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“description”: “Phenylketonuria (PKU) is the most common inborn error of amino acid metabolism and is characterized by mild to severe mental disability in untreated patients.”, “last_modified”: “2017-10-24T02:37:34.608995+00:00” }, “schema_version”: “5”, “modified_by”: { “uuid”: “1db40a7e-e6dc-46dd-9e17-44efbf53d508”, “last_name”: “Thomas”, “title”: “Amanda Thomas”, “email”: “alt2172@cumc.columbia.edu”, “@id”: “/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/”, “@type”: [ “user”, “item” ], “first_name”: “Amanda”, “affiliation”: [ “10009”, “10011”, “10015” ], “lab”: “/labs/curator/” }, “@type”: [ “interpretation”, “item” ], “interpretation_genes”: “”, “@id”: “/interpretations/f6f2fb05-fc57-4712-ad91-80732194a1e8/”, “evaluation_count”: 12, “affiliation”: “10015”, “markAsProvisional”: true, “date_created”: “2018-02-20T18:42:46.798651+00:00”, “submitted_by”: { “uuid”: “1db40a7e-e6dc-46dd-9e17-44efbf53d508”, “last_name”: “Thomas”, “title”: “Amanda Thomas”, “email”: “alt2172@cumc.columbia.edu”, “@id”: “/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/”, “@type”: [ “user”, “item” ], “first_name”: “Amanda”, “affiliation”: [ “10009”, “10011”, “10015” ], “lab”: “/labs/curator/” }, “interpretation_status”: “Provisional”, “extra_evidence_list”: [ { “subcategory”: “allele-data”, “status”: “in progress”, “uuid”: “5f0bf081-6424-4724-b13a-a669cfa7e390”, “category”: “case-segregation”, “variant”: “/variants/574a528a-bc39-44ad-a16e-16c9a03eb507/”, “@type”: [ “extra_evidence”, “item” ], “schema_version”: “2”, “modified_by”: { “uuid”: “1db40a7e-e6dc-46dd-9e17-44efbf53d508”, “last_name”: “Thomas”, “title”: “Amanda Thomas”, “email”: “alt2172@cumc.columbia.edu”, “@id”: “/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/”, “@type”: [ “user”, “item” ], “first_name”: “Amanda”, “affiliation”: [ “10009”, “10011”, “10015” ], “lab”: “/labs/curator/” }, “articles”: [ { “journal”: “Journal of human genetics”, “abstract”: “The aim of this study was to identify the most common genotypes in the phenylketonuria (PKU) population of Andalusia, assessing the correlation with the phenotype and the usefulness in predicting the response to treatment with tetrahydrobiopterin. We conducted a retrospective observational study between January 1980 and January 2010 in 147 Andalusian PKU patients assessing phenotype, genotype and response to a 24-h BH4 loading test. Our cohort of patients exhibited 65 different mutations, 69.2% corresponding to the missense type, in a total of 123 different genotypes. IVS10nt-11g>a was the most common mutation (10.9%). Four novel missense mutations were identified: p.L258P; p.E66K, p.R155C and p.P122S. Although generally there is a good genotype-phenotype correlation, for eight of the repeated genotypes a slightly different phenotype was observed. In 96 PKU subjects BH4 challenge was carried out. Patients with previously reported unresponsive mutations on both alleles showed a negative response, while 95.5% (28/29) of the responsive patients carry at least one missense mutation previously associated to the BH4. Our data reveal a great genetic heterogeneity in the Andalusian population. Genotype is quite a good predictor of the phenotype and of the responsiveness to tetrahydrobiopterin, which is relevant for patient management and follow-up.”, “uuid”: “a412e6b2-7d37-4a9e-8e1d-5794c45936c0”, “pmid”: “23514811”, “doi”: “”, “authors”: [ “Bueno MA”, “González-Lamuño D”, “Delgado-Pecellín C”, “Aldámiz-Echevarría L”, “Pérez B”, “Desviat LR”, “Couce ML” ], “title”: “Molecular epidemiology and genotype-phenotype correlation in phenylketonuria patients from South Spain.”, “date”: “2013 May;58(5):279-84.”, “pmcid”: “”, “@type”: [ “article”, “item” ], “schema_version”: “1”, “@id”: “/articles/23514811/”, “date_created”: “2017-03-29T21:31:47.566413+00:00”, “active”: true, “submitted_by”: { “uuid”: “8f88bcae-5b67-42a2-ac27-0d856a8fbb65”, “last_name”: “Zastrow”, “title”: “Diane Zastrow”, “email”: “thom1618@yahoo.com”, “@id”: “/users/8f88bcae-5b67-42a2-ac27-0d856a8fbb65/”, “@type”: [ “user”, “item” ], “first_name”: “Diane”, “affiliation”: [ “10011”, “10015” ], “lab”: “/labs/curator/” }, “last_modified”: “2017-03-29T21:31:47.566427+00:00” } ], “@id”: “/extra-evidence/5f0bf081-6424-4724-b13a-a669cfa7e390/”, “evidenceDescription”: “Single patient with mild PKU in trans wtih R155C, which has been curated by the Metabolism WG as Likely Pathogenic”, “affiliation”: “10015”, “date_created”: “2018-02-20T18:47:41.413242+00:00”, “submitted_by”: { “uuid”: “1db40a7e-e6dc-46dd-9e17-44efbf53d508”, “last_name”: “Thomas”, “title”: “Amanda Thomas”, “email”: “alt2172@cumc.columbia.edu”, “@id”: “/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/”, “@type”: [ “user”, “item” ], “first_name”: “Amanda”, “affiliation”: [ “10009”, “10011”, “10015” ], “lab”: “/labs/curator/” }, “last_modified”: “2018-02-20T18:47:41.413221+00:00” }, { “subcategory”: “specificity-of-phenotype”, “status”: “in progress”, “uuid”: “3fb04a24-24ef-421e-94e7-c789cb707ef0”, “category”: “case-segregation”, “variant”: “/variants/574a528a-bc39-44ad-a16e-16c9a03eb507/”, “@type”: [ “extra_evidence”, “item” ], “schema_version”: “2”, “modified_by”: { “uuid”: “1db40a7e-e6dc-46dd-9e17-44efbf53d508”, “last_name”: “Thomas”, “title”: “Amanda Thomas”, “email”: “alt2172@cumc.columbia.edu”, “@id”: “/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/”, “@type”: [ “user”, “item” ], “first_name”: “Amanda”, “affiliation”: [ “10009”, “10011”, “10015” ], “lab”: “/labs/curator/” }, “articles”: [ { “journal”: “Metabolism: clinical and experimental”, “abstract”: “To evaluate the protocol we propose for detecting BH(4)-responsive patients and the possibility of delimiting more precisely the population to be tested.”, “uuid”: “3224a3f4-573f-4115-8cf2-c983f4d1e68a”, “pmid”: “22921945”, “doi”: “”, “authors”: [ “Bueno MA”, “Lage S”, “Delgado C”, “Andrade F”, “Couce ML”, “González-Lamuño D”, “Pérez M”, “Aldámiz-Echevarría L” ], “title”: “New evidence for assessing tetrahydrobiopterin (BH(4)) responsiveness.”, “date”: “2012 Dec;61(12):1809-16.”, “pmcid”: “”, “@type”: [ “article”, “item” ], “schema_version”: “1”, “modified_by”: { “uuid”: “1db40a7e-e6dc-46dd-9e17-44efbf53d508”, “last_name”: “Thomas”, “title”: “Amanda Thomas”, “email”: “alt2172@cumc.columbia.edu”, “@id”: “/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/”, “@type”: [ “user”, “item” ], “first_name”: “Amanda”, “affiliation”: [ “10009”, “10011”, “10015” ], “lab”: “/labs/curator/” }, “@id”: “/articles/22921945/”, “date_created”: “2018-02-20T18:48:16.779802+00:00”, “active”: true, “submitted_by”: { “uuid”: “1db40a7e-e6dc-46dd-9e17-44efbf53d508”, “last_name”: “Thomas”, “title”: “Amanda Thomas”, “email”: “alt2172@cumc.columbia.edu”, “@id”: “/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/”, “@type”: [ “user”, “item” ], “first_name”: “Amanda”, “affiliation”: [ “10009”, “10011”, “10015” ], “lab”: “/labs/curator/” }, “last_modified”: “2018-02-20T18:48:16.779784+00:00” } ], “@id”: “/extra-evidence/3fb04a24-24ef-421e-94e7-c789cb707ef0/”, “evidenceDescription”: “BH4 defect excluded in all patients. Single patient with mild PKU”, “affiliation”: “10015”, “date_created”: “2018-02-20T18:48:37.216912+00:00”, “submitted_by”: { “uuid”: “1db40a7e-e6dc-46dd-9e17-44efbf53d508”, “last_name”: “Thomas”, “title”: “Amanda Thomas”, “email”: “alt2172@cumc.columbia.edu”, “@id”: “/users/1db40a7e-e6dc-46dd-9e17-44efbf53d508/”, “@type”: [ “user”, “item” ], “first_name”: “Amanda”, “affiliation”: [ “10009”, “10011”, “10015” ], “lab”: “/labs/curator/” }, “last_modified”: “2018-02-20T18:48:37.216898+00:00” } ], “interpretation_disease”: “/diseases/5bbacce3-3ac8-4911-adbb-5e5369cd79e1/”, “last_modified”: “2018-02-20T18:54:38.381156+00:00” } }, “description”: “The request payload depends on the type of data format you are uploading. Currently only the type vci is supported which follows the format adopted by the ClinGen VCI group. \n\nThe payload should be wrapped in a ‘data’ field when posting/putting the form. The’evidence’ field can either be a list of evidenceUrls that have been provided in support of a tag or in the absence of Urls, could simply be something that has been inferred from the scientific knowledge of the tag provider.” } ] }, “parameters”: [ { “name”: “gid”, “in”: “path”, “type”: “string”, “required”: true } ] }, “/interpretations”: { “get”: { “responses”: { “200”: { “description”: “”, “schema”: { “type”: “object”, “properties”: {} }, “examples”: { “application/json”: { “variantInterpretations”: [ { “gene”: { “label”: “PAH” }, “guidelines”: [ { “label”: “ACMG2015-Guidelines”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001”, “agents”: [ { “label”: “Amanda Thomas”, “@id”: “CG-PCER-AGENT:Amanda_Thomas_153375337633145”, “evidenceCodes”: [ { “label”: “PS1”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PS1” }, { “label”: “PP3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP3” }, { “label”: “PP4”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP4” }, { “label”: “PM3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM3” }, { “label”: “PM2”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM2” } ], “outcome”: { “label”: “Pathogenic”, “@id”: “LN:LA6668-3” } } ], “outcome”: { “label”: “Pathogenic”, “@id”: “LN:LA6668-3” } } ], “hgvs”: [ “NC_000012.12:g.102851734C>G”, “CM000674.2:g.102851734C>G”, “NC_000012.10:g.101769642C>G”, “NC_000012.11:g.103245512C>G”, “CM000674.1:g.103245512C>G”, “NG_008690.1:g.70869G>C”, “ENST00000307000.7:c.850G>C”, “ENST00000549247.6:n.624G>C”, “ENST00000551114.2:n.527G>C”, “ENST00000553106.5:c.865G>C”, “ENST00000635477.1:n.26G>C”, “NM_000277.1:c.865G>C”, “XM_011538422.1:c.865G>C” ], “evidenceLinks”: [ { “@id”: “https://www.ncbi.nlm.nih.gov/pubmed/22921945” }, { “@id”: “https://www.ncbi.nlm.nih.gov/pubmed/23514811” } ], “condition”: { “label”: “phenylketonuria”, “@id”: “MONDO:0009861” }, “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA229830/MONDO:0009861”, “caid”: “CAR:CA229830” }, { “gene”: { “label”: “PAH” }, “guidelines”: [ { “label”: “ACMG2015-Guidelines”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001”, “agents”: [ { “label”: “Amanda Thomas”, “@id”: “CG-PCER-AGENT:Amanda_Thomas_153375337633145”, “evidenceCodes”: [ { “label”: “PP3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP3” }, { “label”: “PP4”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP4” }, { “label”: “PM2”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM2” } ], “outcome”: { “label”: “Uncertain Significance - Insufficient Evidence”, “@id”: “LN:LA26333-7” } } ], “outcome”: { “label”: “Uncertain Significance - Insufficient Evidence”, “@id”: “LN:LA26333-7” } } ], “hgvs”: [ “NC_000012.12:g.102851735C>G”, “CM000674.2:g.102851735C>G”, “NC_000012.10:g.101769643C>G”, “NC_000012.11:g.103245513C>G”, “CM000674.1:g.103245513C>G”, “NG_008690.1:g.70868G>C”, “ENST00000307000.7:c.849G>C”, “ENST00000549247.6:n.623G>C”, “ENST00000551114.2:n.526G>C”, “ENST00000553106.5:c.864G>C”, “ENST00000635477.1:n.25G>C”, “NM_000277.1:c.864G>C”, “XM_011538422.1:c.864G>C” ], “evidenceLinks”: [], “condition”: { “label”: “phenylketonuria”, “@id”: “MONDO:0009861” }, “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA229828/MONDO:0009861”, “caid”: “CAR:CA229828” }, { “gene”: { “label”: “PAH” }, “guidelines”: [ { “label”: “ACMG2015-Guidelines”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001”, “agents”: [ { “label”: “Amanda Thomas”, “@id”: “CG-PCER-AGENT:Amanda_Thomas_153375337633145”, “evidenceCodes”: [ { “label”: “PS3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PS3” }, { “label”: “PP3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP3” }, { “label”: “PP4”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP4” }, { “label”: “PM3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM3” }, { “label”: “PM2”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM2” } ], “outcome”: { “label”: “Pathogenic”, “@id”: “LN:LA6668-3” } } ], “outcome”: { “label”: “Pathogenic”, “@id”: “LN:LA6668-3” } } ], “hgvs”: [ “NC_000012.12:g.102851743C>T”, “CM000674.2:g.102851743C>T”, “NC_000012.10:g.101769651C>T”, “NC_000012.11:g.103245521C>T”, “CM000674.1:g.103245521C>T”, “NG_008690.1:g.70860G>A”, “ENST00000307000.7:c.841G>A”, “ENST00000549247.6:n.615G>A”, “ENST00000551114.2:n.518G>A”, “ENST00000553106.5:c.856G>A”, “ENST00000635477.1:n.17G>A”, “NM_000277.1:c.856G>A”, “XM_011538422.1:c.856G>A” ], “evidenceLinks”: [ { “@id”: “https://www.ncbi.nlm.nih.gov/pubmed/24401910” }, { “@id”: “https://www.ncbi.nlm.nih.gov/pubmed/14722928” } ], “condition”: { “label”: “phenylketonuria”, “@id”: “MONDO:0009861” }, “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA229826/MONDO:0009861”, “caid”: “CAR:CA229826” }, { “gene”: { “label”: “PAH” }, “guidelines”: [ { “label”: “ACMG2015-Guidelines”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001”, “agents”: [ { “label”: “Amanda Thomas”, “@id”: “CG-PCER-AGENT:Amanda_Thomas_153375337633145”, “evidenceCodes”: [ { “label”: “PP3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP3” }, { “label”: “PP4”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP4” }, { “label”: “PM5”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM5” }, { “label”: “PM3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM3” }, { “label”: “PM2”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM2” } ], “outcome”: { “label”: “Likely Pathogenic”, “@id”: “LN:LA26332-9” } } ], “outcome”: { “label”: “Likely Pathogenic”, “@id”: “LN:LA26332-9” } } ], “hgvs”: [ “NC_000012.12:g.102851751A>T”, “CM000674.2:g.102851751A>T”, “NC_000012.10:g.101769659A>T”, “NC_000012.11:g.103245529A>T”, “CM000674.1:g.103245529A>T”, “NG_008690.1:g.70852T>A”, “ENST00000307000.7:c.833T>A”, “ENST00000549247.6:n.607T>A”, “ENST00000551114.2:n.510T>A”, “ENST00000553106.5:c.848T>A”, “ENST00000635477.1:n.9T>A”, “NM_000277.1:c.848T>A”, “XM_011538422.1:c.848T>A” ], “evidenceLinks”: [ { “@id”: “https://www.ncbi.nlm.nih.gov/pubmed/9521426” }, { “@id”: “https://www.ncbi.nlm.nih.gov/pubmed/26413448” } ], “condition”: { “label”: “phenylketonuria”, “@id”: “MONDO:0009861” }, “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA229821/MONDO:0009861”, “caid”: “CAR:CA229821” }, { “gene”: { “label”: “PAH” }, “guidelines”: [ { “label”: “ACMG2015-Guidelines”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001”, “agents”: [ { “label”: “Diane Zastrow”, “@id”: “CG-PCER-AGENT:Diane_Zastrow_153375372705697”, “evidenceCodes”: [ { “label”: “PP3”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PP3” }, { “label”: “PM5”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM5” }, { “label”: “PM2”, “@id”: “https://erepo.genome.network/evidence-repo/api/guideline/GN001/tag/PM2” } ], “outcome”: { “label”: “Uncertain Significance - Insufficient Evidence”, “@id”: “LN:LA26333-7” } } ], “outcome”: { “label”: “Uncertain Significance - Insufficient Evidence”, “@id”: “LN:LA26333-7” } } ], “hgvs”: [ “NC_000012.12:g.102855274C>T”, “CM000674.2:g.102855274C>T”, “NC_000012.10:g.101773182C>T”, “NC_000012.11:g.103249052C>T”, “CM000674.1:g.103249052C>T”, “NG_008690.1:g.67329G>A”, “ENST00000307000.7:c.553G>A”, “ENST00000549111.5:n.664G>A”, “ENST00000553106.5:c.568G>A”, “NM_000277.1:c.568G>A”, “XM_011538422.1:c.568G>A” ], “evidenceLinks”: [], “condition”: { “label”: “phenylketonuria”, “@id”: “MONDO:0009861” }, “@id”: “https://erepo.genome.network/evidence-repo/api/interpretation/CA267660/MONDO:0009861”, “caid”: “CAR:CA267660” } ], “@context”: “https://erepo.genome.network/evidence-repo/api/context/light” } } } }, “summary”: “SearchInterpretations”, “description”: “Search end point for the repository. Accepts one or more of the supported query fields.”, “parameters”: [ { “$ref”: “#/parameters/gene-query” }, { “$ref”: “#/parameters/condition-query” }, { “$ref”: “#/parameters/hgvs-query” }, { “$ref”: “#/parameters/assertion-query” }, { “$ref”: “#/parameters/caid-query” }, { “$ref”: “#/parameters/match-logic-query” }, { “$ref”: “#/parameters/match-mode-query” }, { “$ref”: “#/parameters/match-limit-query” }, { “$ref”: “#/parameters/match-skip-query” } ] } } }, “host”: “erepo.genome.network”, “basePath”: “/evidence-repo/api”, “schemes”: [ “http”, “https” ], “consumes”: [ “application/json” ], “produces”: [ “application/json” ], “securityDefinitions”: { “Redmine API Key”: { “type”: “apiKey”, “in”: “query”, “name”: “key”, “description”: “Select API requests require a Redmine API key, typically because they are write-operations.\n* Even with the API key, there can be restrictive permissions that constrain the request to sensible authorized individuals or Sites.” } }, “parameters”: { “caid”: { “name”: “caid”, “in”: “path”, “type”: “string”, “required”: true, “description”: “Canonical Allele identifier” }, “disease”: { “in”: “path”, “type”: “string”, “required”: true, “name”: “disease”, “description”: “Disease namespace.”, “default”: “OMIM”, “enum”: [ “OMIM”, “MONDO”, “DO” ] }, “did”: { “name”: “did”, “in”: “path”, “type”: “string”, “required”: true, “description”: “The id of the disease. Usually numeric.” }, “gid”: { “in”: “path”, “type”: “string”, “required”: true, “name”: “gid”, “default”: “001”, “description”: “The guideline id.” }, “gene-query”: { “in”: “query”, “type”: “string”, “name”: “gene”, “description”: “HUGO gene name you want to search by.” }, “condition-query”: { “in”: “query”, “type”: “string”, “name”: “condition”, “description”: “name of the condition you want to search by.” }, “hgvs-query”: { “in”: “query”, “type”: “string”, “name”: “hgvs”, “description”: “hgvs expression you want to search by.” }, “assertion-query”: { “in”: “query”, “type”: “string”, “name”: “assertion”, “description”: “assertion you want to search by. Eg. Pathogenic” }, “caid-query”: { “in”: “query”, “type”: “string”, “name”: “caid”, “description”: "Canonical Allele identifier you want to search by. " }, “match-logic-query”: { “name”: “matchLogic”, “in”: “query”, “type”: “string”, “default”: “and”, “enum”: [ “and”, “or” ] }, “match-mode-query”: { “name”: “matchMode”, “in”: “query”, “type”: “string”, “default”: “keyword”, “enum”: [ “keyword”, “prefix” ] }, “match-limit-query”: { “name”: “matchLimit”, “in”: “query”, “type”: “string”, “description”: "Controls the size of the search response. " }, “match-skip-query”: { “name”: “matchSkip”, “in”: “query”, “type”: “string”, “description”: “Skip these many from the beginning when returning a search response. Used in paginating response” }, “upload-type”: { “in”: “query”, “type”: “string”, “name”: “type”, “default”: “vci”, “description”: "Data format for the interpretation document. ", “enum”: [ “vci” ] } }, “responses”: {}, “definitions”: { “success-resp”: { “type”: “object”, “properties”: { “success”: { “type”: “string” }, “status”: { “type”: “integer” } } } } }