Gene Validity Classification Summary

Gene/Disease Pair:

COX15 : Leigh Syndrome

MONDO:0009723 | ORPHA:506 | OMIM:256000
Mode of Inheritance: Autosomal recessive inheritance (HP:0000007)
SOP: Gene Clinical Validity Standard Operating Procedures (SOP), Version 5

Genetic Evidence
Case-Level Data
Evidence Type Case Information Type Guidelines Scores PMIDs/Notes
Default Range Max Points Tally
Variant Evidence
Autosomal Dominant or X-linked Disorder Variant is de novo 2 0-3 12
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
Autosomal Recessive Disease Two variants in trans and at least one de novo or a predicted/proven null variant 2 0-3 12
6.00
Antonicka H et al. 2003 Jan (PMID:12474143); Kennaway NG et al. 1990 Nov (PMID:2175025); Alfadhel M et al. 2011 Apr (PMID:21412973); Bugiani M et al. 2005 May (PMID:15863660); Miryounesi M et al. 2016 Jun 1 (PMID:26959537);
Two variants (not predicted/proven null) with some evidence of gene impact in trans 1 0-1.5
2.00
Oquendo CE et al. 2004 Jul (PMID:15235026); Miryounesi M et al. 2016 Jun 1 (PMID:26959537);
Segregation Evidence Evidence of segregation in one or more families   Sequencing Method 0-3 3
 
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
Case-Control Study Type Case-Control Quality Criteria Guidelines Scores PMIDs/Notes
Points/Study Max Points Tally
Single Variant Analysis 1. Variant Detection Methodology
2. Power
3. Bias and confounding
4. Statistical Significance
0-6 12
Aggregate Variant Analysis 0-6
Total Genetic Evidence Points (Maximum 12) 8
Experimental Evidence
Evidence Category Evidence Type Guidelines Scores PMIDs/Notes
Default Range Max Points Tally
Function Biochemical Function 0.5 0 - 2 2
1.5
Protein Interaction 0.5 0 - 2
Expression 0.5 0 - 2 1.50
Petruzzella V et al. 1998 Dec 15 (PMID:9878253);
Functional Alteration Patient cells 1 0 - 2 2
Non-patient cells 0.5 0 - 1
Models Non-human model organism 2 0 - 4 4 3.50 3.5
Koscielny G et al. 2014 Jan (PMID:24194600); Viscomi C et al. 2011 Jul 6 (PMID:21723506); (One mouse mouse model generated by IMPC.)
Cell culture model 1 0 - 2
Rescue Rescue in human 2 0 - 4
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) 5

 


 

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 8 5 13 YES
CALCULATED CLASSIFICATION LIMITED 1-6
MODERATE 7-11
STRONG 12-18
DEFINITIVE 12-18 AND replication over time
Valid contradictory evidence (Y/N)*
NO
CALCULATED CLASSIFICATION (DATE)
DEFINITIVE
07/13/2017
MODIFY CALCULATED CLASSIFICATION
YES
CURATOR CLASSIFICATION (DATE)
STRONG
08/07/2017
Classification was downgraded from Definitive to Strong after expert review, citing a requirement for more case reports before achieving a Definitive classificaiton.
EXPERT CURATION (DATE)
STRONG
08/07/2017
Curated as part of the Hypertrophic cardiomyopathy Gene Curation Expert Panel and Approved by ClinGen Inborn Errors of Metabolism expert Heather Beaudet