eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| l1 syndrome | ||||
| Disease ID | 1024 |
|---|---|
| Disease | l1 syndrome |
| Definition | A mild to severe congenital X-linked developmental disorder with hydrocephalus of varying degrees of severity, intellectual deficit, spasticity of the legs, and adducted thumbs. Primarily affects males. Affected males have varying degrees of hydrocephalus ranging from subclinical to severe. Intellectual deficit ranges from mild to severe. Adducted thumbs are a characteristic feature of the syndrome, present in about 50% of cases. Caused by mutations in the L1CAM gene (Xq28) encoding the L1 cell adhesion molecule that is expressed mainly in the developing nervous system. Inherited in an X-linked manner. |
| Synonym | adducted thumb with mental retardation clasped thumb and mental retardation crash syndrome gareis-mason syndrome genetic diseases, x-linkeds hypoplasia of corpus callosum and mental retardation with adducted thumbs and spasticity and hydrocephalus syndrome hypoplasia of corpus callosum and mental retardation with adducted thumbs and spasticity and hydrocephalus syndrome (disorder) masa (mental retardation, aphasia, shuffling gait, adducted thumbs) syndrome masa syndrome masa syndrome (disorder) mental retardation, aphasia, shuffling gait, adducted thumbs (masa) mental retardation, aphasia, shuffling gait, and adducted thumbs spastic paraplegia 1, x-linked spastic paraplegia, type 1 spg1 thumb, congenital clasped, with mental retardation x-linked complicated hereditary spastic paraplegia type 1 x-linked corpus callosum agenesis x-linked hydrocephalus with stenosis of the aqueduct of sylvius (hsas) |
| Orphanet | |
| OMIM | |
| DOID | |
| UMLS | C0795953 |
| Comorbidity | UMLS | Disease | Sentences' Count(Total Sentences: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:48) 10555 | AGPAT2 | 1.893 | DISEASES 9179 | AP4M1 | 2.959 | DISEASES 91056 | AP5B1 | 2.006 | DISEASES 393 | ARHGAP4 | 3.075 | DISEASES 51062 | ATL1 | 5.177 | DISEASES 64225 | ATL2 | 3.022 | DISEASES 1822 | ATN1 | 1.725 | DISEASES 6311 | ATXN2 | 1.715 | DISEASES 554 | AVPR2 | 2.096 | DISEASES 26580 | BSCL2 | 3.603 | DISEASES 8556 | CDC14A | 3.103 | DISEASES 6900 | CNTN2 | 1.787 | DISEASES 27255 | CNTN6 | 3.178 | DISEASES 1287 | COL4A5 | 1.455 | DISEASES 113612 | CYP2U1 | 3.045 | DISEASES 80821 | DDHD1 | 3.22 | DISEASES 23259 | DDHD2 | 3.928 | DISEASES 1785 | DNM2 | 1.136 | DISEASES 2157 | F8 | 1.646 | DISEASES 51571 | FAM49B | 3.313 | DISEASES 2705 | GJB1 | 1.278 | DISEASES 57165 | GJC2 | 3.205 | DISEASES 9798 | IST1 | 3.96 | DISEASES 547 | KIF1A | 3.364 | DISEASES 3798 | KIF5A | 3.875 | DISEASES 3897 | L1CAM | 6.464 | DISEASES 3916 | LAMP1 | 1.209 | DISEASES 1130 | LYST | 3.246 | DISEASES 4133 | MAP2 | 1.336 | DISEASES 55384 | MEG3 | 2.912 | DISEASES 4534 | MTM1 | 1.678 | DISEASES 283446 | MYO1H | 4.607 | DISEASES 23114 | NFASC | 2.379 | DISEASES 123606 | NIPA1 | 4.013 | DISEASES 8856 | NR1I2 | 1.192 | DISEASES 4897 | NRCAM | 5.356 | DISEASES 65055 | REEP1 | 4.528 | DISEASES 7905 | REEP5 | 1.795 | DISEASES 64221 | ROBO3 | 2.618 | DISEASES 26278 | SACS | 2.954 | DISEASES 9197 | SLC33A1 | 3.092 | DISEASES 6683 | SPAST | 4.161 | DISEASES 23111 | SPG20 | 4.293 | DISEASES 89910 | UBE3B | 2.227 | DISEASES 10497 | UNC13B | 2.84 | DISEASES 51699 | VPS29 | 3.209 | DISEASES 7454 | WAS | 1.219 | DISEASES 118813 | ZFYVE27 | 3.316 | DISEASES |
| Locus | (Waiting for update.) |
| Disease ID | 1024 |
|---|---|
| Disease | l1 syndrome |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:32) HP:0001263 | Global developmental delay HP:0000486 | Squint eyes HP:0001181 | Adducted thumbs HP:0001258 | Spastic paraplegia, lower limb HP:0000256 | Macrocrania HP:0002251 | Aganglionic megacolon HP:0001274 | Absent corpus callosum HP:0002463 | Language impairment HP:0001257 | Spasticity HP:0004322 | Stature below 3rd percentile HP:0002808 | Gibbus deformity HP:0003307 | Hyperlordosis HP:0002381 | Aphasia HP:0001762 | Talipes equinovarus HP:0002017 | Nausea and vomiting HP:0004374 | Hemiplegia/hemiparesis HP:0003202 | Skeletal muscle atrophy HP:0001249 | Mental retardation HP:0001250 | Seizures HP:0000252 | Small head circumference HP:0001288 | Gait disturbance HP:0002362 | Shuffling gait HP:0001181 | Adducted thumb HP:0001761 | Pes cavus HP:0001249 | Intellectual disability HP:0001347 | Hyperreflexia HP:0002410 | Aqueductal stenosis HP:0000238 | Nonsyndromal hydrocephalus HP:0000716 | Depression HP:0000238 | Hydrocephalus HP:0002315 | Headache HP:0002119 | Ventricular dilatation |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:2) |
| Disease ID | 1024 |
|---|---|
| Disease | l1 syndrome |
| Manually Symptom | (Waiting for update.) |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Manually Genotypes:1) | |||
|---|---|---|---|
| Gene | Mutation | DOI | Article Title |
| L1CAM | - | 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:6) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs137852519 | NA | 3897 | L1CAM | umls:C0795953 | CLINVAR | NA | 0.565428837 | NA | L1CAM | X | 153868034 | C | T |
| rs137852522 | NA | 3897 | L1CAM | umls:C0795953 | CLINVAR | NA | 0.565428837 | NA | L1CAM | X | 153862856 | G | A |
| rs137852523 | NA | 3897 | L1CAM | umls:C0795953 | CLINVAR | NA | 0.565428837 | NA | L1CAM | X | 153870948 | A | C |
| rs137852524 | NA | 3897 | L1CAM | umls:C0795953 | CLINVAR | NA | 0.565428837 | NA | L1CAM | X | 153869818 | C | T |
| rs28933683 | 7920659 | 3897 | L1CAM | umls:C0795953 | UNIPROT | X-linked spastic paraplegia (SPG1), MASA syndrome and X-linked hydrocephalus result from mutations in the L1 gene. | 0.565428837 | 1994 | L1CAM | X | 153870854 | G | T,C,A |
| rs28933683 | NA | 3897 | L1CAM | umls:C0795953 | CLINVAR | NA | 0.565428837 | NA | L1CAM | X | 153870854 | G | T,C,A |
GWASdb Annotation(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
GWASdb Snp Trait(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
Mapped by lexical matching(Total Items:6) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0003202 | Skeletal muscle atrophy | MP:0014068 | abnormal muscle glycogen level | the normal concentration of a readily converted carbohydrate reserve in muscle tissue |
| HP:0001274 | Agenesis of corpus callosum | MP:0013808 | abnormal tunnel of Corti morphology | any structrual anomaly of the triangular, fluid-filled space normally found between the inner and outer rows of supporting pillar cells in the organ of Corti |
| HP:0001263 | Global developmental delay | MP:0002084 | abnormal developmental patterning | abnormal systematic arrangement of the developing body along an axis |
| HP:0002251 | Aganglionic megacolon | MP:0002926 | aganglionic megacolon | extreme dilation of the colon due to defects in innervation from the ganglia, or absence of the ganglia of the myenteric plexus |
| HP:0002017 | Nausea and vomiting | MP:0010426 | abnormal heart and great artery attachment | any anomaly in the in the position or pattern of the connection site of the heart to any of the great arteries, including the pulmonary artery and aorta |
| HP:0002362 | Shuffling gait | MP:0001406 | abnormal gait | abnormal pattern of movement of the limbs of animals, characterized by elements of progression, stability, speed and length over the ground |
Mapped by homologous gene(Total Items:29) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0001258 | Spastic paraplegia | 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:0002381 | Aphasia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0002315 | Headache | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001250 | Seizures | 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:0000486 | Strabismus | 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:0003307 | Hyperlordosis | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0001288 | Gait disturbance | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0002119 | Ventriculomegaly | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0001347 | Hyperreflexia | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0003202 | Skeletal muscle atrophy | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| 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:0000238 | Hydrocephalus | MP:0020080 | increased bone mineralization | increase in the rate at which minerals are deposited into bone |
| HP:0004374 | Hemiplegia/hemiparesis | 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:0001257 | Spasticity | MP:0020316 | decreased vascular endothelial cell proliferation | decrease in the expansion rate of any vascular endothelial cell population by cell division |
| HP:0002410 | Aqueductal stenosis | 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:0002017 | Nausea and vomiting | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0002251 | Aganglionic megacolon | MP:0020220 | decreased tear production | decreased production of the amount of fluid produced in the eye |
| HP:0001761 | Pes cavus | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| 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:0002362 | Shuffling gait | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0002463 | Language impairment | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0001762 | Talipes equinovarus | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0001274 | Agenesis of corpus callosum | 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:0001181 | Adducted thumb | 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:0000716 | Depression | MP:0020329 | decreased capillary density | reduction in the number of capillaries in a given cross-sectional area of a tissue |
| HP:0000256 | Macrocephaly | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| HP:0002808 | Kyphosis | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| 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 |
| Disease ID | 1024 |
|---|---|
| Disease | l1 syndrome |
| Case | (Waiting for update.) |