scholarly journals Unclassified Variant

2019 ◽  
Author(s):  
Keyword(s):  
Unclassified Variant

Patients With an Unclassified Genetic Variant in the BRCA1 or BRCA2 Genes Show Different Clinical Features From Those With a Mutation

2005 ◽  
Vol 23 (10) ◽  
pp. 2185-2190 ◽  
Author(s):  
Encarna B. Gómez-García ◽  
Ton Ambergen ◽  
Marinus J. Blok ◽  
Arthur van den Wijngaard
Keyword(s):  
Standard Deviation ◽  
Family History ◽  
Clinical Features ◽  
Predictive Models ◽  
Genetic Variant ◽  
Pathogenic Mutation ◽  
Unclassified Variant ◽  
The Family ◽  
Novel Variants ◽  
Combined Data

Purpose To obtain and compare the probabilities of finding a mutation in the BRCA1 or BRCA2 genes, the clinical features, and the family history among patients with an unclassified variant (UV) and those with a pathogenic mutation. Patients and Methods The study included 70 patients: 24 with a UV (BRCA1, n = 4; BRCA2, n = 19; both, n = 1), and 46 with a mutation (BRCA1, n = 32; BRCA2, n = 14). Two of the UVs were novel variants; the rest had been reported previously as UVs. Probabilities of finding a mutation were retrospectively obtained using BRCAPRO and Myriad II programs. Results The probability to detect a mutation was significantly lower in the group of patients with a UV than in those with a mutation (BRCAPRO [mean ± standard deviation], 0.297 ± 0.312 v 0.627 ± 0.315, P = .001; and Myriad II, 0.124 ± 0.090 v 0.283 ± 0.176, P = .001, respectively). Independent predictive factors of finding either a UV or a mutation were number of affected relatives (2.9 ± 1.4 v 4.0 ± 1.9; P = .039) and number of tumors among relatives (3.3 ± 1.4 v 4.4 ± 1.8; P = .031), respectively. Conclusion The combined data about the predictive models show significant differences between both groups. Individual probabilities can be regarded as a help to guide the clinical management of patients with a UV in those genes. However, a definitive conclusion about the pathogenicity of a UV can not be obtained from the clinical features alone, but only in combination with biochemical and epidemiologic data.

scholarly journals Identification of an APC Variant in a Patient with Clinical Attenuated Familial Adenomatous Polyposis

2014 ◽  
Vol 2014 ◽  
pp. 1-3 ◽  
Author(s):  
Andrew T. Schlussel ◽  
Susan S. Donlon ◽  
Faye A. Eggerding ◽  
Ronald A. Gagliano
Keyword(s):  
Case Report ◽  
Familial Adenomatous Polyposis ◽  
Apc Gene ◽  
Adenomatous Polyposis ◽  
Invasive Adenocarcinoma ◽  
Unclassified Variant ◽  
Attenuated Familial Adenomatous Polyposis ◽  
Mutant Variant ◽  
Pathogenic Analysis ◽  
Tumor Dna

Introduction.The objective of this case report is to discuss an unclassified germline variant of the adenomatous polyposis coli (APC) gene identified in an older patient with attenuated familial adenomatous polyposis syndrome (AFAP).Methods.We present a case report of a 66-year-old man diagnosed with AFAP. Colonoscopy found multiple polyps and invasive adenocarcinoma arising in the transverse colon. Samples were tested for mutations in the APC gene.Results.DNA sequencing of germline DNA identified a cytosine (C) to thymine (T) transition at nucleotide 1240, heterozygous. The C to T transition at codon 414 is predicted to convert an arginine residue to a cysteine that is possibly pathogenic. Analysis of the patient’s colon tumor DNA indicated that the tumor had lost the mutant variant allele and retained only the normal allele, suggesting that the variant may not be significant.Conclusions.The p.R414C variant has been described previously as a germline mutation of probable pathogenicity. This substitution should be considered an unclassified variant and possibly not pathogenic. These findings support the need for further genetic testing of tissue, as well as for developing a mechanism for testing all variants, as this could significantly impact the lives of patients and their family members.

scholarly journals MSH2 Overexpression Due to an Unclassified Variant in 3’-Untranslated Region in a Patient with Colon Cancer

Biomedicines ◽  
2020 ◽  
Vol 8 (6) ◽  
pp. 167
Author(s):  
Raffaella Liccardo ◽  
Antonio Nolano ◽  
Matilde Lambiase ◽  
Carlo Della Ragione ◽  
Marina De Rosa ◽  
...  
Keyword(s):  
Untranslated Region ◽  
Tumor Development ◽  
Luciferase Reporter ◽  
Luciferase Reporter Gene ◽  
Unclassified Variant ◽  
Dna Mismatch ◽  
Functional Assays ◽  
Mmr Genes ◽  
Uncertain Significance ◽  
Low Expression

Background: The loss or low expression of DNA mismatch repair (MMR) genes can result in genomic instability and tumorigenesis. One such gene, MSH2, is mutated or rearranged in Lynch syndrome (LS), which is characterized by a high risk of tumor development, including colorectal cancer. However, many variants identified in this gene are often defined as variants of uncertain significance (VUS). In this study, we selected a variant in the 3′ untranslated region (UTR) of MSH2 (c*226A > G), identified in three affected members of a LS family and already reported in the literature as a VUS. Methods: The effect of this variant on the activity of the MMR complex was examined using a set of functional assays to evaluate MSH2 expression. Results: We found MSH2 was overexpressed compared to healthy controls, as determined by RTqPCR and Western blot analyses of total RNA and proteins, respectively, extracted from peripheral blood samples. These results were confirmed by luciferase reporter gene assays. Conclusions: We therefore speculated that, in addition to canonical inactivation via a gene mutation, MMR activity may also be modulated by changes in MMR gene expression.

scholarly journals Prognostic impact ofBRCA1 pathogenic andBRCA1/BRCA2 unclassified variant mutations in patients with ovarian carcinoma

Cancer ◽  
2005 ◽  
Vol 104 (5) ◽  
pp. 1004-1012 ◽  
Author(s):  
Ewa Joanna Majdak ◽  
Jaroslaw Debniak ◽  
Tomasz Milczek ◽  
Cees J. Cornelisse ◽  
Peter Devilee ◽  
...  
Keyword(s):  
Ovarian Carcinoma ◽  
Prognostic Impact ◽  
Unclassified Variant

Determination of the Clinical Significance of an Unclassified Variant

2011 ◽  
pp. 337-348 ◽  
Author(s):  
Victor Wei Zhang ◽  
Jing Wang
Keyword(s):  
Clinical Significance ◽  
Unclassified Variant

A previously unclassified variant of sternalis muscle

2017 ◽  
Vol 39 (12) ◽  
pp. 1417-1419 ◽  
Author(s):  
Sarah N. Dudgeon ◽  
Kayla M. Marcotte ◽  
Glenn M. Fox ◽  
B. Kathleen Alsup
Keyword(s):  
Unclassified Variant ◽  
Sternalis Muscle

scholarly journals An unclassified variant of CHD7 activates a cryptic splice site in a patient with CHARGE syndrome

2018 ◽  
Vol 5 (1) ◽  
Author(s):  
Yuko Katoh-Fukui ◽  
Shuichi Yatsuga ◽  
Hirohito Shima ◽  
Atsushi Hattori ◽  
Akie Nakamura ◽  
...  
Keyword(s):  
Splice Site ◽  
Charge Syndrome ◽  
Cryptic Splice Site ◽  
Unclassified Variant

scholarly journals [Erratum] BRCA1 homozygous unclassified variant in a patient with non‑Fanconi anemia: A case report

2018 ◽  
Author(s):  
Bondavalli Davide ◽  
Malvestiti Francesca ◽  
Pensotti Valeria ◽  
Feroce Irene ◽  
Bonanni Bernardo
Keyword(s):  
Case Report ◽  
Fanconi Anemia ◽  
Unclassified Variant

scholarly journals Origin of hepatitis C virus genotype 3 in Africa as estimated through an evolutionary analysis of the full-length genomes of nine subtypes, including the newly sequenced 3d and 3e

2014 ◽  
Vol 95 (8) ◽  
pp. 1677-1688 ◽  
Author(s):  
Chunhua Li ◽  
Ling Lu ◽  
Donald G. Murphy ◽  
Francesco Negro ◽  
Hiroaki Okamoto
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Middle East ◽  
South Asia ◽  
Common Ancestor ◽  
Full Length ◽  
Evolutionary Analysis ◽  
Genotype 3 ◽  
Virus Genotype ◽  
Unclassified Variant

We characterized the full-length genomes of nine hepatitis C virus genotype 3 (HCV-3) isolates: QC7, QC8, QC9, QC10, QC34, QC88, NE145, NE274 and 811. To the best of our knowledge, NE274 and NE145 were the first full-length genomes for confirming the provisionally assigned subtypes 3d and 3e, respectively, whereas 811 represented the first HCV-3 isolate that had its extreme 3′ UTR terminus sequenced. Based on these full-length genomes, together with 42 references representing eight assigned subtypes and an unclassified variant of HCV-3, and 10 sequences of six other genotypes, a timescaled phylogenetic tree was reconstructed after an evolutionary analysis using a coalescent Bayesian procedure. The results indicated that subtypes 3a, 3d and 3e formed a subset with a common ancestor dated to ~202.89 [95 % highest posterior density (HPD): 160.11, 264.6] years ago. The analysis of all of the HCV-3 sequences as a single lineage resulted in the dating of the divergence time to ~457.81 (95 % HPD: 350.62, 587.53) years ago, whereas the common ancestor of all of the seven HCV genotypes dated to ~780.86 (95 % HPD: 592.15, 1021.34) years ago. As subtype 3h and the unclassified variant were relatives, and represented the oldest HCV-3 lineages with origins in Africa and the Middle East, these findings may indicate the ancestral origin of HCV-3 in Africa. We speculate that the ancestral HCV-3 strains may have been brought to South Asia from Africa by land and/or across the sea to result in its indigenous circulation in that region. The spread was estimated to have occurred in the era after Vasco da Gama had completed his expeditions by sailing along the eastern coast of Africa to India. However, before this era, Arabians had practised slave trading from Africa to the Middle East and South Asia for centuries, which may have mediated the earliest spread of HCV-3.

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