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Table 1 NRXN1 variants identified in this study

From: Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia

Chr Position dbSNP ID Ref Val Amino acid variant Our cohort iJGVDa HGVDa gnomADa ClinVar Tools for predicting the deleteriousness of missense variants
NP_004792 MAF MAF MAF MAF PolyPhen-2 MutationTaster REVELb CADDc
NP_620072
2 50091401 C T V1214I 1 SCZ 6/7100 4/2420 12/251454 0.245 29 0.242 22.1
rs752722196 V179I 8.9 × 10− 4 8.4 × 10 − 4 1.7 × 10 − 3 4.8 × 10 − 5 Benign Polymorphism
2 50091446 C T A1199T 2 ASD/1 SCZ 17/7086 10/2420 107/282828 Likely benign 0.087 58 0.233 16.98
rs201336161 A164T 2.7 × 10 − 3 2.4 × 10 − 3 4.1 × 10 − 3 3.8 × 10 − 4 Benign Polymorphism
2 50236845 C T V1164I 1 ASD 2/7104 1/2054 12/282134 0.460 29 0.15 14.39
  rs201881725    V129I 8.9 × 10 − 4 2.8 × 10 − 4 4.9 × 10 − 4 4.3 × 10 − 5   Probably damaging Polymorphism   
2 50497646 G A R856W 1 SCZ Uncertain 1.0 101 0.706 27.8
rs796052777 8.9 × 10 4 Significance Probably damaging Disease causing
2 50531259 T C D772G 1 ASD 1/248460 1.0 94 0.761 29.6
rs1457374261 8.9 × 10 4 4.0 × 10 6 Probably damaging Disease causing
2 50531364 G A T737M 1 ASD/1 SCZ 2/247276 Uncertain 1.0 81 0.686 28.4
rs199970666 1.8 × 10 3    8.1 × 10 6 Significance Probably damaging Disease causing
  1. Genomic position based on NCBI build GRCh38.p12 (Ensembl Transcript IDs ENST00000406316.6 and ENST00000342183.9). The amino acid position is based on NCBI reference sequences NP_004792 and NP_620072, respectively
  2. Chr chromosome, dbSNP dbSNP build 151, Ref reference, Val variant, MAF minor allele frequency, SCZ schizophrenia, ASD autism spectrum disorders, iJGVD integrative Japanese Genome Variation Database, HGVD Human Genetic Variation Database, gnomAD Genome Aggregation Database, ClinVar NCBI ClinVar, PolyPhen-2 polymorphism phenotyping v.2, REVEL Rare Exome Variant Ensemble Learner, CADD Combined Annotation–Dependent Depletion v1.4
  3. For details of each database, see Supplemental methods. None of the SNVs detected in our study were registered in the DECIPHER database
  4. aMinor allele count/total allele count
  5. bThe REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing
  6. cReference genome SNVs at the 10th-% of CADD scores are assigned to 10, top 1 to 20% and top 0.1 to 30%