15 Matching Annotations
  1. Oct 2024
    1. Disease: Von Willebrand Disease (VWD) Type 2A

      Patient: 31 yo, Female

      Variant1: VWF NC_000012.12: c.875-5T>Gdel, p.(Ser292_Glu333delinsLys) Causes complete exon 8 skipping

      Variant2: VWF NM_000552.5: c.813C>G, p.(Tyr271*)

      Phenotypes: History of bleeding (epistaxis, uncontrollable by conventional hemostatic treatment), Easy bruising, gum bleeding, excessive menstrual bleeding, mild decrease in plasma VWF:Ag, severe impairment in VWF function, VWF:Ab/VWF:Ag ratio decreased, VWF:CB/VWF:Ag ratio decreased, FVIII:C lvs slighly below normal range

      Family: Son had bleeding diathesis and spontaneous epistaxis (less severe than proband), normal parents

      In silico data available: SpliceAI delta score of 0.51 for loss of splice acceptor caused by variant 1

      Alamut showed small to moderate effects of the variant on normal splicing of VWF

      NetGene2 showed weak strength of 3' splice sites in exon 8

      SpliceAid2 showed TIA-1 and TIAL 1, which bind to U-rich motifs and facilitate 5' splice site recognition where destroyed in the mutated sequence

  2. 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: 7.3

      AssayResultAssertion: Normal

      StandardErrorMean: 0.08

    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.1145G>T p.(Ser382Ile)

    1. SUPPLEMENTARY DATA

      AssayResult: 58

      AssayResultAssertion: Indeterminate

      PValue: < 0.0001

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

    2. SUPPLEMENTARY DATA

      AssayResult: -32

      AssayResultAssertion: Abnormal

      PValue: < 0.0001

    3. SUPPLEMENTARY DATA

      AssayResult: 76.45

      AssayResultAssertion: Indeterminate

      PValue: 0.0001

      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.23C>T p.(Pro8Leu)

    1. Source Data

      AssayResult: 83.96

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardErrorMean: 9.89

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

    2. Source Data

      AssayResult: 66.19

      AssayResultAssertion: Not reported

      ReplicateCount: 2

      StandardDeviation: 21.26

      StandardErrorMean: 15.03

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

    3. 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.1250C>A p.(S417Y)

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

      AssayResult: 1.2

      AssayResultAssertion: Abnormal

      ReplicateCount: 11

      StandardErrorMean: 0.7

      Comment: This variant had loss of function of peak current (<10% of wildtype), therefore it was considered abnormal (in vitro features consistent with Brugada Syndrome Type 1). (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.1156G>A p.(Gly386Arg)

  3. Feb 2021
    1. Supplemental material

      AssayResult: 86

      AssayResultAssertion: Normal

      Comment: See Table S3 for details

    2. Supplemental material

      AssayResult: 6.1

      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.215C>A p.(Pro72His)