Table 4. Damaging mutations identified in five Egyptian familial breast cancer families*.
| Gene | Affected | Member | Chr. | Position | Ref. | Variant | Genotype | Var type | Coding change | dbSNP144 | Damage | Frequency | ClinVar | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SIFT | PolyPhen2 | All | African | Egypt | |||||||||||||||
| Family 1 | No. | 1 | 2 | 3 | 4 | ||||||||||||||
| Status | A. | A. | U. | U. | |||||||||||||||
| ABCA10 | 2 | + | + | - | + | 17 | 67145196 | AG | - | Het. | Frameshift deletion | c.4510_4511del:p.L1504fs | - | - | - | - | - | - | - |
| CHST15 | 2 | + | + | - | - | 10 | 125780753 | GG | - | Hom. | Frameshift deletion | c.1365_1366del:p.P455fs | rs746518074 | - | - | - | - | - | - |
| GRIP1 | 2 | + | + | + | + | 12 | 66935707 | C | T | Het. | Nonsynonymous SNV | c.G160A:p.V54I | rs199768740 | - | D | 0.0004 | - | - | - |
| LOC100129697 | 2 | + | + | - | - | 16 | 89016677 | G | C | Het. | Nonsynonymous SNV | c.G151C:p.V51L | rs71395347 | D | - | - | - | - | - |
| LOC100129697 | 2 | + | + | - | - | 16 | 89017569 | G | C | Het. | Nonsynonymous SNV | c.G1043C:p.G348A | rs34847212 | D | - | - | - | - | - |
| LOC100129697 | 2 | + | + | + | - | 16 | 89017602 | C | T | Het. | Nonsynonymous SNV | c.C1076T:p.P359L | rs188085712 | D | - | - | - | - | - |
| LOC388813 | 2 | + | + | + | - | 21 | 15974379 | A | C | Het. | Nonsynonymous SNV | c.T280G:p.Y94D | rs370454293 | D | - | 0.0020 | 0.0008 | - | - |
| NBPF10 | 2 | + | + | + | - | 1 | 145296478 | G | T | Het. | Nonsynonymous SNV | c.G400T:p.D134Y | rs6663523 | D | - | - | - | - | - |
| PABPC3 | 2 | + | + | - | - | 13 | 25671271 | AAGC | GAT | Het. | Frameshift substitution | c.935_938GAT | - | - | - | - | - | - | - |
| Family 2 | No. | 1 | 2 | 3 | |||||||||||||||
| Status | A. | A. | U. | ||||||||||||||||
| C16orf62 | 2 | + | + | - | 16 | 19566981 | C | G | Het. | Nonsynonymous SNV | c.C197G:p.A66G | rs564734737 | D | - | 0.0002 | - | - | - | |
| KRTAP21-3 | 2 | + | + | - | 21 | 32090989 | C | T | Het. | Nonsynonymous SNV | c.G89A:p.C30Y | rs760518532 | D | - | - | - | - | - | |
| LOC100129697 | 2 | + | + | - | 16 | 89016677 | G | C | Het. | Nonsynonymous SNV | c.G151C:p.V51L | rs71395347 | D | - | - | - | - | - | |
| LOC100129697 | 2 | + | + | - | 16 | 89017569 | G | C | Het. | Nonsynonymous SNV | c.G1043C:p.G348A | rs34847212 | D | - | - | - | - | - | |
| NBPF10 | 2 | + | + | + | 1 | 145296478 | G | T | Het. | Nonsynonymous SNV | c.G400T:p.D134Y | rs6663523 | D | - | - | - | - | - | |
| NPIPB11 | 2 | + | + | + | 16 | 29394758 | G | T | Hom. | Nonsynonymous SNV | c.C1495A:p.P499T | - | D | - | - | - | - | - | |
| PABPC3 | 2 | + | + | - | 13 | 25671271 | AAGC | GAT | Het. | Frameshift substitution | c.935_938GAT | - | - | - | - | - | - | - | |
| PDE4DIP | 2 | + | + | + | 1 | 144852379 | G | T | Het. | Nonsynonymous SNV | c.C7064A:p.P2355H | - | D | - | - | - | - | - | |
| Family 3 | No. | 1 | 2 | 3 | |||||||||||||||
| Status | A. | U. | U. | ||||||||||||||||
| CCDC7 | 2 | + | + | + | 10 | 33136820 | AA | - | Het. | Frameshift deletion | c.1477_1478del:p.K493fs | - | - | - | - | - | - | - | |
| CFAP46 | 2 | + | + | + | 10 | 134736204 | G | A | Het. | Nonsynonymous SNV | c.C1265T:p.T422M | rs140185143 | D | - | 0.0022 | - | - | - | |
| CXorf23 | 2 | + | - | + | X | 19984574 | G | T | Het. | Nonsynonymous SNV | c.C235A:p.P79T | rs143234295 | - | D | 0.0082 | 0.0299 | - | - | |
| LOC100129697 | 2 | + | + | + | 16 | 89017334 | C | T | Het. | Nonsynonymous SNV | c.C808T:p.R270W | rs28617399 | D | - | - | - | - | - | |
| NBPF10 | 2 | + | + | + | 1 | 145296478 | G | T | Het. | Nonsynonymous SNV | c.G400T:p.D134Y | rs6663523 | D | - | - | - | - | - | |
| NPIPB11 | 2 | + | + | + | 16 | 29394758 | G | T | Hom. | Nonsynonymous SNV | c.C1495A:p.P499T | - | D | - | - | - | - | - | |
| PABPC3 | 2 | + | + | + | 13 | 25671271 | AAGC | GAT | Het. | Frameshift substitution | c.935_938GAT | - | - | - | - | - | - | - | |
| SMIM13 | 2 | + | + | + | 6 | 11134683 | C | T | Het. | Nonsynonymous SNV | c.C124T:p.R42W | - | - | D | - | - | - | - | |
| Family 4 | No. | 1 | 2 | 3 | |||||||||||||||
| Status | A. | A. | U. | ||||||||||||||||
| C16orf62 | 2 | + | + | - | 16 | 19566981 | C | G | Het. | Nonsynonymous SNV | c.C197G:p.A66G | rs564734737 | D | - | 0.0002 | - | - | - | |
| GAGE2A | 2 | + | + | + | X | 49237474 | A | T | Het. | Nonsynonymous SNV | c.A179T:p.D60V | rs782582454 | D | - | - | - | - | - | |
| NPIPB11 | 2 | + | + | + | 16 | 29394758 | G | T | Hom. | Nonsynonymous SNV | c.C1495A:p.P499T | - | D | - | - | - | - | - | |
| PHIP | 2 | + | + | + | 6 | 79671522 | C | A | Het. | Nonsynonymous SNV | c.G3541T:p.A1181S | rs147526156 | - | D | 0.0002 | - | - | - | |
| SLC15A5 | 2 | + | + | - | 12 | 16430451 | A | T | Het. | Nonsynonymous SNV | c.T169A:p.F57I | rs79942763 | D | - | 0.0066 | 0.0227 | - | - | |
| ZNF750 | 2 | + | + | - | 17 | 80789339 | T | C | Het. | Nonsynonymous SNV | c.A992G:p.Y331C | - | - | D | - | - | - | - | |
| Family 5 | No. | 1 | 2 | 3 | 4 | ||||||||||||||
| Status | A. | U. | A. | U. | - | ||||||||||||||
| ATP10B | 2 | + | + | + | + | 5 | 160016684 | A | G | Het. | Nonsynonymous SNV | c.T3665C:p.I1222T | rs144497343 | - | D | 0.0094 | 0.0061 | - | - |
| NPIPB11 | 2 | + | + | + | + | 16 | 29394758 | G | T | Hom. | Nonsynonymous SNV | c.C1495A:p.P499T | - | D | - | - | - | - | - |
| PIGN | 2 | + | + | + | - | 18 | 59828420 | G | A | Het. | Nonsynonymous SNV | c.C167T:p.A56V | rs61755362 | - | D | 0.0044 | - | - | - |
| PRR14L | 2 | + | - | + | + | 22 | 32108801 | G | T | Het. | Nonsynonymous SNV | c.C5024A:p.A1675E | rs750572033 | - | D | - | - | - | - |
*A.: affected; U.: unaffected; Chr.: Chromosome; Ref.: Reference genome hg19; Het.: Heterozygote; Hom.: homozygote; D: Damaging variant