A detailed analysis of the role of non-sarcomeric genes in HCM - incorporating clinical sequencing data from the OMGL and LMM labs, a cohort of over 800 HCM probands from the Royal Brompton Hospital, London and the National Heart Centre, Singapore (sequenced on a broad cardiac NGS panel) and published sequencing, segregation and functional data - has clarified the involvement of FHL1 variants in this condition (see our study published in the European Heart Journal for further details).
Based on this analysis, FHL1 is classified as having: Strong Evidence
|Case excess (gene)||Max LOD score||Case excess (variant)||De novo variant|
|See details below||p.N38S (4/2061 cases vs. 0/60706 ExAC samples, p < 1x10-4)||c.134delA (PMID:22523091)|
|Cohort (reference)||HCM patients tested||Rare variants||Case Frequency||Significance vs ExAC|
Summary of the frequency of rare FHL1 variants (ExAC frequency < 0.0001) in published cohorts of HCM probands. P-values shown are from Fisher' Exact test compared to rare variants in ExAC (ExAC frequency = 0.00123). Significance is based on multiple testing correction of 31 genes tested (p<0.0016).
By comparing the frequency of FHL1 variants in large HCM clinical cohorts to the background population rate in the ExAC database, the proportion of HCM patients with pathogenic mutations in FHL1 can be estimated, as well as the likelihood that a rare (population allele frequency <0.0001) FHL1 variant identified in a HCM patient is disease-causing. Summary data for different variant classes (all protein-altering variants, loss of function truncating variants and non-truncating variants) is highlighted - see the table below for full details of this analysis.
Excess of FHL1 variants in HCM: 0.79% (p<0.0001)
Based on an analysis of all rare protein-altering variants (MAF<0.0001 in ExAC) in FHL1 found in 1535 HCM samples sequenced by OMGL and LMM and in reference samples of the ExAC population database.
|Excess in HCM||0.79%
0.74 - 0.93
0.79 - 1.00
0.72 - 0.92
3.90 - 13.40
3.53 - 12.66
The Etiological Fraction (EF) is the proportion of affected carriers where the variant caused HCM. The Odds Ratio (OR) describes the odds of having a rare variant in the patient cohort to the odds in the ExAC cohort. Fisher's exact test p-values are displayed for case excess, 95% confidence intervals for EFs and ORs.
1. Roddy Walsh, Kate L. Thomson, James S. Ware, Birgit H. Funke, Jessica Woodley, Karen J. McGuire, Francesco Mazzarotto, Edward Blair, Anneke Seller, Jenny C. Taylor, Eric V. Minikel, Exome Aggregation Consortium, Daniel G. MacArthur, Martin Farrall, Stuart A. Cook and Hugh Watkins. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med. 2016 doi:10.1038/gim.2016.90.
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3. Roddy Walsh, Rachel Buchan, Alicja Wilk, Shibu John, Leanne E. Felkin, Kate L. Thomson, Tang Hak Chiaw, Calvin Chin Woon Loong, Chee Jian Pua, Claire Raphael, Sanjay Prasad, Paul J. Barton, Birgit Funke, Hugh Watkins, James S. Ware, Stuart A. Cook. Defining the genetic architecture of hypertrophic cardiomyopathy: re-evaluating the role of non-sarcomeric genes. Eur Heart J. 2017 doi:10.1093/eurheartj/ehw603.