Table 2. Sequence variants detected in VSX1 in 85 probands from unrelated keratoconus families.
| Reference SNP ID reported by |
Position in the gene |
Nucleotide change |
Protein change |
Observed genotypes |
Ethnicity of probands with alleles ab or bb | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Variant 1 | Variant 2 | Variant 1 | Variant 2 | Isoform A | Isoform B | aa | ab | bb | ||
| rs8123716 | Exon 1 | Exon 1 | c.18G>T | c.18G>T | p=(S6S) | p=(S6S) | 76 | 9 | 0 |
Asian (3), White (5), Unclassified (1) |
| Aldave et al. [34] | Exon 1 | Exon 1 | c.174G>T | c.174G>T | p=(P58P) | p=(P58P) | 83 | 2 | 0 | White (2) |
| rs6115023 | Exon 1 | Exon 1 | c.315C>A | c.315C>A | p.D105E | p.D105E | 83 | 2 | 0 | Black (2) |
| rs6037016 | Exon 1 | Exon 1 | c.339C>T | c.339C>T | p=(G113G) | p=(G113G) | 83 | 2 | 0 | Black (2) |
| rs6050307 | Exon 1 | Exon 1 | c.391C>A | c.391C>A | p.R131S | p.R131S | 80 | 4 | 1 | Black (5) |
| Heon et al. [17] | Exon 2 | Exon 2 | c.432C>G | c.432C>G | p.D144E | p.D144E | 84 | 1 | 0 | White (1) |
| Novel 1 | Intron 2 | Intron 2 | c.504-10G>A | c.504-10G>A | - | - | 84 | 1 | 0 | Unclassified (1) |
| Novel 2 | Intron 2 | Intron 2 | c.504-24C>T | c.504-24C>T | - | - | 82 | 3 | 0 | Asian (3) |
| rs12480307 | Exon 3 | Exon 3 | c.546A>G | c.546A>G | p=(A182A) | p=(A182A) | 32 | 44 | 9 |
Asian (15), White (24), Black (11), Unclassified (3) |
| rs6138482 | Intron 3 | Exon 3 | c.627+23G>A | c.650 G>A | - | p.R217H | 67 | 17 | 1 |
Asian (4), White (13), Black (1) |
| Bisceglia et al. [31] | Intron 3 | Exon 3 | c.627+84T>A | c.711T>A | - | p=(P237P) | 32 | 44 | 9 |
Asian (15), White (24), Black (11), Unclassified (3) |
Allele ‘a’ represents the nucleotide of the reference sequence. The nomenclature of the sequence variants follows current recommendations of the Human Genome Variation Society and was described by den Dunnen et al. [39]. The “A” of the ATG-translation initiation codon is referred as nucleotide +1. The last column shows the ethnic backgrounds of the probands. Black represents African or African-Caribbean, Asian stands for Indian or Pakistani, white for white British and white ‘others’ as self reported categories by the study participants.