Table 4.
Variants corresponding to genes intersecting with the list of 2,383 high-risk HL genes from a study by Rotunno et al. (2016).
| HL variants from Rotunno et al. (2016) | Variant in matched gene from present study | |||||||
|---|---|---|---|---|---|---|---|---|
| Gene symbol | Variant position | IDS | HL family | Variant position | CADD_PHRED score | Variant type | Variant consequence | Protein effect |
| ABHD16A | 6_31670740_A_T | 3 | 6_31671105_G_A | 13.23 | SNVs | UTR5 | – | |
| C6orf62 | 6_24719009_T_C | rs147402940 | 3 | 6_24705773_T_C | 12.31 | SNVs | UTR3 | – |
| CEP120 | 5_122758609_G_T | rs141808885 | 1 | 5_122681069_C_T | 12.31 | SNVs | UTR3 | – |
| EDEM1 | 3_5257909_A_G | rs139745426 | 3 | 3_5246773_C_T | 34 | SNVs | Non-synonymous SNV | p.T160M |
| EIF4G3 | 1_21494519_T_C | 3 | 1_21267855_C_T | 14.54 | SNVs | stopgain SNV | p.W7X | |
| EPB41L2 | 6_131202023_A_G | 3 | 6_131191103_G_A | 22.1 | SNVs | Non-synonymous SNV | p.S736F | |
| EXTL3 | 8_28609630_G_A | rs191528081 | 3 | 8_28575243_G_A | 23 | SNVs | Non-synonymous SNV | p.R172H |
| FAM35A | 10_88917757_A_G | rs371636091 | 1 | 10_88911115_AGT_A | 25.8 | Indel | Frameshift deletion | p.2_2del |
| FUK | 16_70507153_G_A | 1 | 16_70501193_C_T | 10.08 | SNVs | UTR3 | - | |
| HLTF | 3_148757909_A_G | rs61750365 | 1 | 3_148802664_C_T | 37 | SNVs | stopgain SNV | p.W11X |
| LPP | 3_188464149_C_T | 3 | 3_188608373_A_T | 10.5 | SNVs | UTR3 | – | |
| LPP | 3_188464149_C_T | 3 | 3_188123978_G_T | 40 | SNVs | stopgain SNV | p.E24X | |
| LPP | 3 | 3_188123979_A_T | 32 | SNVs | Non-synonymous SNV | p.E24V | ||
| LRP6 | 12_12419973_G_T | 3 | 12_12272924_AATATATATATATATATATATATATATATATATATATAT_A | 12.55 | Indel | UTR3 | – | |
| LTBP2 | 14_74983553_G_A | rs145851939 | 3 | 14_74970734_C_T | 27.7 | SNVs | Non-synonymous SNV | p.G1493R |
| MAPKAP1 | 9_128199718_AT_ | 3 | 9_128199770_TAA_T | 14.3 | Indel | UTR3 | – | |
| MARCH10 | 17_60827878_G_A | rs112201730 | 3 | 17_60885673_G_A | 12.03 | SNVs | UTR5 | – |
| MYO18A | 17_27448659_C_T | rs371862120 | 3 | 17_27441099_G_A | 24.3 | SNVs | Non-synonymous SNV | p.A843V |
| NCAM1 | 11_113113556_A_G | 1 | 11_113134920_C_A | 11.07 | SNVs | UTR3 | – | |
| NIPBL | 5_36876673_G_A | 1 | 5_36962227_G_A | 27.5 | SNVs | Non-synonymous SNV | p.R154Q | |
| PHC2 | 1_33820711_G_A | 3 | 1_33896663_C_A | 15.12 | SNVs | upstream | – | |
| RCN1 | 11_32126524_C_T | 3 | 11_32112681_C_T | 10.66 | SNVs | UTR5 | – | |
| SBF2 | 11_9985135_TAAT_ | 3 | 11_9838541_C_T | 33 | SNVs | Non-synonymous SNV | p.R1275H | |
| SLMAP | 3_57914019_A_C | rs191613999 | 1 | 3_57742023_C_G | 13.51 | SNVs | UTR5 | – |
| SZT2 | 1_43885320_C_T | 3 | 1_43891311_G_A | 31 | SNVs | Non-synonymous SNV | p.A96T | |
Variant details from both databases the present study and the study by Rotunno et al. (2016) are shown.