Validated somatic variants identified by WGS in WM patients
| Gene . | N . | Chr . | Position . | Reference . | Variant . | Zygosity . | Protein . | Notes . |
|---|---|---|---|---|---|---|---|---|
| ARID1A | 1 | 1 | 27057944 | C | — | hom | Y551Frameshift | Homozygous by aUPD |
| ARID1A | 1 | 1 | 27099946 | C | T | het | R1276Stop | |
| ARID1A | 1 | 1 | 27101665 | C | T | het | Q1650Stop | |
| ARID1A | 1 | 1 | 27106497 | C | T | het | Q2037Stop | Opposite copy loss |
| ARID1A | 1 | 1 | 27107136 | — | A | het | S2249Frameshift | |
| NOTCH2 | 1 | 1 | 120478125 | A | C | het | F1209V | |
| CXCR4 | 1 | 2 | 136872467 | GAAGACTCAG | AC | het | S344Frameshift | |
| CXCR4 | 1 | 2 | 136872481 | AGAT | — | het | S339Frameshift | |
| CXCR4 | 2 | 2 | 136872485 | G | C | het | S338STOP | WHIM associated rs104893626 |
| CXCR4 | 3 | 2 | 136872485 | G | T | het | S338STOP | WHIM associated rs104893626 |
| CXCR4 | 1 | 2 | 136872570 | — | T | het | T311Frameshift | |
| MAP2 | 1 | 2 | 210557805 | G | C | het | W304C | |
| MYD88 | 1 | 3 | 38182032 | C | G | het | S219C | |
| MYD88 | 27 | 3 | 38182640 | T | C | het | L265P | Homozygous by aUPD × 4 |
| MED23 | 1 | 6 | 131915434 | C | T | het | E1013K | |
| SYNE1 | 1 | 6 | 152708319 | C | T | hom | R2792H | Opposite copy loss |
| TRRAP | 1 | 7 | 98530988 | A | T | het | D1326V | |
| TRAF2 | 1 | 9 | 139815501 | G | — | hom | L324Frameshift | Homozygous by aUPD |
| RAG2 | 1 | 11 | 36615549 | A | G | hom | L57P | Opposite copy loss |
| MLL2 | 1 | 12 | 49425598 | A | G | het | S4297L | |
| MLL2 | 1 | 12 | 49448412 | C | — | het | G101Frameshift | |
| TRAF3 | 1 | 14 | 103371839 | — | T | het | L448Frameshift | Opposite copy loss |
| MYBBP1A | 1 | 17 | 4457136 | G | A | het | P177S | |
| MYBBP1A | 1 | 17 | 4457323 | C | T | het | R148Q | |
| TP53 | 1 | 17 | 7577114 | C | T | het | C275Y | |
| TP53 | 1 | 17 | 7577569 | A | C | hom | C238G | Homozygous by aUPD |
| CD79B | 1 | 17 | 62006799 | A | T | het | Y197N | |
| CD79B | 1 | 17 | 62007129 | C | G | het | Exon boundary | |
| MUC16 | 1 | 19 | 9014687 | G | T | het | A12763E |
| Gene . | N . | Chr . | Position . | Reference . | Variant . | Zygosity . | Protein . | Notes . |
|---|---|---|---|---|---|---|---|---|
| ARID1A | 1 | 1 | 27057944 | C | — | hom | Y551Frameshift | Homozygous by aUPD |
| ARID1A | 1 | 1 | 27099946 | C | T | het | R1276Stop | |
| ARID1A | 1 | 1 | 27101665 | C | T | het | Q1650Stop | |
| ARID1A | 1 | 1 | 27106497 | C | T | het | Q2037Stop | Opposite copy loss |
| ARID1A | 1 | 1 | 27107136 | — | A | het | S2249Frameshift | |
| NOTCH2 | 1 | 1 | 120478125 | A | C | het | F1209V | |
| CXCR4 | 1 | 2 | 136872467 | GAAGACTCAG | AC | het | S344Frameshift | |
| CXCR4 | 1 | 2 | 136872481 | AGAT | — | het | S339Frameshift | |
| CXCR4 | 2 | 2 | 136872485 | G | C | het | S338STOP | WHIM associated rs104893626 |
| CXCR4 | 3 | 2 | 136872485 | G | T | het | S338STOP | WHIM associated rs104893626 |
| CXCR4 | 1 | 2 | 136872570 | — | T | het | T311Frameshift | |
| MAP2 | 1 | 2 | 210557805 | G | C | het | W304C | |
| MYD88 | 1 | 3 | 38182032 | C | G | het | S219C | |
| MYD88 | 27 | 3 | 38182640 | T | C | het | L265P | Homozygous by aUPD × 4 |
| MED23 | 1 | 6 | 131915434 | C | T | het | E1013K | |
| SYNE1 | 1 | 6 | 152708319 | C | T | hom | R2792H | Opposite copy loss |
| TRRAP | 1 | 7 | 98530988 | A | T | het | D1326V | |
| TRAF2 | 1 | 9 | 139815501 | G | — | hom | L324Frameshift | Homozygous by aUPD |
| RAG2 | 1 | 11 | 36615549 | A | G | hom | L57P | Opposite copy loss |
| MLL2 | 1 | 12 | 49425598 | A | G | het | S4297L | |
| MLL2 | 1 | 12 | 49448412 | C | — | het | G101Frameshift | |
| TRAF3 | 1 | 14 | 103371839 | — | T | het | L448Frameshift | Opposite copy loss |
| MYBBP1A | 1 | 17 | 4457136 | G | A | het | P177S | |
| MYBBP1A | 1 | 17 | 4457323 | C | T | het | R148Q | |
| TP53 | 1 | 17 | 7577114 | C | T | het | C275Y | |
| TP53 | 1 | 17 | 7577569 | A | C | hom | C238G | Homozygous by aUPD |
| CD79B | 1 | 17 | 62006799 | A | T | het | Y197N | |
| CD79B | 1 | 17 | 62007129 | C | G | het | Exon boundary | |
| MUC16 | 1 | 19 | 9014687 | G | T | het | A12763E |
List of all variants validated by Sanger sequencing ordered by chromosome and position.
aUPD, acquired uniparental disomies; Chr, chromosome; WHIM, warts, hypogammaglobulinemia, infection, and myelokathexis.