Table 1.
All private CTSK variants following Human Genome Variation Society (HGVS) nomenclature
| Chromosome: position | Ref/alt | Allele counts | Allele frequencies | No. of alleles | No. of hetero | No. of homo | Sequence ontology | Effect | HGVS c (cDNA) | HGVS p (protein) | Exon | Distance of transcript (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| C1:105944311 | C/T | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.894-49G>A | 8 | ||
| C1:105945321 | C/T | 43 | 0.5375 | 80 | 19 | 12 | Intron_variant | Other | ENSFCAT00000003643:c.893+73G>A | 7 | ||
| C1:105945347 | G/A | 2 | 0.025 | 80 | 2 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.893+47C>T | 7 | ||
| C1:105945453 | T/C | 1 | 0.0125 | 80 | 1 | 0 | Synonymous_variant | Other | ENSFCAT00000003643:c.834A>G | p.Ala278= | 7 | 83.8872 |
| C1:105945516 | C/T | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.788-17G>A | 7 | ||
| C1:105945532 | G/– | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.788-33delC | 7 | ||
| C1:105945562 | C/T | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.788-63G>A | 7 | ||
| C1:105945563 | A/G | 1 | 0.0125 | 80 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.788-64T>C | 7 | |||
| C1:105945702 | G/A | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.787+61C>T | 6 | ||
| C1:105945725 | G/A | 25 | 0.3125 | 80 | 15 | 5 | Intron_variant | Other | ENSFCAT00000003643:c.787+38C>T | 6 | ||
| C1:105945734 | C/G | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.787+29G>C | 6 | ||
| C1:105945746 | A/C | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.787+17T>G | 6 | ||
| C1:105945826 | G/A | 2 | 0.025 | 80 | 0 | 1 | Stop_gained | LoF | ENSFCAT00000003643:c.724C>T | p.Arg242Ter | 6 | 72.8097 |
| C1:105945848 | T/– | 80 | 1 | 80 | 0 | 40 | Splice_acceptor_variant | LoF | ENSFCAT00000003643:c.702+1delA | 5 | ||
| C1:105945876 | A/G | 1 | 0.0125 | 80 | 1 | 0 | Synonymous_variant | Other | ENSFCAT00000003643:c.675T>C | p.Tyr225= | 5 | 67.8751 |
| C1:105949867 | G/C | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.621+38C>G | 4 | ||
| C1:105949894 | G/A | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.621+11C>T | 4 | ||
| C1:105950155 | G/A | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.403-32C>T | 4 | ||
| C1:105951023 | A/G | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.402+90T>C | 3 | ||
| C1:105951040 | T/C | 28 | 0.35 | 80 | 18 | 5 | Intron_variant | Other | ENSFCAT00000003643:c.402+73A>G | 3 | ||
| C1:105951045 | G/A | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.402+68C>T | 3 | ||
| C1:105951061 | A/C | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.402+52T>G | 3 | ||
| C1:105951157 | T/C | 1 | 0.0125 | 80 | 1 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.358A>G | p.Ile120Val | 3 | 35.9517 |
| C1:105951484 | G/T | 2 | 0.025 | 80 | 2 | 0 | Splice_region_variant | Other | ENSFCAT00000003643:c.124-8C>A | 2 | ||
| C1:105951516 | –/TACA | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.124-43_124-40dupTGTA | 2 | ||
| C1:105951529 | A/– | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.124-53delT | 2 | ||
| C1:105951875 | G/A | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.123+71C>T | 1 | ||
| C1:105951898 | C/G | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.123+48G>C | 1 | ||
| C1:105951908 | G/A | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.123+38C>T | 1 | ||
| C1:105951921 | C/T | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.123+25G>A | 1 | ||
| C1:105951923 | –/CTT | 1 | 0.0125 | 80 | 1 | 0 | Intron_variant | Other | ENSFCAT00000003643:c.123+21_123+23dupAAG | 1 | ||
| C1:105951951 | T/C | 1 | 0.0125 | 80 | 1 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.118A>G | p.Asn40Asp | 1 | 11.7825 |
| C1:105951964 | C/T | 1 | 0.0125 | 80 | 1 | 0 | Synonymous_variant | Other | ENSFCAT00000003643:c.105G>A | p.Gly35= | 1 | 10.4733 |
| C1:105951982 | T/A | 1 | 0.0125 | 80 | 1 | 0 | Synonymous_variant | Other | ENSFCAT00000003643:c.87A>T | p.Leu29= | 1 | 8.66062 |
| C1:105952007 | A/G | 1 | 0.0125 | 80 | 1 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.62T>C | p.Val21Ala | 1 | 6.143 |
| C1:105952050 | G/T | 1 | 0.0125 | 80 | 1 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.19C>A | p.Leu7Ile | 1 | 1.81269 |
| C1:105945848 | T/– | 388 | 1 | 388 | 0 | 194 | Splice_acceptor_variant | LoF | ENSFCAT00000003643:c.702+1delA | 5 | ||
| C1:105952056 | T/G | 2 | 0.00518135 | 386 | 0 | 1 | Missense_variant | Missense | ENSFCAT00000003643:c.13A>C | p.Lys5Gln | 1 | 1.20846 |
| C1:105951157 | T/C | 1 | 0.00259067 | 386 | 1 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.358A>G | p.Ile120Val | 3 | 35.9517 |
| C1:105951210 | C/T | 1 | 0.0025641 | 390 | 1 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.305G>A | p.Arg102His | 3 | 30.6143 |
| C1:105951951 | T/C | 1 | 0.00257732 | 388 | 1 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.118A>G | p.Asn40Asp | 1 | 11.7825 |
| C1:105952050 | G/T | 1 | 0.00259067 | 386 | 1 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.19C>A | p.Leu7Ile | 1 | 1.81269 |
| C1:105952007 | A/G | 2 | 0.00515464 | 388 | 2 | 0 | Missense_variant | Missense | ENSFCAT00000003643:c.62T>C | p.Val21Ala | 1 | 6.143 |
| C1:105951484 | G/T | 9 | 0.0230769 | 390 | 5 | 2 | Splice_region_variant | Other | ENSFCAT00000003643:c.124-8C>A | 2 |
Ref = reference (the allele in the reference genome); alt = alternative (any other allele found at that locus); hetero = heterozygous; homo = homozygous; LoF = loss of function