Case | (Waiting for update.) |