eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| seckel syndrome | ||||
| Disease ID | 242 |
|---|---|
| Disease | seckel syndrome |
| Definition | A rare autosomal recessive inherited syndrome caused by mutations in the ATR gene, RBBP8 gene, CENPJ gene, CEP152 gene, CEP63 gene, NIN gene, DNA2 gene, or TRAIP gene. It is characterized by intrauterine growth retardation, dwarfism, microcephaly, mental retardation, and a "bird-headed" facial appearance. |
| Synonym | bird-headed dwarf bird-headed dwarf of seckel bird-headed dwarfism microcephalic primordial dwarfism microcephalic primordial dwarfism 1 microcephalic primordial dwarfism i nanocephalic dwarf nanocephalic dwarfism sckl sckl1 seckel bird head syndrome seckel syndrome (disorder) seckel syndrome 1 seckel's syndrome seckel-type dwarfism seckels syndrome |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C0265202 |
| SNOMED-CT | |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences:2) |
| Curated Gene | Entrez_id | Symbol | Resource(Total Genes:8) |
| Inferring Gene | (Waiting for update.) |
| Text Mined Gene | Entrez_id | Symbol | Score | Resource(Total Genes:46) 23365 | ARHGEF12 | 2.001 | DISEASES 64283 | ARHGEF28 | 2.526 | DISEASES 545 | ATR | 5.696 | DISEASES 84126 | ATRIP | 3.024 | DISEASES 282991 | BLOC1S2 | 1.323 | DISEASES 8318 | CDC45 | 2.694 | DISEASES 983 | CDK1 | 1.776 | DISEASES 55755 | CDK5RAP2 | 2.823 | DISEASES 55835 | CENPJ | 4.78 | DISEASES 91687 | CENPL | 3.944 | DISEASES 22995 | CEP152 | 5.62 | DISEASES 80254 | CEP63 | 5.281 | DISEASES 1111 | CHEK1 | 4.04 | DISEASES 54875 | CNTLN | 5.658 | DISEASES 64421 | DCLRE1C | 2.282 | DISEASES 1763 | DNA2 | 3.494 | DISEASES 26052 | DNM3 | 2.841 | DISEASES 8813 | DPM1 | 1.543 | DISEASES 146956 | EME1 | 3.082 | DISEASES 668 | FOXL2 | 1.425 | DISEASES 3014 | H2AFX | 2.998 | DISEASES 3481 | IGF2 | 1.028 | DISEASES 3486 | IGFBP3 | 1.257 | DISEASES 3981 | LIG4 | 3.633 | DISEASES 4134 | MAP4 | 2.516 | DISEASES 79648 | MCPH1 | 4.711 | DISEASES 9656 | MDC1 | 3.036 | DISEASES 54820 | NDE1 | 2.401 | DISEASES 79840 | NHEJ1 | 2.784 | DISEASES 51199 | NIN | 4.236 | DISEASES 9378 | NRXN1 | 1.92 | DISEASES 4998 | ORC1 | 3.935 | DISEASES 5116 | PCNT | 5.843 | DISEASES 11284 | PNKP | 2.848 | DISEASES 5429 | POLH | 2.271 | DISEASES 5932 | RBBP8 | 3.741 | DISEASES 100151683 | RNU4ATAC | 3.222 | DISEASES 3921 | RPSA | 1.076 | DISEASES 7341 | SUMO1 | 1.59 | DISEASES 6890 | TAP1 | 2.802 | DISEASES 7158 | TP53BP1 | 2.397 | DISEASES 10293 | TRAIP | 3.823 | DISEASES 8295 | TRRAP | 2.637 | DISEASES 7337 | UBE3A | 1.347 | DISEASES 10785 | WDR4 | 3.904 | DISEASES 7518 | XRCC4 | 2.864 | DISEASES |
| Locus | Symbol | Locus(Total Locus:9) |
| Disease ID | 242 |
|---|---|
| Disease | seckel syndrome |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:26) HP:0000363 | Abnormality of earlobe HP:0000682 | Abnormality of dental enamel HP:0100543 | Cognitive impairment HP:0004322 | Short stature HP:0007495 | Prematurely aged appearance HP:0000347 | Micrognathia HP:0005692 | Joint hyperflexibility HP:0001852 | Sandal gap HP:0001511 | Intrauterine growth retardation HP:0000494 | Downslanted palpebral fissures HP:0000275 | Narrow face HP:0000252 | Microcephaly HP:0002209 | Sparse scalp hair HP:0002650 | Scoliosis HP:0011342 | Mild global developmental delay HP:0004209 | Clinodactyly of the 5th finger HP:0001249 | Intellectual disability HP:0004326 | Cachexia HP:0001385 | Hip dysplasia HP:0001363 | Craniosynostosis HP:0002750 | Delayed skeletal maturation HP:0000444 | Convex nasal ridge HP:0010579 | Cone-shaped epiphysis HP:0009804 | Reduced number of teeth HP:0000501 | Glaucoma HP:0000387 | Absent earlobe |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:9) HP:0001636 | Tetrology of fallot | 1 HP:0000501 | Glaucoma | 1 HP:0010636 | Schizencephaly | 1 HP:0001688 | Sinus bradycardia | 1 HP:0001510 | Growth deficiency | 1 HP:0011662 | Tricuspid atresia | 1 HP:0005214 | Bowel obstruction | 1 HP:0001087 | Childhood glaucoma | 1 HP:0003510 | Proportionate dwarfism | 1 |
| Disease ID | 242 |
|---|---|
| Disease | seckel syndrome |
| Manually Symptom | UMLS | Name(Total Manually Symptoms:11) C0751617 | semilobar holoprosencephaly C0741916 | cardiac defects C0497552 | nervous system anomalies C0266484 | schizencephaly C0042373 | vascular disease C0031036 | polyarteritis nodosa C0030312 | bone marrow failure C0023467 | acute myeloid leukaemia C0013336 | dwarfism C0011615 | atopic dermatitis C0007766 | intracranial aneurysms |
| Text Mined Symptom | UMLS | Name | Sentences' Count(Total Symptoms:2) |
Manually Genotype(Total Text Mining Genotypes:0) |
|---|
| (Waiting for update.) |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:8) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0001511 | Intrauterine growth retardation | MP:0011109 | lethality throughout fetal growth and development, incomplete penetrance | the appearance of lower than Mendelian ratios of organisms of a given genotype due to death of some, but not all of the organisms between the completion of organogenesis and birth (Mus: E14 to approximately E18.5) |
| HP:0009804 | Reduced number of teeth | 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 |
| 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:0000444 | Convex nasal ridge | MP:0004471 | short nasal bone | reduced length of either of two rectangular bone plates forming the bridge of the nose |
| HP:0002209 | Sparse scalp hair | MP:0011195 | increased hair follicle apoptosis | greater than expected levels of programmed cell death of cells in the epidermis from which the hair shaft develops |
| HP:0000363 | Abnormality of earlobe | MP:0008163 | increased diameter of ulna | increased width of the cross-sectional distance that extends from one lateral edge of the ulna, through its center and to the opposite lateral edge |
| HP:0000682 | Abnormality of dental enamel | 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 |
| HP:0002750 | Delayed skeletal maturation | MP:0003379 | absent sexual maturation | failure to initiate pubertal changes that result in achievement of full sexual capacity |
Mapped by homologous gene(Total Items:26) | ||||
|---|---|---|---|---|
| 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:0001385 | Hip dysplasia | MP:0013293 | embryonic lethality prior to tooth bud stage | death prior to the appearance of tooth buds (Mus: E12-E12.5) |
| HP:0000275 | Narrow face | 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:0004326 | Cachexia | 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: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:0000682 | Abnormality of dental enamel | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000501 | Glaucoma | 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: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:0100543 | Cognitive impairment | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0001363 | Craniosynostosis | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0011342 | Mild global developmental delay | 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: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:0001511 | Intrauterine growth retardation | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0009804 | Reduced number of teeth | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000363 | Abnormality of earlobe | MP:0013785 | abnormal mammary gland bud morphology | any structural anomaly of the morphologically distinct bulb of epithelial cells formed once each mammary placode expands and invaginates into the underlying mesenchyme; in mouse embryos at E12.5, each epithelial bud with its contiguous mesenchyme is eleva |
| HP:0000387 | Absent earlobe | MP:0011098 | embryonic lethality during organogenesis, complete penetrance | death of all organisms of a given genotype in a population between embryo turning and the completion of organogenesis (Mus: E9-9.5 to less than E14) |
| HP:0000444 | Convex nasal ridge | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| 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:0000494 | Downslanted palpebral fissures | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| 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:0007495 | Prematurely aged appearance | MP:0020321 | increased vascular endothelial cell apoptosis | increase in the timing or the number of vascular endothelial cells undergoing programmed cell death |
| HP:0002750 | Delayed skeletal maturation | MP:0020169 | increased thyroid gland weight | higher than average weight of the thyroid gland |
| HP:0005692 | Joint hyperflexibility | MP:0012125 | decreased bronchoconstrictive response | reduction in the expected bronchoconstrictive response to provocation challenge with lipopolysaccharide, bradykinin, histamine or other antigen/allergen or agent, often measured by plethysmography |
| 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:0002209 | Sparse scalp hair | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| Disease ID | 242 |
|---|---|
| Disease | seckel syndrome |
| Case | (Waiting for update.) |