Table 5.
Cathepsin L polymorphisms.
|
CTSL (Cathepsin L) |
MAF (%) in populations with different ancestry |
Potential functional effect |
||||||
|---|---|---|---|---|---|---|---|---|
| Variant ID | Minor allele | AMER (MXL) | AFR (YRI) | EUR (GBR) | EAS (CHB) | Amino acid position and change | Y | N |
| Coding sequence | ||||||||
| rs11541204G/A | A | 0 | 0 | 5.0 | 0 | Gln134Gln | X | |
| Promoter and 5′ near the gene | ||||||||
| rs78985072G/A | A | 4.7* | 0 | 0 | 15.5± | X | ||
| rs142421833C/T | T | 4.7* | 0 | 0 | 15.5± | X | ||
| rs3128509G/A | A | 45.3 | 13.0 | 41.8 | 3.4 | Both alleles can create binding sites for BRCA, GATA4, MYB, and RFX | ||
| rs111786311T/G | G | 1.6 | 16.2 | 2.8‡ | 0 | X | ||
| rs11389221C/CAAA (INDEL) | CAAA | 43.8 | 15.3 | 51.7 | 76.7 | X | ||
| rs56952354A/T | T | 2.3 | 4.6 | 0 | 0 | Both alleles can create binding sites for GATA, GFI1, and TEL2 | ||
| rs75567776G/C | C | 2.3 | 7.9 | 0 | 0 | X | ||
| rs3118869C/A | A | 39.8 | 46.8 | 47.3 | 32.5 | The C allele creates binding sites for SREBP, AHR, and AHRHIF | ||
| rs41307457C/A | A | 3.1 | 23.6 | 2.8‡ | 0 | Both alleles can create binding sites for BRCA, DBP, LRF, MYB, and STAT4 | ||
| 5′ UTR | ||||||||
| rs41312184C/T | T | 1.6 | 0.5 | 11.0 | 0 | Both alleles can create binding sites for STAT, and RFX. The C allele can create a binding site for SF2ASF1 | ||
| 3′ near the gene | ||||||||
| rs59063901G/A | A | 0.8 | 3.7 | 2.8‡ | 0 | Both alleles can create binding sites for STAT, SPZ1, and GABP | ||
*, ‡, ± Variants in high LD or are tagSNPs between them in an American, European, and Asian population, respectively.
MAF; Minor allele frequency, AMER; American, AFR; Africans, EUR; Europeans, EAS; East Asia, MXL; Mexicans from Los Angeles, YRI; Yoruba in Ibadan, Nigeria, CHB; Han Chinese in Beijing, China, GBR; British in England and Scotland, Y; Yes, N; No, INDEL; Insertion/Deletion, UTR; untranslated region, LD; Linkage disequilibrium. CCDS; consensus coding sequence.
CTSL is located on chromosome 9q21.33. Six transcripts have been reported for CTSL, three produce CCDS, and two of them synthesize the 333 amino acid protein. The first transcript consists of 8 exons and 7 introns, 7 exons encode this protein, transcript length; 1436 bps. The second transcript consists of 8 exons and 7 introns, 7 exons encode this protein, transcript length; 1654 pb.