Table 2.
PALB2 missense variants predicted to affect protein function by Align-GVGD and Polyphen2 identified in 1,240 probands participating in the clinic-based resource of the BCFR
| Nucleotide changea | Protein change | rs numberb | LOVDc | PolyPhen2d | Align-GVGD | Frequency (n = 1,240) | % |
|---|---|---|---|---|---|---|---|
| PALB2:c.53A>G | p.K18R | rs138789658 | Yes | D, 1.000 | C0 | 11 | 0.89 |
| PALB2:c.2087C>T | p.T696M | – | No | P, 0.954 | C0 | 1 | 0.08 |
| PALB2:c.2674G>A | p.E892K | rs45476495 | Yes | D, 1.000 | C0 | 3 | 0.24 |
| PALB2:c.2816T>G | p.L939W | rs45478192 | Yes | D, 1.000 | C55 | 7 | 0.56 |
| PALB2:c.2897T>C | p.I966T | – | No | D, 1.000 | C0 | 1 | 0.08 |
| PALB2:c.3054G>C | p.E1018D | rs183489969 | Yes | D, 0.998 | C0 | 1 | 0.08 |
| PALB2:c.3061G>A | p.G1021R | rs143808171 | Yes | D, 1.000 | C65 | 1 | 0.08 |
| PALB2:c.3278T>C | p.I1093T | rs45616636 | Yes | D, 0.999 | C25 | 1 | 0.08 |
| PALB2:c.3356T>C | p.L1119P | – | Yes | D, 1.000 | C65 | 1 | 0.08 |
| PALB2:c.3513G>C | p.L1171F | – | No | D, 1.000 | C0 | 1 | 0.08 |
a
Number based on transcript sequence LRG_308; NM_024675.3, +1 as A of ATG start codon
b
rs number from dbSNP v.137
c
Present (yes) or absent (no) from the LOVD v.2.0 Build 36, PALB2 version 140217 [29]
d
PolyPhen2 prediction (D probably damaging, P possibly damaging), PolyPhen2 score [23]