| Literature DB >> 35402282 |
Hikmat Abdel-Razeq1,2, Faris Tamimi1, Lama Abujamous3, Rashid Abdel-Razeq4, Mahmoud Abunasser1, Sara Edaily1, Hazem Abdulelah1, Razan Abu Khashabeh3, Rayan Bater1.
Abstract
Purpose: Contrary to BRCA pathogenic variants, recommendations for management of variants of uncertain significance (VUS) are not clear and focus more on the patient's family and personal history of cancer. Local and regional data on VUS are scarce. In this paper, we study patterns and frequency of VUS among breast cancer patients undergoing genetic testing. Patients andEntities:
Keywords: BRCA; VUS; breast cancer; genetic testing; variants of uncertain significance
Year: 2022 PMID: 35402282 PMCID: PMC8989924 DOI: 10.3389/fonc.2022.673094
Source DB: PubMed Journal: Front Oncol ISSN: 2234-943X Impact factor: 6.244
Patients’ characteristics (n = 110).
| Characteristics | Number | (%) | |
|---|---|---|---|
| Age at diagnosis (years) | Median | 39 | |
| Range | 25–66 | ||
| Hormonal status | ER-positive | 81 | 73.6 |
| PR-positive | 85 | 77.3 | |
| HER-2 status | HER2-positive | 21 | 19.1 |
| HER2-negative | 86 | 78.2 | |
| Unknown | 3 | 2.7 | |
| Triple negative | 13 | 11.8 | |
| Disease stage | Early stage | 103 | 93.6 |
| Metastatic | 7 | 6.4 | |
ER, estrogen receptor; PR, progesterone receptor; HER2, human epidermal growth factor receptor 2.
VUS rates in relation to indications for genetic testing (n = 1,197).
| Indication for genetic testing | Number of patients | VUS Number (rate) | p-value | |
|---|---|---|---|---|
| Age at diagnosis (years) | ≤40 | 645 | 65 (10.1%) | 0.294 |
| >40 | 552 | 45 (8.2%) | ||
| Triple-negative, age ≤ 60 years | Yes | 157 | 13 (8.3%) | 0.699 |
| No | 1040 | 97 (9.3%) | ||
| Diagnosed at age ≤50 years with ≥1 close relative with breast cancer at any age, ≥1 close relative with pancreatic cancer, or ≥1 close relative with prostate cancer (Gleason score ≥7) | Yes | 593 | 51 (8.6%) | 0.524 |
| No | 604 | 59 (9.8%) | ||
| Diagnosed at any age with ≥1 close relative with breast cancer diagnosed at age 50 years or younger | Yes | 339 | 29 (8.6%) | 0.662 |
| No | 858 | 81 (9.4%) | ||
| Diagnosed at any age with two or more additional diagnosis of breast cancer at any age (synchronously or asynchronously) | Yes | 151 | 12 (8.0%) | 0.604 |
| No | 1046 | 98 (9.4%) | ||
Figure 1Rates of Variants of Uncertain Significance (VUS) by testing panel (n = 1197).
Variants of Uncertain Significance (VUS) Mutations in BRCA1 and BRCA2.
| Gene | Nucleotide change | Amino acid change | Variant type | Frequency |
|---|---|---|---|---|
| BRCA2 | c.9875C>T | p.Pro3292Leu | missense | 4 |
| BRCA2 | c. 9613_9614delinsCT | p.Ala3205Leu | missense | 4 |
| BRCA2 | c.62A>G | p.Lys21Arg | missense | 2 |
| BRCA2 | c.502C>G | p.Pro168Ala | missense | 2 |
| BRCA2 | c.4621A>C | p.Lys1541Gln | missense | 2 |
| BRCA1 | c.994C>T | p.Arg332Trp | missense | 2 |
| BRCA2 | c.4252A>G | p.Ile1418Val | missense | 3 |
| BRCA2 | c.865A>G | p.Asn289Asp | missense | 2 |
| BRCA2 | c.5126A>C | p.Asp1709Ala | missense | 2 |
| BRCA1 | c.5333-6T>C | NA | Intron Variant | 2 |
| BRCA2 | c.9586A>G | p.Lys3196Glu | missense | 2 |
| BRCA1 | c.851A>G | p.Gln284Arg | missense | 2 |
| BRCA2 | c.8632G>C | p.Glu2878Gln | missense | 3 |
| BRCA2 | c.8332-3C>G | NA | Intron Variant | 2 |
| BRCA2 | c.7534C>T | p.Leu2512Phe | missense | 4 |
| BRCA2 | c.6521T>C | p.Val2174Ala | missense | 2 |
| BRCA2 | c.8774A>G | p.Gln2925Arg | missense | 2 |
| BRCA1 | c.2604A>G | p.Ser868= | synonymous | 1 |
| BRCA2 | c.5976A>G | p.Ser1992= | synonymous | 1 |
| BRCA1 | c.693G>A | p.Thr231= | synonymous | 1 |
| BRCA2 | c.122C>T | p.Pro41Leu | missense | 3 |
| BRCA2 | c.10202C>T | p.Thr3401Met | missense | 1 |
| BRCA2 | c.7806-6G>T | NA | Intron Variant | 1 |
| BRCA2 | c.1915T>C | p.= | synonymous | 1 |
| BRCA1 | c.3367G>T | p.Asp1123Tyr | missense | 1 |
| BRCA1 | c.4028A>T | p.Asp1343Val | missense | 1 |
| BRCA1 | c.5555C>T | p.Thr1852Ile | missense | 1 |
| BRCA1 | c.2123 C>A | p.Ser708Tyr | missense | 1 |
| BRCA1 | c.5504G>A | p.Arg1835Gln | missense | 1 |
| BRCA2 | c.2396A>G | p.Lys799Arg | missense | 1 |
| BRCA2 | c.2366 A>G | p.Leu2366Val | missense | 1 |
| BRCA2 | c.4943C>T | p.Ala1648Val | missense | 1 |
| BRCA1 | c.4185+10G>A | NA | Intron Variant | 1 |
| BRCA2 | c.7462A>G | p.Arg2488Gly | missense | 1 |
| BRCA2 | c.8755-19 A>G | NA | Intron Variant | 2 |
| BRCA2 | c.3676A>C | p.Lys1226Gln | missense | 2 |
| BRCA2 | c.10078A>G | p.Lys3360Glu | missense | 1 |
| BRCA1 | c.4412G>A | p.Gly1471Asp | missense | 1 |
| BRCA2 | c.5897A>G | p.His1966Arg | missense | 2 |
| BRCA1 | c.4045A>C | p.Thr1349Pro | missense | 1 |
| BRCA2 | c.2332G>C | p.Val778Ile | missense | 1 |
| BRCA2 | c.277T>G | p.Ser93Ala | missense | 1 |
| BRCA2 | c.5590G>A | p.Asp1864Asn | missense | 1 |
| BRCA1 | c.5074+6 C>G | NA | Intron Variant | 1 |
| BRCA1 | c.478G>A | p.Gly160Arg | missense | 1 |
| BRCA2 | c.1769T>G | p.Phe590Cys | missense | 1 |
| BRCA2 | c.1793C>T | p.Thr598Ile | missense | 1 |
| BRCA2 | c.9839C>A | p.Pro3280His | missense | 1 |
| BRCA2 | c.280 C>T | p.Pro94Ser | missense | 1 |
| BRCA2 | c.9754_9765del | p.Ser3252_Gly3255del | deletion | 1 |
| BRCA2 | c.800G>A | p.Gly267Glu | missense | 1 |
| BRCA1 | c.3149G>C | p.Gly2748Asp | missense | 1 |
| BRCA1 | c.539T>C | p.Ile180Thr | missense | 1 |
| BRCA1 | c.3587C >T | p.Thr1196Ile | missense | 2 |
| BRCA2 | c.4954G>A | p.Ala1652Pro | missense | 1 |
| BRCA1 | c.3642G>T | p.Glu1214Asp | missense | 1 |
| BRCA2 | c.7301A>C | p.Lys2434Thr | missense | 1 |
| BRCA1 | exon 5-8 duplication | NA | duplication | 1 |
| BRCA2 | c.1550A>G | p.Asn517Ser | missense | 1 |
| BRCA2 | c.9502-12T>G | NA | Intron Variant | 1 |
| BRCA2 | c.6986 C>T | p.Pro2329Leu | missense | 1 |
| BRCA2 | c.752C>G | p.Thr251Arg | missense | 1 |
| BRCA1 | c.3526 G>A | p.Val1176Ile | missense | 1 |
| BRCA1 | c.1662G>C | p.Glu554Asp | missense | 1 |
| BRCA2 | c.2072 C>T | p.Ala691Val | missense | 1 |
| BRCA2 | c.9378G>C | p.Gln3126= | synonymous | 1 |
| BRCA1 | c.509G>A | p.Arg170Gln | missense | 1 |
| BRCA2 | c.9781G>A | p.Asp3261Asn | missense | 1 |
| BRCA2 | c.1263 A>G | p.= | synonymous | 1 |
| BRCA1 | c.1446_1448del | p.Ile483del | missense | 1 |
| BRCA2 | c.4594G>T | p.Val1532Phe | missense | 1 |
| BRCA2 | c.9418G>A | p.Ala3140Thr | missense | 1 |
| BRCA2 | c.2779A>G | p.Met927Val | missense | 1 |
| BRCA1 | c.4357+5G>A | NA | Intron Variant | 1 |
| BRCA2 | c.7992T>G | p.Ile2664Met | missense | 1 |
| BRCA2 | c.644_646del | p.Glu215del | deletion | 1 |
| BRCA1 | Exons 1-2 Duplication | NA | duplication | 1 |
| BRCA2 | c.6945 A>G | p.Ile2315Met | missense | 1 |
| BRCA2 | c.340C>T | p.His114Tyr | missense | 1 |
| BRCA2 | c.8382C>G | p.Phe2794Leu | missense | 1 |
| BRCA2 | c.1691C>G | p.Pro564Leu | missense | 1 |
| BRCA1 | c.1333G>C | p.Glu445Gln | missense | 1 |
| BRCA2 | c.6916G>C | p.Ala2306Pro | missense | 1 |
| BRCA1 | c.4434G>C | p.Glu1478Asp | missense | 1 |
| BRCA2 | c.6805G>A | p.Gly2748Asp | missense | 1 |
Many patients had more than one variant, so total number of variants is more than the total number of patients.
p.= means the entire protein coding region was analyzed and no variant was found that changes (or is predicted to change) the protein sequence.
Variants of Uncertain Significance (VUS) Mutations in Non-BRCA1 or BRCA2.
| Gene | Nucleotide change | Amino acid change | Variant type | Frequency |
|---|---|---|---|---|
| ATM | c.5892 G>C | p.Lys1964Asn | missense | 1 |
| ATM | c.37C>T | p.Arg13Cys | missense | 1 |
| ATM | c.8712G>C | p.Glu2904Asp | missense | 1 |
| ATM | c.4421 A>G | p.His1474Arg | missense | 1 |
| ATM | c.6733G>C | p.Glu2245Gln | missense | 1 |
| ATM | c.6975G>A | p.Ala2325= | synonymous | 1 |
| ATM | c.133C>T | p.Arg45Trp | missense | 2 |
| BARD1 | c.59C>T | p.Pro20Leu | missense | 1 |
| BARD1 | c.1108C>T | p.Arg370Cys | missense | 1 |
| BARD1 | c.195A<G | p.= | synonymous | 1 |
| BARD1 | c.1148T>A | p.Met383Lys | missense | 1 |
| BARD1 | c.247T>C | p.Cys83Arg | missense | 1 |
| BARD1 | c.1267A>G | p.Lys423Glu | missense | 1 |
| BARD1 | c.1793C>T | p.Thr598Ile | missense | 2 |
| BRIP1 | c.3178G>A | p.Val1060Ile | missense | 1 |
| BRIP1 | c.1846A>G | p.Thr616Ala | missense | 1 |
| BRIP1 | c.1198G>T | p.Asp400Tyr | missense | 3 |
| CDH1 | c.2369C>T | p.Thr790Ile | missense | 1 |
| CDH1 | c.1914G>C | p.Trp638Cys | missense | 1 |
| CHEK2 | c.1556G>T | p.Arg519Leu | missense | 1 |
| CHEK2 | c.246_260del | p.77_81DQEPE | microsatellite | 1 |
| CHEK2 | c.886G>T | p.Asp296Tyr | missense | 1 |
| CHEK2 | c.1336A>G | p.Asn446Asp | missense | 1 |
| CHEK2 | c.544C>A | p.Pro182Thr | missense | 1 |
| CHEK2 | c.1216 C>T | p.Arg406Cys | missense | 1 |
| CHEK2 | c.1570G>A | p.Glu524Lys | missense | 1 |
| CHEK2 | c.953G>A | p.Arg318His | missense | 1 |
| CHEK2 | c.592+3A>T | NA | Intron Variant | 5 |
| MLH1 | c.650G>A | p.Arg217His | missense | 1 |
| MLH1 | c.919G>A | p.Val307Met | missense | 1 |
| MSH2 | c.2141C>T | p.Ala714Val | missense | 1 |
| MSH2 | c.2T>C | p.Met1? | in-frame shift | 1 |
| MSH6 | c.3029C>G | p.Thr1010Ser | missense | 1 |
| MSH6 | c.1649C>G | p.Ser550Cys | missense | 1 |
| MSH6 | c.1774G>A | p.Val592Ile | missense | 1 |
| MSH6 | c.3104G>A | p.Arg1035Gln | missense | 2 |
| NBN | c.602A>G | p.Asp201Gly | missense | 1 |
| NBN | c.703-3T | NA | Intron Variant | 1 |
| NBN | c.353_355del | p.Ser118del | Deletion | 1 |
| NBN | c.1369A>G | p.Asn457Asp | missense | 1 |
| NF1 | c.1438A>G | p.Lys480Glu | missense | 1 |
| NF1 | c.1662G>T | p.Gln554His | missense | 1 |
| NF1 | c.5788C>G | p.Pro1930Ala | missense | 1 |
| NF1 | c.8431 C>T | p.Arg2811Cys | missense | 1 |
| PALB2 | c.3296C>G | p.Thr1099Arg | missense | 1 |
| PALB2 | c.995 T>C | p.Leu332His | missense | 1 |
| PALB2 | c.3320 T>C | p.Leu1107Pro | missense | 1 |
| PALB2 | c.1497 G>C | p.Leu499= | synonymous | 1 |
| PALB2 | c.1748T>G | p.Leu583Trp | missense | 1 |
| PALB2 | c.1123C>A | p.Leu375Ile | missense | 1 |
| PMS2 | c.655G>A | p.Gly219Arg | missense | 1 |
| PMS2 | c.2335G>A | p.Gly779Arg | missense | 1 |
| PMS2 | c.113C>T | p.Ala38Val | missense | 1 |
| PMS2 | c.2068A>C | p.Lys690Gln | missense | 2 |
| PMS2 | c.2012C>T | p.Thr671Met | missense | 1 |
| RAD51C | c.431T<C | p.Ile144Thr | missense | 2 |
Many patients had more than one variant, so total number of variants is more than the total number of patients.
p.= means the entire protein coding region was analyzed and no variant was found that changes (or is predicted to change) the protein sequence.
Figure 2Surgical interventions. Surgical interventions among patients with results of VUS known prior to surgery (n = 34) and those without (n = 69). No difference in the rates of MRM (p = 0.272) or BCS (p = 0.207). MRM, modified radical mastectomy; BCS, breast-conserving surgery; VUS, variants of uncertain significance.