Gene/Disease Pair: | BRAF : Costello syndrome |
HGNC:1097 | MONDO_0009026 | |
Mode of Inheritance: | Autosomal dominant inheritance (HP:0000006) |
Expert Panel: | RASopathy EP |
SOP: | Gene Clinical Validity Standard Operating Procedures (SOP), Version 5 |
Genetic Evidence
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Case-Level Data
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Evidence Type | Case Information Type | Guidelines | Points | PMIDs/Notes | ||||||
Default | Range | Max | Total | Counted | ||||||||
Variant Evidence
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Autosomal Dominant or X-linked Disorder | Variant is de novo | 2 | 0-3 | 12 |
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Proband with predicted or proven null variant | 1.5 | 0-2 | 10 | |||||||||
Proband with other variant type with some evidence of gene impact | 0.5 | 0-1.5 | 7 |
0
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0 |
Rauen KA et al. 2006 Aug 1 (PMID:16804887);
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Autosomal Recessive Disease | Two variants in trans and at least one de novo or a predicted/proven null variant | 2 | 0-3 | 12 |
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Two variants (not predicted/proven null) with some evidence of gene impact in trans | 1 | 0-1.5 | ||||||||||
Segregation Evidence | Evidence of segregation in one or more families | Sequencing Method | 0-3 | 3 |
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Total LOD Score | Canditate Gene Sequencing | Exome/Genome or all genes sequenced in linkage region | ||||||||||
2-2.99 | 0.5 | 1 | ||||||||||
3-4.99 | 1 | 2 | ||||||||||
≥5 | 1.5 | 3 | ||||||||||
Case-Control Data
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Case-Control Study Type | Case-Control Quality Criteria | Guidelines | Points | PMIDs/Notes | |||||||
Points/Study | Max | Total | Counted | |||||||||
Single Variant Analysis | 1. Variant Detection Methodology 2. Power 3. Bias and confounding 4. Statistical Significance |
0-6 | 12 |
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Aggregate Variant Analysis | 0-6 |
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Total Genetic Evidence Points (Maximum 12) | 0 |
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Experimental Evidence
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Evidence Category | Evidence Type | Guidelines | Points | PMIDs/Notes | |||||||
Default | Range | Max | Total | Counted | ||||||||
Function | Biochemical Function | 0.5 | 0 - 2 | 2 |
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=PrintWrapperPmid($inputThisData["ExperimentalEvidence"]["Function"]["BiochemicalFunction"], "scoreJson[ExperimentalEvidence][Function][BiochemicalFunction]") ?> | ||||||
Protein Interaction | 0.5 | 0 - 2 | ||||||||||
Expression | 0.5 | 0 - 2 | ||||||||||
Functional Alteration | Patient cells | 1 | 0 - 2 | 2 |
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Non-patient cells | 0.5 | 0 - 1 | ||||||||||
Models | Non-human model organism | 2 | 0 - 4 | 4 | ||||||||
Cell culture model | 1 | 0 - 2 | ||||||||||
Rescue | Rescue in human | 2 | 0 - 4 |
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Rescue in non-human model organism | 2 | 0 - 4 | ||||||||||
Rescue in cell culture model | 1 | 0 - 2 | ||||||||||
Rescue in patient cells | 1 | 0 - 2 | ||||||||||
Total Experimental Evidence Points (Maximum 6) | 0 |
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Assertion criteria | Genetic Evidence (0-12 points) | Experimental Evidence
(0-6 points) |
Total Points
(0-18) |
Replication Over Time (Y/N) | ||
Description | Case-level, family segregation, or case-control data that support the gene-disease association | Gene-level experimental evidence that support the gene-disease association | Sum of Genetic & Experimental
Evidence |
> 2 pubs w/ convincing evidence over time (>3 yrs) | ||
Assigned Points | =$inputThisData["summary"]["GeneticEvidenceTotal"]?> 0 | =$inputThisData["summary"]["ExperimentalEvidenceTotal"]?> 0 | =$inputThisData["summary"]["EvidencePointsTotal"]?> 0 | NO | ||
CALCULATED CLASSIFICATION | LIMITED | 1-6 | ||||
MODERATE | 7-11 | |||||
STRONG | 12-18 | |||||
DEFINITIVE | 12-18 AND replication over time | |||||
Valid contradictory evidence (Y/N)*
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CALCULATED CLASSIFICATION (DATE) |
No Classification
07/24/2018
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MODIFY CALCULATED CLASSIFICATION |
YES
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MODIFIED CLASSIFICATION (DATE) |
Disputed
07/24/2018
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REASON(S) FOR CHANGE |
No score-able cases have been described but there have been assertions made.
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EXPERT CURATION (DATE) |
Disputed
07/24/2018
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EVIDENCE SUMMARY |
Only one study to date has identified variants in BRAF in patients diagnosed with suspected Costello syndrome. However, due to lack of further evidence of impact of these variants as well as variable expressivity, age of ascertainment and outdated clinical assessments of affected individuals, these cases were not scored and, therefore, the evidence for this association is Disputed. Furthermore, the HRAS gene is believed to be the only gene definitively associated with Costello syndrome (Aoki et al., 2005; Estep, Tidyman, Teitell, Cotter, & Rauen, 2006; Gripp et al., 2006; Kerr et al., 2006; Zampino et al., 2007).
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