Table 2.
Gene | Chrom | Location | rsID | Ref | Var | AA/protein change | Allele freq# | CDKN2A carrier | History of smoking: yes/no/unk | Family/Patient ID |
---|---|---|---|---|---|---|---|---|---|---|
Loss of function [stopgain, frameshift] variants: | ||||||||||
ATM | chr11 | 108155142 | AG | E1313fs | 0 | no | no | M595 | ||
ATM | chr11 | 108183151 | rs587779852 | G | T | E1978* | 1.05E-04 | no | unk | AJ7379 |
BRCA2 | chr13 | 32914288 | rs80359537 | AT | H1932fs | 0 | no | yes | P153 | |
PALB2 | chr16 | 23646627 | rs180177100 | G | A | R414* | 0 | no | unk | AJ7379 |
Deleterious missense or inframe deletion variants classified by Meta LRP: | ||||||||||
MSH2 | chr2 | 47630331 | rs267607911 | A | G | M1V | 0 | yes | no^ | LUMC6_019 |
MSH2 | chr2 | 47637248 | rs145649774 | C | G | L128V | 0.000349 | yes | no | P147 |
MSH2 | chr2 | 47641430 | rs34136999,, | C | T | A272V | 0.000581 | no | no | P149 |
MSH6 | chr2 | 48026852 | rs376220212 | G | A | R577H | 0.000116 | yes | no | P176 |
PMS2 | chr7 | 6013076 | G | A | P848L | 0 | no | unk | P1 | |
PMS2 | chr7 | 6022617 | rs587780046 | G | A | T671M | 6.34E-04 | no | yes | P282 |
CFTR | chr7 | 117171037 | rs201958172 | G | A | A120T | 1.36E-04 | yes | no | M402 |
CFTR | chr7 | 117171152 | rs397508725 | G | C | S158T | 1.73E-05 | yes | no | P61 |
CFTR | chr7 | 117243784 | rs151048781 | G | C | M952I | 1.20E-04 | no | yes | P115 |
CFTR | chr7 | 117250625 | rs149279509 | A | G | Y1014C | 0.001 | yes | unk | K_1001, K_1002 |
ATM | chr11 | 108122581 | T | G | L542W | 0 | no | no | P268 | |
ATM | chr11 | 108196797 | rs567060474 | G | A | A2274T | 0.001 | no | yes | P115 |
FANCA | chr16 | 89858430 | CTT | E377del | 0 | no | yes | P282 | ||
TP53 | chr17 | 7576911 | rs145151284 | G | C | T312S | 8.99E-05 | no | no | P268 |
BRCA1 | chr17 | 41256266 | rs28897673 | T | C | Y105C | 0.000116 | yes | no, yes | LUMC19_013, LUMC19_016 |
Maximum allele frequency from public databases (see Supplemental Table 4 for details)
Extensive passive smoking exposure
Chrom, chromosome; Ref, referent allele; Var, variant allele; AA, amino acid; freq, frequency; unk, unknown