Table 1 Clinical features and genetic variants confirmed in index cases and available affected relatives.
Index number /FIPA type | Sex (F/M)/ Age (yrs) | Adenoma type/ size (mm) | Gene | Chr Position GRCh37 - hg19 | Variant | Consequence | Pathogenicity | In Silico Tools | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
GERP++ | DANN | SIFT | LIST-S2 | ALPHA MISSENSE | ||||||||
1/ HO | F/23 | PRL-secreting/9 | NR5A1 (SF1) | Chr9:127262707 C > T | NM_004959.5:c.532 G > A | p.(Gly178Arg) | ACMG: VUS ClinVar: Not reported | 4.84 | D (0.9989) | T (0.56) | T (0.8883) | A (0.378) |
PKD1 | Chr16:2150248 C > T | NM_001009944.3:c.9631 G > A | p.(Ala3211Thr) | ACMG: VUS ClinVar: VUS | 4.69 | T (0.7633) | T (0.56) | T (0.3465) | LB (0.057) | |||
2/HO | M/22 | GH-secreting/15 | TINF2 | Chr14:24710039 T > TC | NM_001099274.3: c.646dup | p.(Glu216GlyfsTer61) | ACMG: Pathogenic ClinVar: Not reported | NA | NA | NA | NA | NA |
ATP2B3 | ChrX:152830460 G > C | NM_001001344.3:c.3241 G > C | p.(Glu1081Gln) | ACMG: VUS ClinVar: Not reported | 4.63 | D (0.9977) | T (0.07) | D (0.9383) | LB (0.114) | |||
3/HO | M/33 | GH-secreting/14 | RUNX2 | Chr6:45630999 C > T | NM_001024630.4:c.1169 C > T | p.(Pro390Leu) | ACMG: VUS ClinVar: Not reported | 5.31 | D (0.9950) | T (0.14) | T (0.4790) | LP (0.626) |
4/HO | M/59 | PRL-secreting/22 | LGALS3 | Chr14:55604881 C > G | NM_002306.3 :c.137 C > G | p.(Pro46Arg) | ACMG: VUS ClinVar: Not reported | 5.34 | T (0.9829) | D (0) | D (0.8980) | A (0.5) |
DRD4 | Chr11:640307 G > A | NM_000797.4: c.1057 + 1 G > A | splice donor | ACMG: VUS ClinVar: Not reported | NA | NA | NA | NA | NA | |||
5/HO | F/27 | PRL-secreting/6 | SYTL3 | Chr6:159129392 G > T | NM_001242395.1:c.485 G > T | p.(Ser162Ile) | ACMG: LB ClinVar: Not reported | 4.59 | T (0.9879) | D (0.16) | NA | LB (0.152) |
6/HO | F/43 | GH-secreting/14 | SQSTM1 | Chr5:179260612 CAGG > C | NM_003900.4:c.1001_1003del | p.(Gly334del) | ACMG: VUS ClinVar: VUS | NA | NA | NA | NA | NA |
AIP | Chr11:67258381 C > T | NM_003977.2:c.910 C > T | p.(Arg304Ter) | ACGM: VUS ClinVar: Pathogenic | 5.39 | D (0.9964) | NA | NA | NA | |||
7/HO | M/32 | GH-secreting/60 | ATP2B3 | ChrX:152818590 G > A | NM_001001344.2:c.1921 G > A | p.(Asp641Asn) | ACMG: VUS ClinVar: Not reported | 5.44 | D (0.9986) | T (0.23) | D (0.9018) | LB (0.102) |
TSC1 | Chr9:135781415 C > T | NM_001162427.1: c.1550 G > A | p.(Arg517Gln) | ACGM: VUS ClinVar: LB | 6.05 | D (0.991) | T (0.23) | NA | LB (0.084) | |||
SSTR4 | Chr20:23017082 T > C | NM_001052.2:c.962 T > C | p.(Phe321Ser) | ACMG: VUS ClinVar: Not reported | 3.65 | T (0.7532) | T (1) | T (0.5168) | LB (0.099) | |||
FGFR2 | Chr10:123260394 T > G | NM_022970.3:c.1510 A > C | p.(Ile504Leu) | ACGM : VUS ClinVar: Not reported | 5.76 | T (0.9756) | T (0.36) | T ( 0.6349) | LB (0.105) | |||
8/HO | F/38 | GH-secreting/18 | BRAF | Chr7:140434597 G > GA | NM 004333.4:c.2128-28dup | Intronic | ACGM: VUS ClinVar: VUS | NA | NA | NA | NA | NA |
9/HO | M/51 | PRL-secreting/15 | RUNX2 | Chr6:45390433 G > GCAGCAGCAGCAA | NM_001024630.4:c.174_185dup | p.(Gln68_Gln71dup) | ACGM: VUS ClinVar: Conflicting classifications of pathogenicity | NA | NA | NA | NA | NA |
10/HO | M/32 | GH-secreting/7 | APC | Chr5:112173317 A > G | NM_000038.5:c.2026 A > G | p.(Ile676Val) | ACGM : VUS ClinVar: VUS | 5.99 | D (0.9966) | T (0) | NA | LB (0.232) |
11/HE | F/47 | GH-secreting/12 | RARB | Chr3:25215908 C > T | NM_001290216.3:c.20 C > T | p.(Ala7Val) | ACMG : VUS ClinVar: Not reported | 5.88 | D (0.9972) | D (0.03) | T (0.5300) | LB (0.075) |
SYTL3 | Chr6:159086521 G > A | NM_001242395.2:c.205 G > A | p.(Val69Met) | ACGM: LB ClinVar: Not reported | 5.8 | T (0.9575) | T (0.05) | NA | LB (0.102) | |||
12/HE | M/37 | GH-secreting/23 | AIP | Chr11:67257786 G > C | NM_003977.2:c.646-1 G > C | Splice acceptor site (intron 4–5) | ACMG: Pathogenic ClinVar: Not reported | NA | NA | NA | NA | NA |
LGALS3 | Chr14:55611955 T > C | NM_002306.3:c.719 T > C | p.(Ile240Thr) | ACMG : VUS ClinVar: Not reported | 5.77 | D (0.9971) | D (0) | D (0.8707) | LP (0.658) | |||
SUFU | Chr10:104356982 C > T | NM_016169.3:c.842 C > T | p.(Pro281Leu) | ACGM : VUS ClinVar: VUS | 6.03 | D (0.9952) | D (0.3) | D (0.9881) | LB (0.14) | |||
13/HE | M/27 | GH-secreting/40 | AIP | Chr11:67254618 C > T | NM_003977.2:c.241 C > T | p.(Arg81Ter) | ACMG: Pathogenic ClinVar: Pathogenic | 5.22 | D (0.9978) | NA | NA | NA |
14/HE | M/30 | PRL-secreting/29 | SDHB | Chr1:17354257 T > C | NM_003000.2:c.527 A > G | p.(Glu176Gly) | ACGM : VUS ClinVar: VUS | 5.76 | D (0.9978) | D (0) | D (0.9671) | A (0.388) |
15/HE | F/42 | ACTH-secreting/12 | RARB | Chr3:25216009 C > A | NM_001290216.3:c.121 C > A | p.(Leu41Ile) | ACMG : VUS ClinVar: Not reported | 5.88 | D (0.9935) | T (0.04) | T (0.3260) | LB (0.071) |
16/HE | M/60 | PRL-secreting/45 | DRD3 | Chr3:113890746 A > G | NM_000796.3:c.94 T > C | p.(Tyr32His) | ACGM : VUS ClinVar: Not reported | 5 | D (0.9982) | D (0) | D (0.8829) | LB (0.203) |
17/HE | F/22 | PRL-secreting/12 | NF1 | Chr17:29562948 A > G | NM_000267.3:c.3883 A > G | p.(Thr1295Ala) | ACGM: VUS ClinVar: Conflicting classifications of pathogenicity | 5.94 | T (0.9850) | T (0.43) | T (0.7980) | LB (0.055) |
18/HE | F/19 | PRL-secreting/18 | NPR2 | Chr9:35800044 A > G | NM_003995.3:c.1013 A > G | p.(Tyr338Cys) | ACGM: VUS ClinVar: VUS | 5.69 | D (0.9984) | D (0) | D (0.9622) | LP (0.656) |
19/HE | M/36 | ACTH-secreting/6 | PTTG1 | Chr5:159851328 A > G | NM_004219.2:c.361 A > G | p.(Asn121Asp) | ACGM : VUS ClinVar: Not reported | 5.17 | T (0.9866) | T (0.73) | NA | LB (0.106) |
20/HE | F/46 | ACTH-secreting/5 | CDH23 | Chr10:73570263 C > T | NM_001171934.1:c.2294 C > T | p.(Ala765Val) | ACGM : VUS ClinVar: VUS | 5.67 | D (0.9973) | (0.02) | D (0.9498) | A (0.516) |
KCNQ1 | Chr11:2683253 G > A | NM_181798.1:c.1456 G > A | p.(Ala486Thr) | ACGM: VUS ClinVar: VUS | 4.59 | T (0.9082) | T (0.19) | T (0.8037) | LB (0.078) | |||
