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Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants
- Source :
- Loong, L, Cubuk, C, Choi, S, Allen, S, Torr, B, Garrett, A, Loveday, C, Durkie, M, Callaway, A, Burghel, GJ, Drummond, J, Robinson, R, Berry, IR, Wallace, A & CanVIG-UK 2021, ' Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants. ', Genetics in medicine : official journal of the American College of Medical Genetics, vol. 24, no. 3, pp. 552-563 . https://doi.org/10.1016/j.gim.2021.11.011
- Publication Year :
- 2021
- Publisher :
- American College of Medical Genetics and Genomics, 2021.
-
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.
- Subjects :
- Concordance
Mutation, Missense
Biology
PM5
CanVIG-UK
Humans
Missense mutation
Genetic Predisposition to Disease
Variant
Codon
Genetics (clinical)
Genetics
Genetics & Heredity
0604 Genetics
BRCA1 Protein
Genetic Variation
1103 Clinical Sciences
Pathogenicity
Classification
MutS Homolog 2 Protein
Genetic Variation/genetics
Mutation, Missense/genetics
MSH2
ACMG
BRCA1 Protein/genetics
MutS Homolog 2 Protein/genetics
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Loong, L, Cubuk, C, Choi, S, Allen, S, Torr, B, Garrett, A, Loveday, C, Durkie, M, Callaway, A, Burghel, GJ, Drummond, J, Robinson, R, Berry, IR, Wallace, A & CanVIG-UK 2021, ' Quantifying prediction of pathogenicity for within-codon concordance (PM5) using 7541 functional classifications of BRCA1 and MSH2 missense variants. ', Genetics in medicine : official journal of the American College of Medical Genetics, vol. 24, no. 3, pp. 552-563 . https://doi.org/10.1016/j.gim.2021.11.011
- Accession number :
- edsair.doi.dedup.....4a638418e559b935daf78b3ef4e1f05a