Gene Validity Curation

Gene Validity Classification Summary

Gene/Disease Pair:

LAMP2 : Danon disease

MONDO:0010281 | ORPHA:34587 | OMIM:300257
Mode of Inheritance: X-linked inheritance (HP:0001427)
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
14.00
12
Charron P et al. 2004 Aug (PMID:15253947); Arad M et al. 2005 Jan 27 (PMID:15673802);
Proband with predicted or proven null variant 1.5 0-2 10 4.50 4.5
Charron P et al. 2004 Aug (PMID:15253947); Garcia-Pavia P et al. 2011 Nov (PMID:21896538);
Proband with other variant type with some evidence of gene impact 0.5 0-1.5 7
1.50
1.5
Arad M et al. 2005 Jan 27 (PMID:15673802);
Autosomal Recessive Disease Two variants in trans and at least one de novo or a predicted/proven null variant 2 0-3 12
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
 
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
2.00
Walsh R et al. 2017 Feb (PMID:27532257);
Total Genetic Evidence Points (Maximum 12) 12
Experimental Evidence
Evidence Category Evidence Type Guidelines Scores PMIDs/Notes
Default Range Max Points Tally
Function Biochemical Function 0.5 0 - 2 2
1
Protein Interaction 0.5 0 - 2
Expression 0.5 0 - 2 1.00
Konecki DS et al. 1995 Oct 13 (PMID:7488019); Lichter-Konecki U et al. 1999 Jul (PMID:10448712);
Functional Alteration Patient cells 1 0 - 2 2
0
Non-patient cells 0.5 0 - 1 0.00
Stypmann J et al. 2006 Jul (PMID:16604439); (Genes altered not involved in heart, and mechanism unclear.)
Models Non-human model organism 2 0 - 4 4 4.00 4
Tanaka Y et al. 2000 Aug 24 (PMID:10972293); Stypmann J et al. 2006 Jul (PMID:16604439);
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 12 5 17 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
01/24/2017
EXPERT CURATION (DATE)
DEFINITIVE
10/11/2017
Curated as part of the ClinGen Hypertrophic cardiomyopathy Gene Curation Expert Panel and approved by ClinGen expert Jonathan S. Berg.