eRAM
encyclopedia of Rare Disease Annotation for Precision Medicine
| brachytelephalangic chondrodysplasia punctata | ||||
| Disease ID | 1524 |
|---|---|
| Disease | brachytelephalangic chondrodysplasia punctata |
| Synonym | bcdp cdpx1 chondrodysplasia punctata 1, x-linked recessive chondrodysplasia punctata, brachytelephalangic chondrodysplasia punctata, brachytelephalangic, autosomal cpxr |
| Orphanet | |
| OMIM | |
| UMLS | C1844853 |
| 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:1) ARSE | Xp22.33 |
| Disease ID | 1524 |
|---|---|
| Disease | brachytelephalangic chondrodysplasia punctata |
| Integrated Phenotype | HPO | Name(Total Integrated Phenotypes:14) HP:0000925 | Abnormality of the vertebral column HP:0004322 | Stature below 3rd percentile HP:0000252 | Small head circumference HP:0001263 | Developmental retardation HP:0000518 | Cataract HP:0003196 | Short nose HP:0000420 | Short nasal septum HP:0005280 | Flat, nasal bridge HP:0000458 | Anosmia HP:0000365 | Hearing impairment HP:0009882 | Hypoplastic terminal phalanges HP:0008064 | Ichthyosis HP:0000135 | Hypogonadism HP:0010655 | Stippled epiphyses |
| Text Mined Phenotype | HPO | Name | Sentences' Count(Total Phenotypes:1) |
| Disease ID | 1524 |
|---|---|
| Disease | brachytelephalangic chondrodysplasia punctata |
| Manually Symptom | (Waiting for update.) |
| Text Mined Symptom | (Waiting for update.) |
Manually Genotype(Total Manually Genotypes:30) | |||
|---|---|---|---|
| Gene | Mutation | DOI | Article Title |
| ARSE | exon 3, c. 126_128delTCT, Leu43del | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 3, c. 139 G→A, D47N | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 4, c. 217G→A, G73S | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 4, c. 235 C→T, H79Y | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 4, c. 268A→G, R90G | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 4, c. 284 C→T, T95M | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 5, c. 359 G→A, G120E | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 6, c. 445G→T, G149C | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 7, c. 916 A→G, T306A | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 7, c. 949 G→A, G317R | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 9, c. 1130 G→A, G377E | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 9, c. 1171G→A, G391R | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 10, c. 1300G→A, G434S | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 10, c. 1387G→A, A463T | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 11, c. 1442 C→T, T481M | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 1–11, c. (?_67)_(1770_?)del, Nulle | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 3, c. 119 T→G, I40S | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 3, c. 169 G→A, G57S | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 5, c. 349 G→A, G117R | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 5, c. 410 G→C, G137A | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 8, c. 1063 G→A, G355S | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | exon 9, c. 1226 C→T, T409M | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 36 G>C, R12S | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 410 G>T, G137V | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 733 G>C, G245R | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 332 G>C, R111P | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 1475 G>A, C492Y | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 239 T>A, I80N | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 1442 C>T, T481M | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
| ARSE | 1732 C>T, P578S | doi:10.1038/gim.2013.13 | A prospective study of brachytelephalangic chondrodysplasia punctata: identification of arylsulfatase E mutations, functional analysis of novel missense alleles, and determination of potential phenocopies |
Text Mining Genotype(Total Genotypes:0) | |
|---|---|
| (Waiting for update.) | |
All Snps(Total Genotypes:12) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| snpId | pubmedId | geneId | geneSymbol | diseaseId | sourceId | sentence | score | Year | geneSymbol_dbSNP | CHROMOSOME | POS | REF | ALT |
| rs122460151 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2958423 | C | G |
| rs122460152 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2953224 | C | T |
| rs122460153 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2953241 | C | G |
| rs122460154 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2949425 | C | G |
| rs122460155 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2935127 | C | T |
| rs145946864 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2953236 | G | A |
| rs28935474 | 12567415 | 415 | ARSE | umls:C1844853 | UNIPROT | X-linked chondrodysplasia punctata (CDPX1), due to mutations of the arylsulfatase E (ARSE) gene, is a congenital disorder characterized by abnormalities in cartilage and bone development. | 0.480814326 | 2003 | ARSE | X | 2934870 | G | A |
| rs28935474 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2934870 | G | A |
| rs80338710 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2958340 | A | C |
| rs80338711 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2953163 | C | G,A |
| rs80338713 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2935160 | G | A |
| rs80338714 | NA | 415 | ARSE | umls:C1844853 | CLINVAR | NA | 0.480814326 | NA | ARSE | X | 2934859 | 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:6) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0003196 | Short 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:0001263 | Global developmental delay | MP:0002084 | abnormal developmental patterning | abnormal systematic arrangement of the developing body along an axis |
| HP:0000925 | Abnormality of the vertebral column | MP:0009005 | abnormal sesamoid bone of gastrocnemius morphology | any structural anomaly of the small sesamoid bones situated behind the condyles of the femur |
| HP:0005280 | Depressed nasal bridge | MP:0013582 | abnormal lateral nasal gland morphology | any structural anomaly of the lateral nasal glands (the largest nasal secretory glands in rodents) which surround the maxillary sinus located in the lateral wall adjacent to each nasal passage and are characterized by cytologic features similar to those d |
| HP:0000420 | Short nasal septum | MP:0009903 | abnormal medial nasal prominence morphology | any structural anomaly of the central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the form |
| HP:0009882 | Short distal 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 |
Mapped by homologous gene(Total Items:14) | ||||
|---|---|---|---|---|
| HP ID | HP Name | MP ID | MP Name | Annotation |
| HP:0009882 | Short distal phalanx of finger | 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:0008064 | Ichthyosis | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000518 | Cataract | 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:0000420 | Short nasal septum | MP:0013550 | abnormal secondary palate morphology | |
| HP:0010655 | Epiphyseal stippling | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0000135 | Hypogonadism | 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:0000365 | Hearing impairment | MP:0020254 | decreased collagen level | decreased level of the main structural protein of the various connective tissues in animals |
| HP:0005280 | Depressed nasal bridge | 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 |
| HP:0003196 | Short nose | MP:0020309 | increased creatine kinase activity | increased ability of to catalyze the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+). |
| 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:0000458 | Anosmia | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| HP:0000925 | Abnormality of the vertebral column | MP:0020137 | decreased bone mineralization | decrease in the rate at which minerals are deposited into bone |
| Disease ID | 1524 |
|---|---|
| Disease | brachytelephalangic chondrodysplasia punctata |
| Case | (Waiting for update.) |