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. 2022 Mar;24(3):552-563.
doi: 10.1016/j.gim.2021.11.011. Epub 2021 Nov 18.

Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants

Lucy Loong  1 , Cankut Cubuk  1 , Subin Choi  1 , Sophie Allen  1 , Beth Torr  1 , Alice Garrett  1 , Chey Loveday  1 , Miranda Durkie  2 , Alison Callaway  3 , George J Burghel  4 , James Drummond  5 , Rachel Robinson  6 , Ian R Berry  7 , Andrew Wallace  4 , Diana M Eccles  8 , Marc Tischkowitz  9 , Sian Ellard  10 , James S Ware  11 , Helen Hanson  12 , Clare Turnbull  13 ; CanVIG-UK
Collaborators, Affiliations

Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants

Lucy Loong et al. Genet Med. 2022 Mar.

Abstract

Purpose: Conditions and thresholds applied for evidence weighting of within-codon concordance (PM5) for pathogenicity vary widely between laboratories and expert groups. Because of the sparseness of available clinical classifications, there is little evidence for variation in practice.

Methods: We used as a truthset 7541 dichotomous functional classifications of BRCA1 and MSH2, spanning 311 codons of BRCA1 and 918 codons of MSH2, generated from large-scale functional assays that have been shown to correlate excellently with clinical classifications. We assessed PM5 at 5 stringencies with incorporation of 8 in silico tools. For each analysis, we quantified a positive likelihood ratio (pLR, true positive rate/false positive rate), the predictive value of PM5-lookup in ClinVar compared with the functional truthset.

Results: pLR was 16.3 (10.6-24.9) for variants for which there was exactly 1 additional colocated deleterious variant on ClinVar, and the variant under examination was equally or more damaging when analyzed using BLOSUM62. pLR was 71.5 (37.8-135.3) for variants for which there were 2 or more colocated deleterious ClinVar variants, and the variant under examination was equally or more damaging than at least 1 colocated variant when analyzed using BLOSUM62.

Conclusion: These analyses support the graded use of PM5, with potential to use it at higher evidence weighting where more stringent criteria are met.

Keywords: ACMG; Classification; Codon; PM5; Variant.

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Conflict of interest statement

Conflict of Interest The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Schematic of PM5 analyses comparing prediction (lookup of colocated variants in the lookup data set) with a reference truthset. Combinations of lookup data set and reference truthset for each analysis approach (top). Assignation of true positive, true negative, false positive, and false negative (middle). Binary PM5 definitions of increasing stringency (a-e) and nonoverlapping banded PM5 definitions (x, y) (bottom). DEL, deleterious; MAVE, multiplex assay of variant effect; TOL, tolerated.
Figure 2
Figure 2
Distribution of assay results by codon. By codon, number of multiplex assay of variant effect (MAVE)-deleterious missense variants (red), number of MAVE-tolerated missense variants (blue), and number of eligible missense (green) for (A) BRCA1 and (B) MSH2.
Figure 3
Figure 3
Distribution of codon typesin BRCA1 and MSH2. Number of codons which are MAVE-deleterious only (red), MAVE-tolerated only (green), and MAVE-mixed (blue) against the total number of missense variants at the codon for which there is dichotomous assay data (x-axis) for (A) BRCA1 and (B) MSH2.
See this image and copyright information in PMC

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