Table 2 Identified ANXA1 novel variants and SNPs absent in controls
From: Recurrent duplications of the annexin A1 gene (ANXA1) in autism spectrum disorders
Genomic position (hg18) | Nucleotide change | Amino acid change | Location | Transcript | Novel/SNP | Frequency cases | Genotype | In silico analysis | PhastCons (primates) |
|---|---|---|---|---|---|---|---|---|---|
74956445 | G > A | – | 5' of the gene | ENST00000257497 | Novel1 | 0.002 | Homo | TFBS abolished: VDR, CAR, PXR; NF-Y, C-myb, Crx; TFBS created: HNF6, Nkx6-2, OTX, CdxA | 0.48 |
74956718 | CTA > Del.CTA | – | Intron 1–2 | ENST00000257497 | Novel1 | 0.002 | Het | - | 0.23 |
74962617 | C > T | – | 5'UTR | ENST00000376911 | rs27951151 | 0.002 | Het | - | 0.014 |
74964058 | T > C | – | intron 3–4 | ENST00000257497 | rs101143501 | 0.002 | Het | splice-site SNP (ENSEMBL), ISRE down (pfSNP) | 0.81 |
74972178 | G > A | – | intron 10–11 | ENST00000257497 | Novel1 | 0.005 | Het | – | 0.1 |
74972626 | T > G | – | Intron 11–12 | ENST00000257497 | Novel1 | 0.002 | Het | – | 0.18 |
74973075 | G > C | – | Intron 11–12 | ENST00000257497 | rs101196051 | 0.002 | Het | – | 0.11 |
74973545 | T > C | – | Intron 11–12 | ENST00000257497 | Novel1 | 0.002 | Het | – | NA |
74975361 | G > A | – | 3' (intergenic) | – | Novel | 0.002 | Het | – | 0.05 |
74975609 | T > A | – | 3' (intergenic) | – | Novel | 0.002 | Het | – | 0.78 |
74975645 | T > C | – | 3' (intergenic) | – | rs149272288 | 0.001 | Het | – | 0.014 |
74975873 | C > T | – | 3' (intergenic) | – | rs9792653 | 0.051 | Het | – | NA |
74975882 | C > T | – | 3' (intergenic) | – | rs143327464 | 0.004 | Het | – | NA |
74976171 | C > T | – | 3' (intergenic) | – | rs113627562 | 0.004 | Het | – | NA |
74976222 | A > G | – | 3' (intergenic) | – | rs72737044 | 0.017 | Het/Homo | – | 0.18 |
74976536 | C > T | – | 3' (intergenic) | – | Novel | 0.001 | Het | – | 0.03 |
74976574 | T > C | – | 3' (intergenic) | – | rs78798837 | 0.002 | Het | – | NA |
74977215 | T > C | – | 3' (intergenic) | – | Novel | 0.001 | Het | – | 0.006 |
74977218 | C > T | – | 3' (intergenic) | – | rs146061737 | 0.001 | Het | – | 0.003 |
74977655 | A > G | – | 3' (intergenic) | – | rs114240435 | 0.002 | Het | – | 0 |
74977680 | C > A | – | 3' (intergenic) | – | rs114833327 | 0.001 | Het | – | NA |
74977840 | G > A | – | 3' (intergenic) | – | rs11143512 | 0.465 | Het/Homo | – | NA |
74977852 | A > G | – | 3' (intergenic) | – | Novel | 0.001 | Het | – | 0.01 |
74977888 | C > G | – | 3' (intergenic) | – | rs17653109 | 0.089 | Het/Homo | – | 0.07 |
74977928 | C > T | – | 3' (intergenic) | – | rs75260654 | 0.023 | Het | – | NA |
74977965 | C > G | – | 3' (intergenic) | – | Novel | 0.001 | Het | – | 0.08 |
74977981 | C > T | – | 3' (intergenic) | – | rs4443724 | 1 | Homo | – | 0.003 |
74977990 | C > T | – | 3' (intergenic) | – | rs116224215 | 0.007 | Het | – | NA |
74978003 | C > T | – | 3' (intergenic) | – | rs4285546 | 0.04 | Het/Homo | – | 0.003 |