Table 1.
NRXN1 variants identified in this study
| 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 | |||||||
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
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
For details of each database, see Supplemental methods. None of the SNVs detected in our study were registered in the DECIPHER database
aMinor allele count/total allele count
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
cReference genome SNVs at the 10th-% of CADD scores are assigned to 10, top 1 to 20% and top 0.1 to 30%