Ontology type: schema:ScholarlyArticle Open Access: True
2019-12
AUTHORSMagdalena Danyel, Eun Kyung Suk, Vera Raile, Jutta Gellermann, Alexej Knaus, Denise Horn
ABSTRACTBACKGROUND: Two interstitial microdeletions Xp11.22 including the CLCN5 and SHROOM4 genes were recently reported in a male individual affected with Dent disease, short stature, psychomotor delay and minor facial anomalies. Dent disease, characterized by a specific renal phenotype, is caused by truncating mutations of CLCN5 in the majority of affected cases. CASE PRESENTATION: Here, we present clinical and molecular findings in a male patient with clinical signs of Dent disease, developmental delay, short stature, microcephaly, and facial dysmorphism. Using molecular karyotyping we identified a hemizygous interstitial microdeletion Xp11.23p.11.22 of about 700 kb, which was inherited from his asymptomatic mother. Among the six deleted genes is CLCN5, which explains the renal phenotype in our patient. SHROOM4, which is partially deleted in this patient, is involved in neuronal development and was shown to be associated with X-linked intellectual disability. This is a candidate gene, the loss of which is thought to be associated with his further clinical manifestations. To rule out mutations in other genes related to intellectual disability, whole exome sequencing was performed. No other pathogenic variants that could explain the phenotypic features, were found. CONCLUSION: We compared the clinical findings of the patient presented here with the reported case with an Xp11.22 microdeletion including CLCN5 and SHROOM4 and re-defined the phenotypic spectrum associated with this microdeletion. More... »
PAGES6
http://scigraph.springernature.com/pub.10.1186/s12920-018-0471-6
DOIhttp://dx.doi.org/10.1186/s12920-018-0471-6
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1111319126
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/30630535
JSON-LD is the canonical representation for SciGraph data.
TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT
[
{
"@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json",
"about": [
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Genetics",
"type": "DefinedTerm"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Biological Sciences",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"name": [
"Institute of Medical Genetics and Human Genetics, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Berlin, Germany"
],
"type": "Organization"
},
"familyName": "Danyel",
"givenName": "Magdalena",
"type": "Person"
},
{
"affiliation": {
"name": [
"Praxis f\u00fcr Humangenetik-Friedrichstrasse, Berlin, Germany"
],
"type": "Organization"
},
"familyName": "Suk",
"givenName": "Eun Kyung",
"id": "sg:person.01167547063.17",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01167547063.17"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Charit\u00e9",
"id": "https://www.grid.ac/institutes/grid.6363.0",
"name": [
"Department of Pediatric Neurology, Sozialp\u00e4diatrisches Zentrum (SPZ), Center for Chronically Sick Children, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Germany, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Berlin, Germany"
],
"type": "Organization"
},
"familyName": "Raile",
"givenName": "Vera",
"id": "sg:person.013476154017.09",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013476154017.09"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Department of Pediatric Nephrology, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Berlin, Germany"
],
"type": "Organization"
},
"familyName": "Gellermann",
"givenName": "Jutta",
"type": "Person"
},
{
"affiliation": {
"alternateName": "University Hospital Bonn",
"id": "https://www.grid.ac/institutes/grid.15090.3d",
"name": [
"Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Berlin, Germany"
],
"type": "Organization"
},
"familyName": "Knaus",
"givenName": "Alexej",
"id": "sg:person.01366641255.60",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01366641255.60"
],
"type": "Person"
},
{
"affiliation": {
"name": [
"Institute of Medical Genetics and Human Genetics, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health, Berlin, Germany"
],
"type": "Organization"
},
"familyName": "Horn",
"givenName": "Denise",
"id": "sg:person.01035750745.43",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035750745.43"
],
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.1136/jmedgenet-2015-103568",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007361237"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1097/gim.0b013e3182217a3a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009028405",
"https://doi.org/10.1097/gim.0b013e3182217a3a"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1097/gim.0b013e3182217a3a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009028405",
"https://doi.org/10.1097/gim.0b013e3182217a3a"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/379445a0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1012692443",
"https://doi.org/10.1038/379445a0"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/ajmg.a.36807",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013393192"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/bts462",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015488047"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13039-015-0107-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016944014",
"https://doi.org/10.1186/s13039-015-0107-x"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13039-015-0107-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1016944014",
"https://doi.org/10.1186/s13039-015-0107-x"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00439-005-0072-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018995313",
"https://doi.org/10.1007/s00439-005-0072-2"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00439-005-0072-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018995313",
"https://doi.org/10.1007/s00439-005-0072-2"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00439-005-0072-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018995313",
"https://doi.org/10.1007/s00439-005-0072-2"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s10815-014-0342-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1019303886",
"https://doi.org/10.1007/s10815-014-0342-9"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.2890",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020782180",
"https://doi.org/10.1038/nmeth.2890"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00467-016-3343-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025489046",
"https://doi.org/10.1007/s00467-016-3343-3"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00467-016-3343-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025489046",
"https://doi.org/10.1007/s00467-016-3343-3"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1196/annals.1429.019",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030588902"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1101/gr.107524.110",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032096953"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/ajmg.a.20021",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034395570"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btp324",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038266369"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1136/adc.39.205.240",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039148737"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/humu.22049",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044263752"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1002/cm.20167",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048325825"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1086/427887",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1058715349"
],
"type": "CreativeWork"
}
],
"datePublished": "2019-12",
"datePublishedReg": "2019-12-01",
"description": "BACKGROUND: Two interstitial microdeletions Xp11.22 including the CLCN5 and SHROOM4 genes were recently reported in a male individual affected with Dent disease, short stature, psychomotor delay and minor facial anomalies. Dent disease, characterized by a specific renal phenotype, is caused by truncating mutations of CLCN5 in the majority of affected cases.\nCASE PRESENTATION: Here, we present clinical and molecular findings in a male patient with clinical signs of Dent disease, developmental delay, short stature, microcephaly, and facial dysmorphism. Using molecular karyotyping we identified a hemizygous interstitial microdeletion Xp11.23p.11.22 of about 700\u2009kb, which was inherited from his asymptomatic mother. Among the six deleted genes is CLCN5, which explains the renal phenotype in our patient. SHROOM4, which is partially deleted in this patient, is involved in neuronal development and was shown to be associated with X-linked intellectual disability. This is a candidate gene, the loss of which is thought to be associated with his further clinical manifestations. To rule out mutations in other genes related to intellectual disability, whole exome sequencing was performed. No other pathogenic variants that could explain the phenotypic features, were found.\nCONCLUSION: We compared the clinical findings of the patient presented here with the reported case with an Xp11.22 microdeletion including CLCN5 and SHROOM4 and re-defined the phenotypic spectrum associated with this microdeletion.",
"genre": "research_article",
"id": "sg:pub.10.1186/s12920-018-0471-6",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isPartOf": [
{
"id": "sg:journal.1039191",
"issn": [
"1755-8794"
],
"name": "BMC Medical Genomics",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "12"
}
],
"name": "Familial Xp11.22 microdeletion including SHROOM4 and CLCN5 is associated with intellectual disability, short stature, microcephaly and Dent disease: a case report",
"pagination": "6",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"4e8e4e396d5a0528d4bc3039c628ff9c9847af5cc5e4132e1c32e0d4cdfff921"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"30630535"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101319628"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/s12920-018-0471-6"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1111319126"
]
}
],
"sameAs": [
"https://doi.org/10.1186/s12920-018-0471-6",
"https://app.dimensions.ai/details/publication/pub.1111319126"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-11T08:41",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000320_0000000320/records_101381_00000000.jsonl",
"type": "ScholarlyArticle",
"url": "https://link.springer.com/10.1186%2Fs12920-018-0471-6"
}
]
Download the RDF metadata as: json-ld nt turtle xml License info
JSON-LD is a popular format for linked data which is fully compatible with JSON.
curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s12920-018-0471-6'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s12920-018-0471-6'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12920-018-0471-6'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12920-018-0471-6'
This table displays all metadata directly associated to this object as RDF triples.
173 TRIPLES
21 PREDICATES
47 URIs
21 LITERALS
9 BLANK NODES