15 Matching Annotations
  1. Mar 2021
    1. Results for individual PALB2 variants were normalized relative to WT-PALB2 and the p.Tyr551ter (p.Y551X) truncating variant on a 1:5 scale with the fold change in GFP-positive cells for WT set at 5.0 and fold change GFP-positive cells for p.Y551X set at 1.0. The p.L24S (c.71T>C), p.L35P (c.104T>C), p.I944N (c.2831T>A), and p.L1070P (c.3209T>C) variants and all protein-truncating frame-shift and deletion variants tested were deficient in HDR activity, with normalized fold change <2.0 (approximately 40% activity) (Fig. 1a).

      AssayResult: 4.8

      AssayResultAssertion: Normal

      StandardErrorMean: 0.79

    2. A total of 84 PALB2 patient-derived missense variants reported in ClinVar, COSMIC, and the PALB2 LOVD database were selected

      HGVS: NM_024675.3:c.2816T>G p.(Leu939Trp)


      AssayResult: 36

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

      Approximation: Exact assay result value not reported; value estimated from Figure 6C.


      AssayResult: -36

      AssayResultAssertion: Abnormal

      PValue: < 0.0001


      AssayResult: 91.53

      AssayResultAssertion: Not reported

      PValue: > 0.9999

      Comment: Exact values reported in Table S3.

    4. To this end, 44 missense variants found in breast cancer patients were identified in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar) and/or selected by literature curation based on their frequency of description or amino acid substitution position in the protein (Supplemental Table S1).

      HGVS: NM_024675.3:c.83A>G p.(Tyr28Cys)

    1. While 3 VUS (p.W912G, p.L961P, and p.G1043D) had a dramatic impact on the percentage of cells showing RAD51 foci, 2 VUS (p.G937R and p.L947S) displayed a more minor effect.

      AssayResult: 19.52 foci/cell

      AssayResultAssertion: Indeterminate (described as "minor effect")

      Range: 0 - 70

      Comment: Exact values reported in "Source Data" file

    2. Source Data

      AssayResult: 24.27

      AssayResultAssertion: Abnormal

      ReplicateCount: Not reported

      StandardErrorMean: Not reported

      Comment: Exact values reported in “Supplementary Data 1” file; result for this variant not reported in “Source Data” file.

    3. Source Data

      AssayResult: 17.62

      AssayResultAssertion: Abnormal

      ReplicateCount: 2

      StandardDeviation: 1.76

      StandardErrorMean: 1.25

      Comment: Exact values reported in “Source Data” file.

    4. We, therefore, analyzed the effect of 48 PALB2 VUS (Fig. 2a, blue) and one synthetic missense variant (p.A1025R) (Fig. 2a, purple)29 on PALB2 function in HR.

      HGVS: NM_024675.3:c.3073_3074delinsCG p.(A1025R)

    1. Most Suspected Brugada Syndrome Variants Had (Partial) Loss of Function

      AssayResult: 47

      AssayResultAssertion: Indeterminate

      ReplicateCount: 10

      StandardErrorMean: 15.5

      Comment: This variant had a mix of multiple abnormalities: a partial loss of function of peak current (10-50% of wildtype) and a gain of function >10mV shift in activation voltage. Therefore it was considered to have inconclusive in vitro properties (neither normal nor abnormal in vitro function). (Personal communication: A. Glazer)

    2. we selected 73 previously unstudied variants: 63 suspected Brugada syndrome variants and 10 suspected benign variants

      HGVS: NM_198056.2:c.3784G>A p.(Gly1262Ser)

  2. Feb 2021
    1. Supplemental material

      AssayResult: 62

      AssayResultAssertion: Abnormal

      Comment: See Table S3 for details

    2. Supplemental material

      AssayResult: 4.7

      AssayResultAssertion: Abnormal

      Comment: See Table S3 for details

    3. We analysed a total of 82 blood samples derived from 77 individuals (online supplemental table 3). These 77 individuals corresponded either to new index cases suspected to harbour a pathogenic TP53 variant or to relatives of index cases harbouring TP53 variants.

      HGVS: NM_000546.5:c.770del p.(Leu257Argfs*88)