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"type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1765", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/el/0/1663", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/ei/1/1664", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/el/0/1663/1665", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000097", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Info unpublished, but per Dr. Longy, parents of pt 74 are unaffected and both negative for variant.", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000097", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/23335809", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000268", "contribution": [ { "agent": { "@id": 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Pts recruited from National Database for Autism research BUT study ID (14 433) way too similar to O'Roak, appears to be same individual.", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000268", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/28250423", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000269", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "De novo variant identified in Cauc male with autism, non-verbal IQ=50. OFC 57.8 cm at or under 4 yrs old. At least +5SD, z-score +4.7 per article. Pt in study via Simons Simplex Collection. Pt ID 14433.p1. Pt tested via exome but parents tested targeted only.", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000269", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/23160955", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1663/1665", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/1/1664", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1663", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/el/0/1828", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/ei/1/1829", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/el/0/1828/1830", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000272", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Variant demonstrated loss of phosphatase activity on in vitro assay, also showed lack of growth rescue capability.", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000272", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/21828076", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000271", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Variant categorized as \"WT-like\" on VAMPseq high throughput assay assessing protein abundance as a measure of stability.", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000271", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/29785012", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000266", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Variant in hypomorphic range (score -1.91) on high-throughput phosphatase assay", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000266", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/29706350", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1828/1830", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/1/1829", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1828", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/el/0/1699", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/ei/1/1700", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000442/MONDO:0017623/003/el/0/1699/1701", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000097", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Identified in pts 73/74 (child and parent). Child is proband pt 73, had macrocephaly (55.5cm) and MR/autism/ADD. Parent had targeted testing, history of macrocephaly (62cm) , polyps (pseudo polyps and lymphoid hyperplasia), benign thyroid (MNG) and breast disease (mild fibrocystic mastopathy). \n\nReached out to Dr. Longy for details: \nDear Jessica,\n\nThank for your note.\nI confirm that patient 73 is the son of patient 74.\n\nPatient 73: born in 2002, observed in 2005 (3 years old). Macrocephaly: 55.5 cm (+4DS); delay in acquisitions and attention deficit.\nPatient 74: born In 1974, observed in 2005 (31 years old). Macrocephaly: 62 cm; colonoscopy in 2007 showing pseudo polyps with lymphoid hyperplasia, unoperated thyroid goiter and mild fibrocystic mastopathy. \nTo note that the father and the mother of patient 74 , phenotypically normal, are non-carrier of the PTEN T131I.\n\nTo note also that I was contacted by William Foulkes in 2015 because he had to follow a boy with the same mutation and autism disorder.", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000097", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/23335809", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000269", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Identified in child with extreme macrocephaly and autism. See de novo section. 1 point.\nPatient was reported as male with speech delay, low verbal and non-verbal IQ", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000269", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/23160955", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1699/1701", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/1/1700", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1699", "type": "EvidenceLine" }, { "@id": 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child with macrocephaly and autism; variant absent in a sibling, affected status unknown. Pts recruited from National Database for Autism research BUT study ID (14 433) way too similar to O'Roak, appears to be same individual.", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000268", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/28250423", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000442/MONDO:0017623/003/ci/EV000000269", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "De novo variant identified in Cauc male with autism, non-verbal IQ=50. OFC 57.8 cm at or under 4 yrs old. At least +5SD, z-score +4.7 per article. Pt in study via Simons Simplex Collection. Pt ID 14433.p1. Pt tested via exome but parents tested targeted only.", "contributionDate": { "date": "2018/12/10", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": "SEPIO:0000516", "label": "curator role", "type": "ContributoryRole" }, "type": "Contribution" } ], "id": "CA000442/MONDO:0017623/003/ci/EV000000269", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/23160955", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1729/1731", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/1/1730", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003/0/1729", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA000442/MONDO:0017623/003", "metadata": { "created": "2024-09-27T19:54:19.868Z", "note": "DISCLAIMER: While the data/content in this document is approved by ClinGen expert panel(s), the SEPIO schema presented here is an initial prototype and has not been reviewed nor finalized by the ClinGen Data Exchange Modeling Team. We expect it to differ significantly from the final schema.", "producedAtUTC": "Fri, 27 Sep 2024 19:54:19 -0000", "schemaLabel": "Evidence Repository.Beta-1 (Unofficial)", "version": "1.0.0" }, "statementOutcome": { "@id": "https://loinc.org/LA6668-3", "id": "LN:LA6668-3", "label": "Pathogenic" }, "type": "VariantPathogenicityInterpretation", "uuid": "78613fd1-ded6-4249-b54d-0894617cf17d", "variant": { "@id": "https://reg.genome.network/allele/CA000442", "id": "CAR:CA000442", "relatedContextualAllele": [ { "alleleName": [ { "name": "NM_000314.6:c.392C>T" } ], "preferred": true } ], "relatedIdentifier": [ { "label": "NM_000314.6(PTEN):c.392C>T (p.Thr131Ile)" } ], "type": "CAR" } } ], "metadata": { "rendered": { "by": "https://erepo.genome.network/evrepo/api/summary/srvc", "when": "2026-11-03T19:59:12.799Z" } }, "status": { "code": 200, "name": "OK" } }