Gene: TPM1 (HGNC:12010)
Evidence Code: PS4 — Strong
Modification Type: Disease-specific
Currently few well-designed case-control studies have been performed for inherited cardiomyopathies.  Until such studies become available, comparative analyses can be undertaken using case data (e.g., internal and/or published cohorts) and control data from population-level cohorts (e.g., gnomAD). 


Cohorts used in these analyses should meet the following criteria: 




The cases have a clinical diagnosis of the specified disorder or related phenotype (e.g., all cases have HCM or another relevant phenotype*). 


When assessing cases, it's important to consider how likely another potential cause of the phenotype has been excluded.  This includes considering the presence of other variants in relevant genes (particularly those likely to be contributing to phenotype) and the extent of testing performed (i.e., single gene sequencing, panel testing, whole exome/genome sequencing).






The controls should not be derived from study populations that might be enriched for the specified disorder.


The denominator of the cohorts must be available (e.g., variant detected in 5 out of 3,500 cases and 1 out of 60,000 controls).


The cohorts do not include closely related individuals (i.e., family members are not included in the case counts).


The cohorts do not overlap with other cohorts being used in the analysis (i.e., cases are not being counted more than once).


The population diversity of the case and control cohorts are broadly similar.


Consider the size of the case cohort — larger cohorts are likely to provide more accurate estimates of variant frequency; therefore, it may be preferable to use data from the largest available case series for case-control analyses (e.g., Walsh 
et al.
 2017
5
, 
DECIPHER
).




To account for limitations that arise when performing unmatched case-control analyses, the following stringent OR threshold is recommended:




STRONG
 evidence requires the lower bound of the 95% confidence interval (CI) around the odds ratio (OR) estimate to be 
≥20




A PS4 calculator is available at 
www.cardiodb.org
.


If multiple cohorts are available, the final ORs and associated CIs need to be harmonized across all cohorts to determine the final level (e.g., if 2 large cohorts have an OR of ~6 and a third small cohort has an OR of 11, application at a SUPPORTING level should be considered).  


*RELEVANT PHENOTYPES:




Cases of HCM and RCM may be combined as they are considered part of the same disease spectrum. 


For the eight genes covered by these guidelines, the combination of probands with other phenotypes should be reviewed by a clinical expert to determine if grouping is appropriate. 


Additional considerations for LVNC and end-stage HCM: 


Due to the current debate about whether isolated LVNC represents a true disease entity or variation of typical cardiac morphology (Anderson 
et al.
 2017
6
; Oechslin 
et al.
 2017
7
; Hershberger 
et al.
 2017
8
; Ross 
et al.
 2020
9
), individuals with isolated LVNC should NOT be added to proband or segregation counts (including individuals with isolated LVNC in a family with other cardiomyopathies).








HCM and DCM have distinct mechanisms of disease and therefore pathogenetic variants are not anticipated to cause both primary phenotypes. While occurrence in both phenotypes may initially be considered as evidence against pathogenicity, end-stage HCM can present similarly to DCM. Careful consideration is needed before including DCM or related phenotypes in case or segregation data for primarily HCM variants.