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Table 3 Variants with an increase in pathogenicity score due to reanalysis

From: Genomic diagnosis for children with intellectual disability and/or developmental delay

Gene Affected individual ID(s) Variant info Original score Updated score Reason(s) for update Evidence for upgrade
DDX3X 00075-C NM_001356.4(DDX3X):c.745G > T (p.Glu249Ter) VUS Pathogenic Publication [38]
EBF3 00006-C NM_001005463.2(EBF3):c.1101 + 1G > T VUS Pathogenic GeneMatcher Collaboration with several other groups identified patients with comparable genotypes and phenotypes [37]
EBF3 00032-C NM_001005463.2(EBF3):c.530C > T (p.Pro177Leu) VUS Pathogenic GeneMatcher Collaboration with several other groups identified patients with comparable genotypes and phenotypes [37]
KIAA2022 00082-C NM_001008537.2(KIAA2022):c.2999_3000delCT (p.Ser1000Cysfs) VUS Pathogenic Publication/Personal communication [39]
TCF20 00078-C NM_005650.3(TCF20):c.5385_5386delTG (p.Cys1795Trpfs) VUS Pathogenic Publication [16]
ARID2 00026-C NM_152641.2(ARID2):c.1708delT (p.Cys570Valfs) NR Pathogenic Publication [40]
CDK13 00253-C NM_003718.4(CDK13):c.2525A > G (p.Asn842Ser) NR Pathogenic Publication [16]
CLPB 00127-C NM_030813.5(CLPB):c.1222A > G (p.Arg408Gly) NM_030813.5(CLPB):c.1249C > T (p.Arg417Ter) NR Pathogenic Publication [41]
FGF12 00074-C NM_021032.4(FGF12):c.341G > A (p.R114H) NR Pathogenic Publication [42]
MTOR 00040-C NM_004958.3(MTOR):c.4785G > A (p.Met1595Ile) NR Pathogenic Publication For review [26]; see also [27]
MTOR 00028-C, 00028-C2 NM_004958.3(MTOR):c.5663 T > G (p.Phe1888Cys) NR Pathogenic Filter In original filter, required allele count of one; this variant was present in identical twins
HDAC8 00001-C NM_018486.2(HDAC8):c.737 + 1G > A NR Likely pathogenic Filter In original filter, required depth for all members of trio was set to 10 reads; father had only 7
LAMA2 00055-C, 00055-S NM_000426.3(LAMA2):c.715C > T (p.Arg239Cys) NR Likely pathogenic Clarification of clinical phenotype Discussion with clinicians was necessary to determine that patients’ phenotypes did match those observed for LAMA2
MAST1 00270-C NM_014975.2:c.278C > T, p.Ser93Leu NR Likely pathogenic GeneMatcher Collaboration with several other groups identified patients with comparable genotypes and phenotypes
SUV420H1 00056-C NM_017635.3:c.2497G > T, p.Glu833X NR Likely pathogenic Publication [16]
  1. C child/proband, C2 affected identical twin, S affected sibling, NR no returnables, VUS variant of uncertain significance