Gene Validity Curation

Gene Validity Classification Summary

Gene/Disease Pair:

ALPK3 : Hypertrophic cardiomyopathy

MONDO:0005045 | ORPHA:217569 | OMIM:617608
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
8.00
Almomani R et al. 2016 Feb 9 (PMID:26846950); Phelan DG et al. 2016 Sep 1 (PMID:27106955);
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
1.00
1  
Total LOD Score Canditate Gene Sequencing Exome/Genome or all genes sequenced in linkage region  
2-2.99 0.5 1
Phelan DG et al. 2016 Sep 1 (PMID:27106955);
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) 9
Experimental Evidence
Evidence Category Evidence Type Guidelines Scores PMIDs/Notes
Default Range Max Points Tally
Function Biochemical Function 0.5 0 - 2 2
0.50
1
Hosoda T et al. 2001 Sep 21 (PMID:11418590);
Protein Interaction 0.5 0 - 2
Expression 0.5 0 - 2 0.50
Hosoda T et al. 2001 Sep 21 (PMID:11418590);
Functional Alteration Patient cells 1 0 - 2 2
1.00
1.5
Phelan DG et al. 2016 Sep 1 (PMID:27106955);
Non-patient cells 0.5 0 - 1 0.50
Hosoda T et al. 2001 Sep 21 (PMID:11418590);
Models Non-human model organism 2 0 - 4 4 1.00 1
Van Sligtenhorst I et al. 2012 Jan (PMID:21441111);
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) 3.5

 


 

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 9 3.5 12.5 NO
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)
STRONG
12/16/2016
EXPERT CURATION (DATE)
STRONG
02/07/2017