Table 3.
Filtered variants of interest
| Gene | Chromosome | HGVS DNA reference | HGVS protein reference | Variant type | Predicted effect | dbSNP/dbVAR ID | LOH | Tumor tissue detection (VAF) |
|---|---|---|---|---|---|---|---|---|
| IGF2R | 6:160515930 GRCh37 |
c.3949dup | p.Asp1317GlyfsTer5 | Frameshift | LOF, dominant negative | Yes | Primary (NA) Left lung metastasis (0.00) Right lung metastasis (0.70) |
|
| PTPRD | 9:8341226 GRCh37 |
c.3772G>A | p.Ala1258Thr | Missense | Probably damaging | No | Primary (NA) Left lung metastasis (0.40) Right lung metastasis (0.38) |
|
| PTEN | 10:89717672 GRCh37 |
NM_000314.6 c.697C>T |
NP_000305.3 p.Arg233Ter |
Stop gain | LOF | rs121909219 | Yes | Primary (0.00) Left lung metastasis (0.48) Right lung metastasis (0.68) |
| MEN1 | 11:64572093 GRCh37 |
NM_130799.2 c.1561delC |
NP_000235.2 p.Arg521GlyfsTer43 |
Frameshift | LOF | rs794728642 | Yes | Primary (NA) Left lung metastasis (0.00) Right lung metastasis (0.26) |
| RB1 | 13:48941648 GRCh37 |
NM_000321.2 c.958C>T |
NP_000312.2 p.Arg320Ter |
Stop gain | LOF, LOH | rs121913300 | Yes | Primary (0.91) Left lung metastasis (0.63) Right lung metastasis (0.70) |
| TP53 | 17:7577548 GRCh37 |
NM_000546.5 c.733G>A |
NP_000537.3 p.Gly245Ser |
Missense | LOF, LOH | rs28934575 | Yes | Primary (0.90) Left lung metastasis (0.58) Right lung metastasis (0.74) |
| MSH2 | 2:47672676 GRCh37 |
c.1277-9_1292del | Splice critical | LOF, LOH | Yes | Primary (0.95) Left lung metastasis (0.46) Right lung metastasis (0.63) |
||
| MLH1 | 3:37058999 GRCh37 |
NM_000249.3 c.793C>T |
NP_000240.1 p.Arg265Cys |
Missense | LOF | rs63751194 | Yes | Primary (0.03) Left lung metastasis (0.00) Right lung metastasis (0.00) |
(LOF) Loss of function, (LOH) loss of heterozygosity, (NA) not applicable, (VAF) variant allele frequency.