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Table 1 Differentially expressed genes upon QPRT-KO with |log2FC| > 2.5

From: Loss of the Chr16p11.2 ASD candidate gene QPRT leads to aberrant neuronal differentiation in the SH-SY5Y neuronal cell model

Gene Chr del268T vs eCtrl ins395A vs eCtrl WT vs eCtrl SFARI score ASD literature
FDR log2FC FDR log2FC FDR log2FC
COX17 3q13.33 3.33E−138 − 5.94 1.78E−154 − 5.63 0.30 − 0.13 / /
GUCA1A 6p21.1 4.56E−41 − 5.38 3.97E−46 − 5.88 0.20 0.26 / /
COX17P1 13q14.13 1.09E−84 − 5.19 5.82E−93 − 5.28 0.59 − 0.11 / /
VSTM2A 7p11.2 1.81E−10 − 5.00 6.36E−12 − 5.28 0.61 − 0.27 / /
KCNQ3 8q24.22 5.77E−04 − 4.76 1.25E03 − 3.04 0.46 0.49 3 Role for KCNQ3 in epilepsy and autism [75]
CCK 3p22.1 2.56E−04 − 3.18 5.97E−05 − 3.13 0.17 0.68 / Candidate gene for Asperger’s in a microdeletion case study [76]
GABRB3 15q12 3.04E−43 − 3.00 9.43E−54 − 3.58 0.80 0.04 2 CNV Chr15q11-13 implicated in ASD; polymorphisms associated with ASD [62, 77]
BRINP1 9q33.1 8.93E−09 − 2.92 2.09E−09 − 2.85 0.20 − 0.53 / −/− mice: autism-like behavior including reduced sociability and altered vocalization [78]
LINC01760 1p21.3 1.02E−02 2.74 4.93E−03 2.62 0.95 − 0.30 / /
SNTG2 2p25.3 7.04E−04 − 2.71 5.06E−07 − 5.58 0.72 0.22 4 Region linked with ID [64], associated with ASD [65]; interaction partner of neuroligins, interaction altered by ASD associated mutations [66]
ARHGAP20 11q23.1 1.63E−09 − 2.65 4.08E−15 − 3.93 0.45 − 0.30 / /
SRRM4 12q24.23 1.29E−18 − 2.61 2.25E−26 − 3.40 0.54 − 0.20 / −/+ mice: multiple autistic-like features [79]
  1. Chr chromosomal region, del268T CRISPR/Cas9 induced mutation (deletion of one nucleotide) in exon 2 of QPRT, ins395A CRISPR/Cas9-induced mutation (insertion of one nucleotide) in exon 2 of QPRT, eCtrl control cell line with empty CRISPR/Cas9 control vector, WT wild-type SH-SY5Y cell line untreated, FDR False discovery rate, log2 FC log2 fold change, SFARI score score in the SFARI database [58] (a smaller score means higher evidence), ASD references Pubmed was searched for “gene and autism” and “gene and ASD”