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Table 1 Mutations identified in LRP1, ALS2CL, ZNF480 and KPNA1 and occurrence in SCZ and CTR cohorts

From: Investigation of rare variants in LRP1, KPNA1, ALS2CL and ZNF480 genes in schizophrenia patients reflects genetic heterogeneity of the disease

Mutation details Prediction scores Occurrence
Gene Genomic Positiona Nucleotide variantb AA Change Typed dbSNPe ESVf 1000 genomesg Inheritanceh Pantheri Siftj PolyPhenk SCZ l cohort CTR cohort
LRP1 chr12:57,579,450   Y2200X c NS     de novo      
LRP1 chr12:57,538,812 c.506G > A G169D MS - A = 2 / G = 10756 - N/A - 0.01 2.337 1/189 -
LRP1 chr12:57,539,265 c.833G > T S278I MS - - - T (mother) −2.47064 0.08 1.73 1/189 -
LRP1 chr12:57,548,392 c.1135G > A R379H MS - - - N/A −2.23136 0.07 1.571 1/189 -
LRP1 chr12:57,574,263 c.5386 + 1G > A M1795I MS - - - T (mother) - 0.06 1.968 1/189 -
LRP1 chr12:57,577,915 c.5977C > T R1993W MS rs141826184 T = 25 / C = 10733 T = 1 / C = 1093 N/A - 0.05 0.037 2/189 -
LRP1 chr12:57,578,673 c.6238G > A D2080N MS rs34577247 A = 159 / G = 10599 A = 26 / G = 2162 N/A - 0.45 0.375 >5 -
LRP1 chr12:57,579,328 c.6478G > A A2160T MS - A = 1 / G = 10495 - N/A - 0.60 1.147 1/189 -
LRP1 chr12:57,587,040 c.7637G > A G2546S MS rs113379328 A = 24 / G = 10734 - N/A - 0.13 0.836 >5 -
LRP1 chr12:57,587,717 c.7840G > A R2613Q MS rs150340911 A = 12 / G = 10746 - N/A - 0.36 0.898 2/189 -
LRP1 chr12:57,588,275 c.8057G > A R2686H MS rs148104493 A = 1 / G = 10755 - N/A - 0.12 0.999 1/189 -
LRP1 chr12:57,589,784 c.8699A > C Q2900P MS rs7397167 A = 123 / C = 10635 A = 14 / C = 2174 N/A - 0.53 - >5 -
LRP1 chr12:57,590,916 c.9044G > A G3015S MS rs145303173 A = 6 / G = 10752 - N/A - 0.76 0.357 2/189 -
LRP1 chr12:57,598,513 c.11175G > A G3725E MS rs151301245 A = 12 / G = 10746 - T (mother) - 0.03 1.583 1/189 -
LRP1 chr12:57,600,508 c.11843G > A G3948D MS - - - N/A - 0.50 1.357 1/189 -
ALS2CL chr3:46,717,166   R733X c NS     de novo      
ALS2CL chr3:46,717,175 c.2188C > T G730S MS rs142971127 T = 80 / C = 10678 T = 12 / C = 2176 N/A - 0.40 1.483 7/475 1/189
ALS2CL chr3:46,718,458 c.1812G > T P605T MS - - - N/A −1.70789 0.42 1.761 0/475 1/189
ALS2CL chr3:46,718,477 c.1793C > T R598H MS - - - N/A −2.73328 0.01 1.686 0/475 1/189
ALS2CL chr3:46,719,769 c.1737G > A P580S MS - - - T (mother) - 0.62 1.615 1/475 0/189
ALS2CL chr3:46,719,861 c.1645T > C N549S MS rs140347863 C = 9 / T = 10749 - T (father). N/A. T (mother). N/A - 0.35 1.851 3/475 1/189
ALS2CL chr3:46,722,792 c.1380G > A T460M MS - A = 1 / G = 10757 - T (father) −2.00878 0.11 0.374 1/475 0/189
ALS2CL chr3:46,725,290 c.894G > A A298V MS rs141781567 A = 15 / G = 10757 - N/A −1.6125 0.14 1.366 2/475 0/189
ALS2CL chr3:46,725,522 c.802T > A T268S MS - - - T (mother) −1.48254 0.33 1.406 1/475 0/189
ALS2CL chr3:46,728,477 c.530A > G I176T MS rs145807890 G = 8 / A = 10746 - N/A −1.28647 0.39 1.351 0/475 1/189
ALS2CL chr3:46,729,700 c.190C > A E65X NS rs139496961 A = 20 / C = 10738 - N/A. T (father). N/A. N/A - - - 4/475 1/189
ALS2CL chr3:46,729,756 c.134C > G E45Q MS rs7642448 G = 4590 / C = 6166 - N/A - 0.28 1.042 >5 >5
ZNF480 chr19:52,826,001   R500X c NS     de novo      
ZNF480 chr19:52,825,329 c.826C > T R276X NS - - - N/A - - - 1/475 0/189
ZNF480 chr19:52,825,495 c.992C > A A331E MS - - - N/A - 0.95 0.838 0/475 1/189
ZNF480 chr19:52,826,001 c.1498C > T R500X NS - - - N/A - - - 0/475 1/189
KPNA1 chr3:122,146,472   E448X c NS     de novo      
KPNA1 chr3:122,186,188 c.218C > T S73N MS rs4678193 T = 79 / C = 10677 T = 11 / C = 2177 N/A −2.16746 0.45 0.174 >5 -
  1. a according to build Hg19; b variant position according to Mutalyzer 2.0.beta-20 [12] and to Genbank accession number NM_002332.2 for LRP1, NM_147129.3 for ALS2CL, NM_144684.2 for ZNF480 and NM_002264.3 for KPNA1; c MS: missense and NS: nonsense; d nonsense mutations previously identified by exome sequencing [6]; e rs number as obtained in dbSNP database [7]; f observed allele counts according to Exome Variant Server in all populations [9]; g observed allele counts according to 1000 genomes in all populations [8]; h inheritance study when parents available; i according to Panther, sub-PSEC score is the probability that a given coding variant will cause a deleterious functional change when less than −3 [13]; j according to Sift scores (from 0 to 1), the amino acid substitution is predicted to be damaging if the score is < = 0.05 and tolerated if the score is > 0.05 [11]; k according to polyphen, if PSIC score difference is > 1.5, the variation is predicted to be possibly or probably damaging [10, 11]. l > 5 indicates that the variant has been identified in more than 5 individuals.