Table 2.
Clonal Sequence Variants Detected by Exome Sequencing and Their Predicted Effects on Protein Products
| Chr | Pos | Ref | Alta | Gene | clone Ab | clone B | clone C | clone W | clone Y |
| 1 | 21014224 | G | T | KIF17 | S432Y | ||||
| 1 | 90178297 | G | A | LRRC8C | P56P | ||||
| 1 | 149921554 | C | T | OTUD7B | Q367Q | ||||
| 2 | 109347284 | T | C | RANBP2 | F39F | ||||
| 2 | 113820048 | C | A | IL36RN | L88I | ||||
| 2 | 173330424 | C | T | ITGA6 | intronic | ||||
| 3 | 132319348 | T | C | CCRL1 | V36A | ||||
| 3 | 193002674 | G | T | ATP13A5 | intronic | intronic | intronic | ||
| 4 | 113568377 | GAAGA | G | LARP7 | frameshiftc | ||||
| 6 | 152652970 | C | A | SYNE1 | A4284S | ||||
| 7 | 2260574 | C | T | MAD1L1 | G47D | ||||
| 7 | 22179660 | G | C | RAPGEF5 | L601V | ||||
| 8 | 15508246 | C | T | TUSC3 | R117C | ||||
| 9 | 33354142 | G | A | NFX1 | E130K | ||||
| 10 | 75541848 | C | T | CHCHD1 | S5S | ||||
| 11 | 124095534 | G | A | OR8G2 | G46E | ||||
| 12 | 80752469 | G | T | OTOGL | C2026F | ||||
| 12 | 101750754 | G | T | UTP20 | R1862I | R1862I | R1862I | ||
| 12 | 105445861 | G | T | ALDH1L2 | intronic | ||||
| 14 | 21967435 | C | A | METTL3 | intronic | ||||
| 15 | 43827249 | G | T | PPIP5K1 | P1071T | ||||
| 15 | 48805891 | C | A | FBN1 | intronic | ||||
| 15 | 90631649 | C | A | IDH2 | W155L | ||||
| 16 | 20043135 | C | A | GPR139 | S328S | ||||
| 17 | 11998899 | G | A | MAP24K4 | R145Q | R145Q | R145Q | ||
| 17 | 48817653 | AT | A | LUC7L3 | intronicd | ||||
| 17 | 73567174 | G | T | LLGL2 | L712L | ||||
| 17 | 79226178 | C | A | SLC38A10 | A588S | ||||
| 18 | 30992086 | G | T | C18orf34 | intronic | ||||
| 19 | 9028296 | G | T | MUC16 | L12166M | ||||
| 19 | 56552245 | G | T | NLRP5 | intronic | intronic | intronic | ||
| 20 | 60498685 | G | T | CDH44 | E425D | ||||
| 22 | 37325592 | C | A | CSF2RB | D100E | D100E | D100E | ||
| 22 | 39078278 | A | T | TOMM22 | intronic | ||||
| X | 32328257 | G | T | DMD | A1897D | ||||
| X | 48558634 | C | T | SUV39H1 | T106T | ||||
| X | 135956509 | C | A | RBMX | S323I |
a
Alternate allele compared to reference allele in parental HUES 1 cell line (clone X), confirmed by Sanger sequencing
b
Clones A, B, and C are SORT1−/− clones in HUES 1; clone W is a wild-type (SORT1+/+) clone in HUES 1 that was exposed to SORT1 TALENs, from the same pool as clones A–C; clone Y is a wild-type (SORT1+/+) clone that was exposed to a different set of TALENs (targeting CELSR2)
c
The surrounding sequence is: CAGAA GAGAA GAAAA AGAAA AAGAA GAAGA AAGGC CGAAT GAAAA AGGAA GACAA
d
The surrounding sequence is: ATAAT CACAG ATAAT TTATA CAATT ATATT TTTTC CCCCA GGTCC GTGTG AAAAA