ライフサイエンスコーパス: synonymous

1 -5 should not all be considered functionally synonymous.

2 benign missense mutations and the rest were synonymous.

3 tivity and ecosystem C sequestration are not synonymous.

4 domain (ASL) negates wobble decoding of its synonymous A-ending codon, suggesting that this function

5 Using synonymous alleles to enlarge sequence space exploration

6 replacing codons Thr6 and Pro8 of flgM with synonymous alternates produced a 600-fold range in FlgM

7 slational properties distinct from the other synonymous alternatives (CGN).

8 instances of seven codons were replaced with synonymous alternatives across all protein-coding genes.

9 ough dinosaurs and gigantism are practically synonymous, an analysis of body size evolution in dinosa

10 .05% frequency [57% non-synonymous (NS), 42% synonymous and 1% gain or loss of stop codon or splice s

11 Non-synonymous and deleterious variants, segregating with th

12 tagenesis have revealed that synonymous, non-synonymous and intronic mutations frequently alter the i

13 Synonymous and intronic mutations with predicted splice-

14 etation of personal genomes.While non-coding synonymous and intronic variants are often not under str

15 s in genic regions, resulting in overlooking synonymous and intronic variants when searching for dise

16 ative selection observed for synonymous, non-synonymous and loss-of-function mutations.

17 text alterations to predict pathogenicity of synonymous and non-coding genetic variants, and provide

18 intolerant and Z-scores of observed/expected synonymous and non-synonymous mutation ratios.

19 ine and somatic mutations as well as between synonymous and non-synonymous mutations.

20 f leaves in lineage trees branches following synonymous and non-synonymous mutations.

21 To evaluate synonymous and nonsynonymous alternatives to essential A

22 ently intermediate between that operating on synonymous and nonsynonymous sites.

23 lved in photosynthetic metabolism have lower synonymous and nonsynonymous substitutions rates than th

24 results provide a resource for prioritising synonymous and other variants as disease-causing mutatio

25 both the nature of adaptive mutations (often synonymous) and the frequency with which strains success

26 shes known pathogenic and benign variants in synonymous (AUC = 0.88) and intronic (AUC = 0.83) public

27 Recoding viral genomes by numerous synonymous but suboptimal substitutions provides live at

28 Synonymous changes at Thr6 and Leu9 resulted in a twofol

29 though previous studies have shown that some synonymous changes can lead to different final structure

30 RNA folding and reducing R-loop formation by synonymous changes in a reporter gene can lower mutation

31 We quantified nonsynonymous and synonymous changes in both genes and identified sites ex

32 ge leading to this group is enriched for non-synonymous changes within the genomic area of Salmonella

33 nonymous nucleotide changes than the rate of synonymous changes, demonstrating prevalent molecular ad

34 The patient carries a concomitant synonymous CLCN1 variant that likely worsens the myotoni

35 ondrial defect in the synVI strain mapped to synonymous coding changes within PRE4 (YFR050C), encodin

36 ow-frequency (minor allele frequency = 2.5%) synonymous coding variant g.14900931G>A (p.Asp120Asp) (r

37 Synonymous codon choice has diverse and important roles,

38 "Min" variants (excess of underrepresented synonymous codon pairs) are nonviable except for P2(Min)

39 7 "Max" mutations (excess of overrepresented synonymous codon pairs) or up to 2,104 "SD" mutations (r

40 However, synonymous codon substitutions can affect many distinct

41 These results support a model in which synonymous codon substitutions can impair cell fitness b

42 Here we show that synonymous codon substitutions encoding a single essenti

43 ecent reports have identified rare-to-common synonymous codon substitutions that impair folding of th

44 Synonymous codon suppressors that corrected the effect o

45 Synonymous codon usage (SCU) varies widely among human g

46 Synonymous codon usage affects the efficiency/stringency

47 d attempts to deconvolve the extent to which synonymous codon usage can promote or frustrate proper p

48 Synonymous codon usage has been identified as a determin

49 evelopment, suggesting an important role for synonymous codon usage in organism physiology.

50 nables experimental testing of the impact of synonymous codon usage on the production of functional p

51 Synonymous codon usage significantly impacts translation

52 says and for different assumptions regarding synonymous codon usage, tRNA level modifications, or rib

53 nsistent with translation rate modulation by synonymous codon usage.

54 ongation rate, which varies as a function of synonymous codon usage.

55 er, a critical mass of reports suggests that synonymous codon variations may impact protein conformat

56 mino acids are each encoded by more than one synonymous codon.

57 of distinct, functional roles for otherwise synonymous codons and enables experimental testing of th

58 oved by harmonizing selected DNA segments by synonymous codons and reveal additional complexity invol

59 rential transfer RNA supply within the cell, synonymous codons are not used with equal frequency, a p

60 hesis that although the usage frequencies of synonymous codons change from organism to organism, codo

61 The uneven use of synonymous codons in the transcriptome regulates the eff

62 Synonymous codons naturally occur with different frequen

63 multiple codons, and the frequency that such synonymous codons occur in genomes ranges from rare to c

64 Synonymous codons occur with different frequencies in di

65 Synonymous codons provide redundancy in the genetic code

66 Our results demonstrate that optimal synonymous codons speed up translation elongation while

67 To investigate the impact of synonymous codons usage on protein expression and functi

68 to 2,104 "SD" mutations (randomly scrambled synonymous codons).

69 Most amino acids are encoded by multiple synonymous codons, some of which are used more rarely th

70 but disappears after random substitution of synonymous codons, which suggests that the evolution of

71 most amino acids can be encoded by multiple synonymous codons.

72 o the degree of in vivo ribosome stalling at synonymous codons.

73 dues are each encoded by multiple, so-called synonymous codons.

74 mic design based on multiple replacements of synonymous codons.

75 4 codons, the mRNA levels vary >20 fold with synonymous CRD substitutions that accommodate tRNA dynam

76 mple, we identify and directly phase two non-synonymous de novo variants in SAMD9L, (OMIM #159550) in

77 Non-synonymous differences in viral proteins were identified

78 skewed ratio (4.83) of nonsynonymous versus synonymous (dN/dS) mtDNA mutations with high statistical

79 each virus and the ratio of nonsynonymous to synonymous (dN/dS) substitutions of minor variants confi

80 EBV isolates from China, we identify two non-synonymous EBV variants within BALF2 that are strongly a

81 e estimates of the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS ratio) located a

82 ividuals with Wilms tumour and a de-novo non-synonymous FBXW7 mutation in a child with a rhabdoid tum

83 rected the effect of a translation-defective synonymous flgM allele were restricted to two codons fla

84 Manipulative experiments in yeast using 37 synonymous fluorescent proteins confirmed that an exogen

85 rons (HIPP cells) have been considered to be synonymous for DG-SOMIs.

86 Evaluating the impact of non-synonymous genetic variants is essential for uncovering

87 Non-synonymous genetic variation in SLC30A2 is common in hum

88 to understand as numerous mutations and non-synonymous genetic variation in ZnT2 have been detected

89 cal systems or 'tissue chips' (the terms are synonymous), have attracted substantial interest in rece

90 Three substitutions (one synonymous in PB2, one nonsynonymous in M and PA each) w

91 Medical Language System were used to resolve synonymous ingredient names.

92 ing SIRCAS, we create a Salmonella with 1557 synonymous leucine codon replacements across 176 genes,

93 Familial analyses of one variant, a synonymous LMNA VUS, demonstrated segregation with cardi

94 ften conceptually or analytically treated as synonymous markers of gamma activity.

95 Because the approach involves hundreds of synonymous modifications to the genome, the reversion ri

96 Here we show, using synonymous mutagenesis, that CG suppression is essential

97 L deficiency due to homozygosity for a novel synonymous mutation (c.222C->A, p.V74V).

98 ed exonic definition of exon 4 and the MMP20 synonymous mutation decreased exonic definition of exon

99 determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g

100 ighly structured, conserved, and contain low synonymous mutation rates.

101 al excess calculated using non-synonymous to synonymous mutation ratios (dN/dS).

102 and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift bei

103 ores of observed/expected synonymous and non-synonymous mutation ratios.

104 whole genome sequencing, we identified a non-synonymous mutation within an uncharacterized LacI-type

105 n, we found that potentially deleterious non-synonymous mutations (9566 SNPs) explained as much genet

106 The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method

107 y of 1.9 x 10(7) with over 8500 possible non-synonymous mutations and inferred the effects of each mu

108 Missense or non-synonymous mutations are nucleotide substitutions that a

109 more, aside from those that affect splicing, synonymous mutations are typically ignored as potential

110 onymous to synonymous mutations; however, if synonymous mutations are under purifying selection, this

111 Evolving neoplasms accumulate non-synonymous mutations at a high rate, potentially enablin

112 Assuming all non-synonymous mutations cause resistance, we report 90% sen

113 py and hindering their fixations relative to synonymous mutations despite continued population adapta

114 te the distribution of fitness effects among synonymous mutations for a gene under directional select

115 Synonymous mutations had highly variable fitness effects

116 Several mouse models harboring synonymous mutations have shown alterations in synaptic

117 We analyze de novo synonymous mutations identified in autism spectrum disor

118 sing temperature, a CPD RSV containing 2,692 synonymous mutations in 9 of 11 ORFs did not lose temper

119 Nonsynonymous and synonymous mutations in a PEST-like domain near the LLO

120 Furthermore, we found non-synonymous mutations in a set of plausible candidate gen

121 We discovered non-synonymous mutations in ARID1A, FBXW7, PIGR, ZC3H12A, an

122 All non-synonymous mutations in reactive T cell epitopes were te

123 Analysis of both 5' UTR and synonymous mutations in the PEST-like domain that are pr

124 oach, we introduce a barcoded library of non-synonymous mutations into hotspot codons 12 and 13 of Kr

125 Our results reveal that synonymous mutations most likely play an underappreciate

126 Inactivating m(6)A addition sites with synonymous mutations or demethylase resulted in m(6)A-de

127 Synonymous mutations or protein expression losses in ACT

128 ons are detected using the synonymous to non-synonymous mutations ratio.

129 However, a CPD RSV containing 1,378 synonymous mutations solely in the polymerase L ORF quic

130 reover, we show that, despite only a few non-synonymous mutations specifically targeting arginine res

131 lus (mRNA) and minus (vRNA) strands and used synonymous mutations to ablate m(6)A on both strands of

132 f the BC supergene and dragging multiple non-synonymous mutations to high frequency.

133 beta-lactamase CTX-M-15, and find three non-synonymous mutations with increased resistance against m

134 de the most compelling evidence to date that synonymous mutations with non-neutral fitness effects ma

135 resented in dbSNP and included predicted non-synonymous mutations with possible phenotypic effects.

136 oma and these tumours contain only 30-50 non-synonymous mutations(5).

137 es differed by one or two reverse engineered synonymous mutations, and measured the transmission of t

138 er 260 000 somatic alterations including non-synonymous mutations, copy number variants and structura

139 The fitness effects of synonymous mutations, nucleotide changes that do not alt

140 ructures associated with vPAR-CL sites using synonymous mutations, resulting in varied effects to vir

141 Synonymous mutations, such as I507-ATC-->ATT, in deletio

142 ls pervasive weak negative selection against synonymous mutations.

143 ed a constrained evolutionary path, even for synonymous mutations.

144 ations as well as between synonymous and non-synonymous mutations.

145 trees branches following synonymous and non-synonymous mutations.

146 sites with high ratios of non-synonymous to synonymous mutations; however, if synonymous mutations a

147 nd systematic mutagenesis have revealed that synonymous, non-synonymous and intronic mutations freque

148 evidence of negative selection observed for synonymous, non-synonymous and loss-of-function mutation

149 No single non-synonymous (NS) single nucleotide variant (SNV) nor any

150 ng variants down to 0.05% frequency [57% non-synonymous (NS), 42% synonymous and 1% gain or loss of s

151 analysis identified 3 amino acid changes, 16 synonymous nucleotide changes, and a 12-bp insertion str

152 tional selection and capable of adapting via synonymous nucleotide changes.

153 ous nucleotide site diversity (piN/piS), and synonymous nucleotide diversity (piS), avoiding the stat

154 selection, the nonsynonymous relative to the synonymous nucleotide site diversity (piN/piS), and syno

155 with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most p

156 imization, in which codons are replaced with synonymous ones in order to increase protein expression.

157 reased with age, and many mutations were non-synonymous or resided in RNA coding genes and thus can l

158 n pairs more highly conserved than any other synonymous pair.

159 Probands have a significant burden of synonymous PMMs and these mutations are enriched for com

160 n EMC-deficient cells, we identified two non-synonymous point mutations in NS4A and NS4B, which rescu

161 A single non-synonymous polymorphism within a protein synthesis gene

162 n algorithms and conservation scores, 12 non-synonymous prediction algorithms and four cancer-specifi

163 Synonymous rare codons are considered to be sub-optimal

164 Although a general functional role for synonymous rare codons farther within coding sequences h

165 n coding sequences include large clusters of synonymous rare codons.

166 We observed a lower nonsynonymous to synonymous rate ratio in antagonistic changing environme

167 y orders of magnitude among species, whereas synonymous rates among genes within a genome are general

168 To demonstrate their synonymous reactivity to ketenimines, these salts have b

169 Synonymous RNA mutations that lead to severe defects in

170 unprecedented intragenomic heterogeneity in synonymous sequence divergence, but the biological mecha

171 However, 19 non-synonymous showed conventional P-values < 0.05 comparing

172 A non-synonymous single nucleotide polymorphism of the human s

173 Genome-wide genetic mismatches in non-synonymous single nucleotide polymorphisms (nsSNPs) were

174 eness varies widely, which may be due to non-synonymous single nucleotide polymorphisms (nsSNPs) with

175 Synonymous single nucleotide polymorphisms (sSNPs) are c

176 We found several, known and new, non-synonymous single nucleotide polymorphisms in the propel

177 so referred to as missense mutations, or non-synonymous Single Nucleotide Variants - missense SNVs or

178 re-computed predictions of the impact of non-synonymous single nucleotide variants, to facilitate the

179 Nearly one-third of non-synonymous single-nucleotide polymorphism (nsSNPs) are d

180 ons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp g

181 Here we report de novo non-synonymous single-nucleotide variants (SNVs) by conducti

182 ied class of TSAs are those derived from non-synonymous single-nucleotide variants (SNVs), or SNV neo

183 istributions of synonymous substitutions per synonymous site (K(s) ) among paralogs, phylogenomic (ge

184 uency plots for synonymous substitutions per synonymous site (Ks ) between paralogous gene pairs and

185 Using the synplot2 program, synonymous site conservation was found among mammals in

186 the rate of crossing over, and the level of synonymous site diversity and rate of adaptive evolution

187 These variants compensate for synonymous-site variation in host mRNAs.

188 eously expressing multiple variants to cover synonymous-site variation, Cuscuta trans-species sRNAs m

189 We showed that conserved synonymous sites and/or local secondary structures that

190 previous studies indicated that selection at synonymous sites could be strong, this is the first stud

191 nogaster populations to measure selection on synonymous sites in a way that allowed us to estimate th

192 the functional importance of CUB, as well as synonymous sites in general, have been underestimated.

193 ), with strong selection acting on 10-20% of synonymous sites in preferred codons.

194 greater fraction of nonsynonymous sites than synonymous sites subject to high levels of editing.

195 unts for the majority of strong selection on synonymous sites, with secondary contributions of splici

196 o predict long-term evolutionary patterns at synonymous sites.

197 otein structures and identify 45 nsSNVs (non-synonymous small nucleotide variations) near the catalyt

198 A non-synonymous SNP (encoding a Glu415Gly substitution) in th

199 contained de novo mutations, including a non-synonymous SNP conferring antibiotic resistance in one p

200 determinate growth habit is caused by a non-synonymous SNP in CsTFL1 CsTFL1 is expressed in the suba

201 tween airflow obstruction or COPD with a non-synonymous SNP in the TNS1 gene, which encodes tensin1.

202 TYR region, in addition to the rs1042602 non-synonymous SNP located on the TYR gene, variants located

203 HRV SNPs tag non-synonymous SNPs (in NDUFA11 and KIAA1755), expression qu

204 terization and validation of deleterious non-synonymous SNPs (nsSNPs) in the interleukin-8 gene using

205 tion and identified 18 highly pathogenic non-synonymous SNPs (nsSNPs) out of 607 SNPs.

206 We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants.

207 s, Pfcrt, Pfk13 and Pfmdr1), and several non-synonymous SNPs were detected in these genes.

208 utant specific binding, as compared with non-synonymous SNV derived neoantigens.

209 affinity binders was three times that of non-synonymous SNV mutations.

210 Database and 10 002 putatively 'benign' non-synonymous SNVs from UCSC.

211 Here, using synonymous somatic mutations (SSMs) identified in over 4

212 Novel non-synonymous/splice-site variants in extracellular matrix

213 rther genotyping indicated that a single non-synonymous substitution (A120G) in the N-terminal region

214 those in the wild type by only a single, non-synonymous substitution (Gly734Glu) in the psaA gene, wh

215 mous substitutions are more predominant than synonymous substitution and occur across the entire geno

216 e, we studied the ratios of nonsynonymous-to-synonymous substitution rates (d (N)/d (S)) in protein-c

217 Synonymous substitution rates in plant mitochondrial gen

218 A synonymous substitution that results in exon eight skipp

219 relation between fitness and the presence of synonymous substitutions across a phylogeny of related P

220 ce has diverse and important roles, and many synonymous substitutions are detrimental.

221 conversion, despite the presence of some non-synonymous substitutions between plastid genomes of pare

222 analysis provides strong evidence that many synonymous substitutions have been selected to optimize

223 s reveals that relative average rates of non-synonymous substitutions in nuclear versus plastid genes

224 l gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes.

225 g three means of inference: distributions of synonymous substitutions per synonymous site (K(s) ) amo

226 Analyses of frequency plots for synonymous substitutions per synonymous site (Ks ) betwe

227 by the biopharmaceutical industry, involves synonymous substitutions to increase protein expression.

228 At the species level, biased patterns of synonymous substitutions underpin increased codon optimi

229 The ratio of nonsynonymous to synonymous substitutions was higher among the FtsZ2-2 ge

230 In these flies, the presence of multiple non-synonymous substitutions, even at modest heteroplasmy, d

231 Using correlation profiles of synonymous substitutions, we determine recombination rat

232 pecies show lower ratios of nonsynonymous to synonymous substitutions.

233 cleotide data is due solely to fast-evolving synonymous substitutions.

234 , and polyps or adenomas, and colorectal (or synonymous terms), published by March 2016.

235 deleterious mutations are detected using the synonymous to non-synonymous mutations ratio.

236 -wide mutational excess calculated using non-synonymous to synonymous mutation ratios (dN/dS).

237 The ratio of non-synonymous to synonymous mutations (dN/dS) has become a

238 is to identify sites with high ratios of non-synonymous to synonymous mutations; however, if synonymo

239 Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also s

240 on between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the

241 gn strategy to create 27 non-natural and non-synonymous transcription factors using the lactose repre

242 These data describe the first synonymous UPF3B mutation in a patient with prominent sp

243 estigated initially by interrogating a novel synonymous UPF3B variant in a male with absent speech.

244 i, and one new independent low-frequency non-synonymous variant in an established heart rate locus (K

245 + replication p = 6.38 x 10(-10)) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, d

246 We causally linked a non-synonymous variant in the conserved lipoyl domain of DBT

247 ur study reports the first likely pathogenic synonymous variant linked to DFNA10 and provide further

248 strongest enrichment for causality among non-synonymous variants (54x more likely to be causal, 1.4x

249 ), the association seems to be driven by non-synonymous variants (rs1426654, rs16891982, and rs104260

250 wo single-amino-acid deletions and three non-synonymous variants affecting conserved residues within

251 as also observed in association with two non-synonymous variants affecting the fibronectin type III d

252 ts per megabase (v/mb) for samples including synonymous variants and 3.883 +/- 1.38 v/mb for samples

253 s, predicting population-specific impacts of synonymous variants and categorizing genetic biases uniq

254 and 3.883 +/- 1.38 v/mb for samples without synonymous variants compared to tumor-normal paired call

255 We identified 7 rare non-synonymous variants in 7 of 20 genes and performed Sange

256 gnificant enrichment of rare and de novo non-synonymous variants in chromodomain (CHD) genes was obse

257 hypothetical and metabolic proteins, and non-synonymous variants in genes involved in adhesion, iron

258 We highlight the importance of rare synonymous variants in human physiology and argue for th

259 exomes from epilepsy family trios identifies synonymous variants in known epilepsy genes, thus pinpoi

260 frameshift and four different homozygous non-synonymous variants in NFASC.

261 Western HP strains contains a number of non-synonymous variants in relatively high frequencies which

262 and demonstrates how naturally occurring non-synonymous variants in RGS alter signaling.

263 d variants in four of the novel loci are non-synonymous variants in the genes C10orf71, DALDR3, TESK2

264 Affected individuals carrying de novo non-synonymous variants involving the C-terminal region pres

265 functionally characterized rare missense and synonymous variants of GPR39, a family A GPCR, revealing

266 annotated several thousand more reliable non-synonymous variants than other widely used tools (e.g. A

267 c or likely pathogenic, and a subset of rare synonymous variants that cause large changes in local co

268 We filtered rare non-synonymous variants that were predicted to be damaging t

269 hasia, and hypotonia in which homozygous non-synonymous variants were identified in IQSEC1 (GenBank:

270 We selected 520 non-synonymous variants with at least 7.5% frequency in the

271 ified gene-wide associations of uncommon non-synonymous variants within UBAP2 and STARD9.

272 riants (one stop-gain, five missense and six synonymous variants), two promoter variants, 133 introni

273 ds of molecular variation, from noncoding to synonymous variants, can make significant contributions

274 dies, identifying functional implications of synonymous variants, predicting population-specific impa

275 egions have similar effect sizes to those of synonymous variants, whereas pLoF variants in highly exp

276 It had long been presumed that synonymous variants, which, by definition, do not alter

277 gy models using 860,292 missense and 465,886 synonymous variants.

278 ified seven additional PDS/PG-associated non-synonymous variants.

279 controls as normalized by the level of rare synonymous variants.

280 ion against deleterious variants governs non-synonymous variation among very closely related populati

281 metrics to quantify gene-level constraint on synonymous variation, we discover that dosage-sensitive

282 gulated genes are particularly intolerant to synonymous variation.

283 tatic across the observation period; this is synonymous with a constant infection pressure from the s

284 It is also synonymous with a high chemical reactivity and low reduc

285 typical motile fish-pathogenic E. tarda are synonymous with Edwardsiella piscicida, while atypical n

286 incorrect perception that palliative care is synonymous with end-of-life care, with no role earlier i

287 n cancer, precision medicine has been nearly synonymous with genomics.

288 lidene)]]bis[propanedinitrile]), have become synonymous with high power conversion efficiencies (PCEs

289 sed on indacenodithiophene (IDT) have become synonymous with high power conversion efficiencies (PCEs

290 SPG2 (synonymous with IRREGULAR XYLEM9-LIKE [IRX9L]) encodes a

291 mune encephalomyelitis because NFM-deficient synonymous with knockout mice developed an identical dis

292 astly, we surveyed Clinvar variants that are synonymous with respect to the POLG ORF and found that m

293 ated with the acute sepsis event and are not synonymous with risk factors for community-associated at

294 We further demonstrate that AsCYP72A475 is synonymous with Sad6, a previously uncharacterized locus

295 arly dramatic at 18 degrees C, a temperature synonymous with that experienced by patients undergoing

296 Dopamine (DA) responses are synonymous with the 'reward prediction error' of reinfor

297 the clinical finding of a receded NPC is not synonymous with the diagnosis of convergence insufficien

298 dromic repeats' (CRISPR) has recently become synonymous with the genome-editing revolution.

299 ific responses in animal models, have become synonymous with the major histocompatibility complex (MH

300 rinuclear puncta in the cytoplasm, which are synonymous with viral inclusion bodies (IBs), the site f