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If pediatric, minimum peds score = 5. If adult, minimum CC score = 12. Per Dr. Longy, pt was 16yo F, OFC 65cm, and variant occurred de novo. Earns 1 PP4 pt based on this new info.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000097", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/23335809", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/EV000000283", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Seen in 3.5yo Cauc M with extreme macrocephaly (+7SD) and developmental delay. Mother with normal OFC negative, father with large OFC (61.2 cm) not tested. Peds score = 5.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000283", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/15805158", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/EV000000280", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Present in an individual in either the CCF or OSU PTEN study; no phenotype data provided. Could try to obtain if needed for classification.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000280", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/21194675", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/EV000000275", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "1 patient fro OSU PTEN study with clinical features of CS/BRRS. Could be patient overlap.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000275", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/21659347", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/EV000000279", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Article references Butler et al., 2005 which identified a patient with D252G. No additional patient with D252G reported in this article.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000279", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/17286265", "type": "CuratorInference" } ], "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/0/1633/1635", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/1/1634", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/0/1633", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/el/0/1702", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/ei/1/1703", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2023/10/19", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0069", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000328", "id": "SEPIO:0000328", "label": "Benign Strong" }, "id": "0069", "label": "BS2", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/el/0/1702/1704", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/CA000564/MONDO:0017623/003.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/CA000564/MONDO:0017623/003.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/0/1702/1704", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/1/1703", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Not Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/0/1702", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/el/0/1636", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/ei/1/1637", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2023/10/19", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0030", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000329", "id": "SEPIO:0000329", "label": "Pathogenic Supporting" }, "id": "0030", "label": "PM2", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/el/0/1636/1638", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/CA000564/MONDO:0017623/003.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "This variant is completely absent from gnomAD/ExAC databases (PM2_Supporting). 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"@id": "https://obofoundry.org/sepio/clingen/0037", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000330", "id": "SEPIO:0000330", "label": "Pathogenic Strong" }, "id": "0037", "label": "PM6", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/el/0/1729/1731", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/CA000564/MONDO:0017623/003.002", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Variant reportedly de novo in a patient reported by Bubien et al, 2013 (PMID: 23335809) per personal communication with Dr. Longy and the patient has a peds score of 5, which would be 1 point counting toward PS4, which bumps PM6 up to PM6_Strong.\n[PM6_Strong may be used for a proband with presumed de novo occurrence for an individual with a highly specific phenotype (meets criteria to count towards PS4)]", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/CA000564/MONDO:0017623/003.002", "type": "InfFromBkgrndSciKnow" } ], "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/0/1729/1731", "type": "EvidenceLine" } ], "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/1/1730", "statementOutcome": { "@id": "SEPIO:0000224", "label": "Met" }, "type": "CriterionAssessment" } ], "evidenceStrength": { "@id": "https://obofoundry.org/sepio" }, "id": "CG-PCER-VARINT:CA000564/MONDO:0017623/003/0/1729", "type": "EvidenceLine" }, { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/el/0/1825", "evidenceItem": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/ei/1/1826", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "contributionDate": { "date": "2023/10/19", "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" } ], "criterion": { "@id": "https://obofoundry.org/sepio/clingen/0039", "defaultStrength": { "@id": "https://obofoundry.org/sepio/SEPIO:0000216", "id": "SEPIO:0000216", "label": "Pathogenic Moderate" }, "id": "0039", "label": "PS3", "type": "Criterion" }, "evidenceLine": [ { "@id": "https://erepo.genome.network/evrepo/api/interpretation/CA000564/MONDO:0017623/003/el/0/1825/1827", "evidenceItem": [ { "@id": "CG-PCER:curatorInference/CA000564/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 scored in \"hypomorphic\" range (-2.1) on high throughput phosphatase assay - would not consider applying criteria.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000266", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/29706350", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/EV000000281", "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 decreased protein expression and stability (~60% of WT) when introduced in COS-7 or U87MG cells.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000281", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/29706633", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/EV000000282", "contribution": [ { "agent": { "@id": "https://erepo.genome.network/evrepo/api//agent/CG_50012_EP15519033251287", "id": "CG-PCER-AGENT:CG_50012_EP15519033251287", "type": "Agent" }, "comments": "Authors demonstrated that wild-type PTEN can rescue the neuronal hypertrophy, while PTEN D252G failed to rescue this hypertrophy. A subset of these mutations lacked nuclear localization, prompting us to examine the role of nuclear PTEN in regulating neuronal growth. We found that nuclear PTEN alone is sufficient to regulate soma size. Furthermore, forced localization of the D252G into the nucleus partially restores regulation of soma size.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000282", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/29373119", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000564/MONDO:0017623/003/ci/EV000000284", "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 decreased protein expression, pAKT closer to WT than pos control C124S. Also showed decreased protein stability.", "contributionDate": { "date": "2023/10/19", "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": "CA000564/MONDO:0017623/003/ci/EV000000284", "traceableAuthorStatement": "https://www.ncbi.nlm.nih.gov/pubmed/25527629", "type": "CuratorInference" }, { "@id": "CG-PCER:curatorInference/CA000564/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": "D252G demonstrated a partially active protein in yeast.", "contributionDate": { "date": "2023/10/19", "description": "Date on which this evidence was provided" }, "contributionRole": { "@id": "https://obofoundry.org/sepio/0000156", "id": 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