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The current mutation

ID: V8517
DNA: 20397T>C
Protein: S6799S
Position: 20661








COV2Var annotation categories







Summary information of mutation (20397T>C)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1ab
  Gene Name   ORF1ab_pp1ab
  Gene Type   protein_coding
  Genome position   20661
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   synonymous_variant
  DNA Level   DNA Mutation: 20397T>C
  Ref Seq: T
  Mut Seq: C
  Protein Level   Protein 1-letter Mutation: S6799S
  Protein 3-letter Mutation: Ser6799Ser

Overview of the genomic positions of Mutation.
Note: The annotated 12 genes were retrieved from GeneBank (Accession: NC_045512.2). "MP" represents genomic position of mutation.





Analyzing the distribution of mutation (20397T>C) across geographic regions, temporal trends, and lineages

The count of genome sequences harboring this mutation and its distribution across global regions offer insights into regional variations.
Note: The distribution of mutation across 218 geographical regions. Color representation of genome sequence counts. The data is obtained from GISAID's metadata, specifically capturing the regional distribution of genomic sequences.



The dynamic count of genome sequences containing this mutation over time.
Note: Clicking the "Count" or "Cumulative Count" button toggles the view. Count represents the number of genome sequences per month. Cumulative count represents the accumulated total count up to the respective month. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.



For every time point represented in the graph above, identifying the top 3 lineages with the highest count of genome sequences carrying this mutation aids in pinpointing noteworthy lineages for further analysis.
Note: Users can filter the lineages by entering a "Year-Month" term in the search box. For example, entering 2020-01 will display lineages that appeared in January 2020. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.

Collection date Lineage Total lineage monthly counts Lineage-specific monthly counts Lineage-specific monthly frequency
2020-10 B.1.177 936 449 4.80e-1
2020-10 B.1.177.44 936 208 2.22e-1
2020-10 B.1.177.12 936 170 1.82e-1
2020-11 B.1.177.12 2110 753 3.57e-1
2020-11 B.1.177 2110 608 2.88e-1
2020-11 B.1.177.44 2110 374 1.77e-1
2020-12 B.1.177.12 4474 2405 5.38e-1
2020-12 B.1.177 4474 704 1.57e-1
2020-12 B.1.177.44 4474 444 9.92e-2
2020-03 B.1.177.12 1 1 1.00e+0
2020-06 B.1.177 2 1 5.00e-1
2020-06 B.1.240 2 1 5.00e-1
2020-07 B.1.177 2 1 5.00e-1
2020-07 B.1.240 2 1 5.00e-1
2020-08 B.1.177 192 127 6.61e-1
2020-08 B.1.177.44 192 62 3.23e-1
2020-08 B.1.177.12 192 1 5.21e-3
2020-09 B.1.177 458 303 6.62e-1
2020-09 B.1.177.44 458 69 1.51e-1
2020-09 B.1.177.12 458 60 1.31e-1
2021-01 B.1.177.12 5191 2184 4.21e-1
2021-01 B.1.177 5191 948 1.83e-1
2021-01 B.1.177.35 5191 722 1.39e-1
2021-10 AY.88 9 5 5.56e-1
2021-10 AY.103 9 1 1.11e-1
2021-10 AY.20 9 1 1.11e-1
2021-11 AY.122 8 2 2.50e-1
2021-11 AY.4 8 2 2.50e-1
2021-11 AY.103 8 1 1.25e-1
2021-12 AY.25.1.1 8 2 2.50e-1
2021-12 BA.1 8 2 2.50e-1
2021-12 AY.4.2.3 8 1 1.25e-1
2021-02 B.1.177 2216 932 4.21e-1
2021-02 B.1.177.12 2216 574 2.59e-1
2021-02 B.1.177.35 2216 344 1.55e-1
2021-03 B.1.177 677 263 3.88e-1
2021-03 B.1.177.12 677 199 2.94e-1
2021-03 B.1.177.35 677 71 1.05e-1
2021-04 B.1.177 96 42 4.38e-1
2021-04 B.1.177.12 96 35 3.65e-1
2021-04 B.1.177.41 96 9 9.38e-2
2021-05 B.1.177 11 11 1.00e+0
2021-06 AY.20 6 2 3.33e-1
2021-06 B.1.177.44 6 2 3.33e-1
2021-06 B.1.177 6 1 1.67e-1
2021-07 AY.20 4 2 5.00e-1
2021-07 AY.4 4 1 2.50e-1
2021-07 P.1 4 1 2.50e-1
2021-08 AY.14 15 10 6.67e-1
2021-08 AY.4 15 3 2.00e-1
2021-08 AY.122 15 1 6.67e-2
2021-09 AY.14 15 9 6.00e-1
2021-09 AY.88 15 3 2.00e-1
2021-09 AY.20 15 1 6.67e-2
2022-01 BA.1.1 15 9 6.00e-1
2022-01 BA.1 15 4 2.67e-1
2022-01 BA.1.21 15 2 1.33e-1
2022-10 BF.7 1 1 1.00e+0
2022-11 BN.1.3 1 1 1.00e+0
2022-12 BN.1.3 8 7 8.75e-1
2022-12 BQ.1.3 8 1 1.25e-1
2022-02 BA.1.1 11 8 7.27e-1
2022-02 BA.1.21 11 2 1.82e-1
2022-02 BA.2 11 1 9.09e-2
2022-03 BA.1.1 15 4 2.67e-1
2022-03 BA.2.12 15 4 2.67e-1
2022-03 BA.2.9 15 4 2.67e-1
2022-04 BA.2.12 12 7 5.83e-1
2022-04 BA.2 12 4 3.33e-1
2022-04 BA.1.1 12 1 8.33e-2
2022-05 BA.2.12 2 2 1.00e+0
2022-07 BF.5 5 3 6.00e-1
2022-07 BA.2.18 5 1 2.00e-1
2022-07 BA.5 5 1 2.00e-1
2022-08 BF.5 6 3 5.00e-1
2022-08 BA.2.76 6 1 1.67e-1
2022-08 BA.4.6 6 1 1.67e-1
2023-01 XBF 10 6 6.00e-1
2023-01 XBB.1.5 10 2 2.00e-1
2023-01 BQ.1.1.32 10 1 1.00e-1
2023-02 XBF 10 9 9.00e-1
2023-02 XBB.1.5 10 1 1.00e-1

The count of genome sequences and the frequency of this mutation in each lineage.
Note: Displaying mutation frequencies (>0.01) among 2,735 lineages. Mutation Count represents the count of sequences carrying this mutation. Users can filter the lineages by entering a search term in the search box. For example, entering "A.1" will display A.1 lineages. The data is obtained from GISAID's metadata, specifically capturing the lineage of genomic sequences. Mutation count: Count of sequences carrying this mutation.

Mutation ID Lineage Mutation frequency Mutation count Earliest lineage emergence Latest lineage emergence
V8517 B.1.177.35 9.57e-1 1487 2020-10-17 2021-4-23
V8517 B.1.177.42 9.99e-1 855 2020-10-26 2021-3-22
V8517 B.1.177.43 9.71e-1 605 2020-8-17 2021-12-29
V8517 B.1.177.44 9.70e-1 1742 2020-8-7 2021-6-7
V8517 B.1.177.12 9.97e-1 6382 2020-3-30 2021-4-12
V8517 B.1.177 6.13e-2 4390 2020-2-2 2022-5-25
V8517 B.1.160.10 1.69e-2 2 2020-8-27 2021-2-20
V8517 B.1.160.32 1.09e-2 2 2020-10-2 2021-1-26
V8517 B.1.177.31 3.94e-1 13 2020-8-24 2021-2-3
V8517 B.1.177.36 9.48e-1 55 2020-9-14 2021-3-2
V8517 B.1.177.37 1.00e+0 34 2020-10-12 2021-2-25
V8517 B.1.177.38 1.00e+0 93 2020-9-11 2021-3-17
V8517 B.1.177.39 1.00e+0 59 2020-10-5 2021-3-2
V8517 B.1.177.40 9.88e-1 170 2020-10-14 2021-3-10
V8517 B.1.177.41 9.92e-1 368 2020-9-20 2021-4-24






Examining mutation (20397T>C) found in abundant sequences of non-human animal hosts

Exploring mutation presence across 35 non-human animal hosts for cross-species transmission.
Note: We retained the mutation that appear in at least three non-human animal hosts' sequences. The data is obtained from GISAID's metadata, specifically capturing the host of genomic sequences.

Animal host Lineage Source region Collection date Accession ID




Association between mutation (20397T>C) and patients of different ages, genders, and statuses

Note: The logistic regression model was employed to examine changes in patient data before and after the mutation. The logistic regression model was conducted using the glm function in R. The data is obtained from GISAID's metadata, specifically capturing the patient status, gender, and age of genomic sequences.

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient statuses (ambulatory, deceased, homebound, hospitalized, mild, and recovered) based on GISAID classifications. In the analysis exploring the association between mutation and patient status, the model included mutation, patient status, patient age, gender, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient status Ambulatory 8.33e+0 2.96e+0 2.82e+0 4.85e-3 Increase
Deceased -6.67e-1 7.70e-1 -8.66e-1 3.87e-1 Decrease
Homebound -1.50e+1 1.70e+3 -8.80e-3 9.93e-1 Decrease
Hospitalized 1.25e+0 3.95e-1 3.16e+0 1.55e-3 Increase
Mild -8.89e-1 1.21e+0 -7.36e-1 4.62e-1 Decrease
Recovered -2.42e+0 6.79e-1 -3.57e+0 3.59e-4 Decrease

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient age (0-17, 18-39, 40-64, 65-84, and 85+). In the analysis exploring the association between mutation and patient age, the model included mutation, patient age, gender, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient age, years 0-17 -1.14e-1 1.06e-1 -1.07e+0 2.84e-1 Decrease
18-39 -1.35e-2 6.41e-2 -2.10e-1 8.34e-1 Decrease
40-64 6.18e-2 5.83e-2 1.06e+0 2.90e-1 Increase
65-84 -4.25e-2 7.14e-2 -5.95e-1 5.52e-1 Decrease
>=85 3.95e-2 9.66e-2 4.09e-1 6.83e-1 Increase

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient gender (male and female). In the analysis exploring the association between mutation and patient gender, the model included mutation, patient gender, patient age, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient gender Male -1.00e-1 5.66e-2 -1.77e+0 7.66e-2 Decrease





Investigating natural selection at mutation (20397T>C) site for genetic adaptation and diversity

Note: Investigating the occurrence of positive selection or negative selection at this mutation site reveals implications for genetic adaptation and diversity.

The MEME method within the HyPhy software was employed to analyze positive selection. MEME: episodic selection.
Note: List of sites found to be under episodic selection by MEME (p < 0.05). "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site P-value Lineage Method

The FEL method within the HyPhy software was employed to analyze both positive and negative selection. FEL: pervasive selection on samll datasets.
Note: List of sites found to be under pervasive selection by FEL (p < 0.05). A beta value greater than alpha signifies positive selection, while a beta value smaller than alpha signifies negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Alpha Beta P-value Lineage Method

The FUBAR method within the HyPhy software was employed to analyze both positive and negative selection. FUBAR: pervasive selection on large datasets.
Note: List of sites found to be under pervasive selection by FUBAR (prob > 0.95). A prob[alpha < beta] value exceeding 0.95 indicates positive selection, while a prob[alpha > beta] value exceeding 0.95 indicates negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Prob[alpha>beta] Prob[alpha<beta] Lineage Method




Alterations in protein physicochemical properties induced by mutation (20397T>C)

Understanding the alterations in protein physicochemical properties can reveal the evolutionary processes and adaptive changes of viruses
Note: ProtParam software was used for the analysis of physicochemical properties. Significant change threshold: A change exceeding 10% compared to the reference is considered a significant change. "GRAVY" is an abbreviation for "grand average of hydropathicity".

Group Protein name Molecular weight Theoretical PI Extinction coefficients Aliphatic index GRAVY




Alterations in protein stability induced by mutation (20397T>C)

The impact of mutations on protein stability directly or indirectly affects the biological characteristics, adaptability, and transmission capacity of the virus
Note: iMutant 2.0 was utilized to analyze the effects of mutations on protein stability. pH 7 and a temperature of 25°C are employed to replicate the in vitro environment. pH 7.4 and a temperature of 37°C are utilized to simulate the in vivo environment.

Mutation Protein name Mutation type Position ΔDDG Stability pH Temperature Condition




Impact on protein function induced by mutation (20397T>C)

The impact of mutations on protein function
Note: The MutPred2 software was used to predict the pathogenicity of a mutation and gives the molecular mechanism of pathogenicity. A score above 0.5 indicates an increased likelihood of pathogenicity. "Pr" is the abbreviation for "proportion. P" is the abbreviation for "p-value.

Mutation Protein name Mutation type Score Molecular mechanisms




Exploring mutation (20397T>C) distribution within intrinsically disordered protein regions

Intrinsically Disordered Proteins (IDPs) which refers to protein regions that have no unique 3D structure. In viral proteins, mutations in the disordered regions s are critical for immune evasion and antibody escape, suggesting potential additional implications for vaccines and monoclonal therapeutic strategies.
Note: The iupred3 software was utilized for analyzing IDPs. A score greater than 0.5 is considered indicative of an IDP. In the plot, "POS" represents the position of the mutation.





Alterations in enzyme cleavage sites induced by mutation (20397T>C)

Exploring the impact of mutations on the cleavage sites of 28 enzymes.
Note: The PeptideCutter software was used for detecting enzymes cleavage sites. The increased enzymes cleavage sites refer to the cleavage sites in the mutated protein that are added compared to the reference protein. Conversely, the decreased enzymes cleavage sites indicate the cleavage sites in the mutated protein that are reduced compared to the reference protein.

Mutation Protein name Genome position Enzyme name Increased cleavage sites Decreased cleavage sites




Impact of spike protein mutation (20397T>C) on antigenicity and immunogenicity

Investigating the impact of mutations on antigenicity and immunogenicity carries important implications for vaccine design and our understanding of immune responses.
Note: An absolute change greater than 0.0102 (three times the median across sites) in antigenicity score is considered significant. An absolute changegreater than 0.2754 (three times the median across sites) in immunogenicity score is considered significant. The VaxiJen tool was utilized for antigenicity analysis. The IEDB tool was used for immunogenicity analysis. Antigens with a prediction score of more than 0.4 for this tool are considered candidate antigens. MHC I immunogenicity score >0, indicating a higher probability to stimulate an immune response.

Group Protein name Protein region Antigenicity score Immunogenicity score




Impact of mutation (20397T>C) on viral transmissibility by the affinity between RBD and ACE2 receptor

Unraveling the impact of mutations on the interaction between the receptor binding domain (RBD) and ACE2 receptor using deep mutational scanning (DMS) experimental data to gain insights into their effects on viral transmissibility.
Note: The ΔBinding affinity represents the disparity between the binding affinity of a mutation and the reference binding affinity. A positive Δbinding affinity value (Δlog10(KD,app) > 0) signifies an increased affinity between RBD and ACE2 receptor due to the mutation. Conversely, a negative value (Δlog10(KD,app) < 0) indicates a reduced affinity between RBD and ACE2 receptor caused by the mutation. A p-value smaller than 0.05 indicates significance. "Ave mut bind" represents the average binding affinity of this mutation. "Ave ref bind" refers to the average binding affinity at a site without any mutation (reference binding affinity).

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Mutation Protein name Protein region Mutation Position Ave mut bind Ave ref bind ΔBinding affinity P-value Image


The interface between the receptor binding domain (RBD) and ACE2 receptor is depicted in the crystal structure 6JM0.
Note: The structure 6M0J encompasses the RBD range of 333 to 526. The binding sites (403-406, 408, 417, 439, 445-447, 449, 453, 455-456, 473-478, 484-498, and 500-506) on the RBD that interface with ACE2 are indicated in magenta. The binding sites on the RBD that have been identified through the interface footprints experiment. The ACE2 binding sites within the interface are shown in cyan, representing residues within 5Å proximity to the RBD binding sites. The mutation within the RBD range of 333 to 526 is depicted in red.

        Show as:

        Show interface residues:





Impact of mutation (20397T>C) on immune escape by the affinity between RBD and antibody/serum

By utilizing experimental data from deep mutational scanning (DMS), we can uncover how mutations affect the interaction between the receptor binding domain (RBD) and antibodies/serum. This approach provides valuable insights into strategies for evading the host immune response.
Note: We considered a mutation to mediate strong escape if the escape score exceeded 0.1 (10% of the maximum score of 1). A total of 1,504 antibodies/serum data were collected for this analysis. "Condition name" refers to the name of the antibodies/serum. "Mut escape score" represents the escape score of the mutation in that specific condition. "Avg mut escape score" indicates the average escape score of the mutation site in that condition, considering the occurrence of this mutation and other mutations. Class 1 antibodies bind to an epitope only in the RBD “up” conformation, and are the most abundant. Class 2 antibodies bind to the RBD both in “up” and “down” conformations. Class 3 and class 4 antibodies both bind outside the ACE2 binding site. Class 3 antibodies bind the RBD in both the open and closed conformation, while class 4 antibodies bind only in the open conformation.

Mutation Condition name Condition type Condition subtype Condition year Mut escape score Avg mut escape score




Investigating the co-mutation patterns of mutation (20397T>C) across 2,735 viral lineages

Investigating the co-mutation patterns of SARS-CoV-2 across 2,735 viral lineages to unravel the cooperative effects of different mutations. In biological research, correlation analysis of mutation sites helps us understand whether there is a close relationship or interaction between certain mutations.
Note: The Spearman correlation coefficient is used to calculate the correlation between two mutations within each Pango lineage. Holm–Bonferroni method was used for multiple test adjustment. We retained mutation pairs with correlation values greater than 0.6 or less than -0.6 and Holm–Bonferroni corrected p-values less than 0.05.

Associated mutation ID DNA mutation Mutation type Protein name Protein mutation correlation coefficient Lineage
V5600 1093C>T missense_variant N P365S 7.47e-1 B.1.177
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 8.15e-1 B.1.177
V9790 1113C>T synonymous_variant N D371D 9.59e-1 B.1.177
V1626 7034C>T missense_variant ORF1ab_pp1a A2345V 6.07e-1 AY.20
V392 997A>G missense_variant ORF1ab_pp1a T333A 8.33e-1 B.1.429
V5329 118C>T missense_variant N R40C 1.00e+0 AY.79
V6219 2445C>T synonymous_variant ORF1ab_pp1a L815L 1.00e+0 AY.88
V7358 11409C>T synonymous_variant ORF1ab_pp1a Y3803Y 1.00e+0 AY.88
V1828 8507C>T missense_variant ORF1ab_pp1a T2836I 7.06e-1 B.1.1.141
V5575 976C>T missense_variant N P326S 7.06e-1 B.1.1.141
V9287 15C>T synonymous_variant M N5N 7.06e-1 B.1.1.141
V3508 21204G>T missense_variant ORF1ab_pp1ab M7068I 1.00e+0 B.1.1.189
V5505 659C>T missense_variant N A220V 1.00e+0 B.1.1.189
V5600 1093C>T missense_variant N P365S 1.00e+0 B.1.1.189
V5713 88G>T missense_variant ORF10 V30L 1.00e+0 B.1.1.189
V5866 180T>C synonymous_variant ORF1ab_pp1a V60V 1.00e+0 B.1.1.189
V6689 6021C>T synonymous_variant ORF1ab_pp1a T2007T 1.00e+0 B.1.1.189
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.189
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 1.00e+0 B.1.1.189
V9322 279C>G synonymous_variant M L93L 1.00e+0 B.1.1.189
V9790 1113C>T synonymous_variant N D371D 1.00e+0 B.1.1.189
V2182 11114C>T missense_variant ORF1ab_pp1a A3705V 7.07e-1 B.1.1.39
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 7.07e-1 B.1.1.39
V3748 665C>T missense_variant S A222V 6.32e-1 B.1.1.39
V4796 3G>T start_lost ORF6 M1? 7.07e-1 B.1.1.39
V5505 659C>T missense_variant N A220V 7.07e-1 B.1.1.39
V5600 1093C>T missense_variant N P365S 1.00e+0 B.1.1.39
V5713 88G>T missense_variant ORF10 V30L 6.32e-1 B.1.1.39
V6689 6021C>T synonymous_variant ORF1ab_pp1a T2007T 6.32e-1 B.1.1.39
V8436 19620C>T synonymous_variant ORF1ab_pp1ab Y6540Y 7.07e-1 B.1.1.39
V8886 1989C>T synonymous_variant S D663D 7.07e-1 B.1.1.39
V9322 279C>G synonymous_variant M L93L 7.07e-1 B.1.1.39
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 6.52e-1 B.1.160
V2182 11114C>T missense_variant ORF1ab_pp1a A3705V 1.00e+0 B.1.1.70
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 1.00e+0 B.1.1.70
V4390 148G>A missense_variant ORF3a V50I 1.00e+0 B.1.1.70
V5505 659C>T missense_variant N A220V 1.00e+0 B.1.1.70
V5600 1093C>T missense_variant N P365S 1.00e+0 B.1.1.70
V8300 18540C>T synonymous_variant ORF1ab_pp1ab S6180S 1.00e+0 B.1.1.70
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 7.07e-1 B.1.1.70
V9322 279C>G synonymous_variant M L93L 1.00e+0 B.1.1.70
V9790 1113C>T synonymous_variant N D371D 1.00e+0 B.1.1.70
V3508 21204G>T missense_variant ORF1ab_pp1ab M7068I 8.94e-1 B.1.177.17
V5628 1148C>T missense_variant N P383L 7.74e-1 B.1.177.17
V6170 2151C>T synonymous_variant ORF1ab_pp1a Y717Y 8.94e-1 B.1.177.17
V6457 4305C>T synonymous_variant ORF1ab_pp1a I1435I 8.94e-1 B.1.177.17
V7505 12519C>T synonymous_variant ORF1ab_pp1a N4173N 7.74e-1 B.1.177.17
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.177.17
V9790 1113C>T synonymous_variant N D371D 8.94e-1 B.1.177.17
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 6.32e-1 B.1.177.43
V6170 2151C>T synonymous_variant ORF1ab_pp1a Y717Y 1.00e+0 B.1.214.2
V677 2041C>T missense_variant ORF1ab_pp1a L681F 1.00e+0 B.1.214.2
V2927 17254C>T missense_variant ORF1ab_pp1ab L5752F 6.42e-1 B.1.221
V3785 770G>A missense_variant S G257D 9.82e-1 B.1.221
V4919 186_188delATT disruptive_inframe_deletion ORF7a Q62_F63delinsH 9.31e-1 B.1.221
V5505 659C>T missense_variant N A220V 8.50e-1 B.1.221
V5600 1093C>T missense_variant N P365S 9.16e-1 B.1.221
V5601 1094C>T missense_variant N P365L 8.38e-1 B.1.221
V5713 88G>T missense_variant ORF10 V30L 6.00e-1 B.1.221
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 7.78e-1 B.1.221
V9117 3690G>T synonymous_variant S V1230V 9.64e-1 B.1.221
V9322 279C>G synonymous_variant M L93L 8.62e-1 B.1.221
V9790 1113C>T synonymous_variant N D371D 9.47e-1 B.1.221
V6467 4368C>T synonymous_variant ORF1ab_pp1a G1456G 6.67e-1 B.1.258
V3508 21204G>T missense_variant ORF1ab_pp1ab M7068I 1.00e+0 B.1.36
V5505 659C>T missense_variant N A220V 1.00e+0 B.1.36
V9322 279C>G synonymous_variant M L93L 7.07e-1 B.1.36
V6176 2184C>T synonymous_variant ORF1ab_pp1a G728G 7.07e-1 B.1.565
V7263 10521A>G synonymous_variant ORF1ab_pp1a Q3507Q 8.89e-1 BA.2.12
V5368 307G>T missense_variant N D103Y 7.07e-1 BA.2.18
V7607 13251C>T synonymous_variant ORF1ab_pp1ab G4417G 7.07e-1 BA.2.18
V1220 4702A>G missense_variant ORF1ab_pp1a I1568V 1.00e+0 BA.5.2.21
V2088 10628C>T missense_variant ORF1ab_pp1a T3543I 1.00e+0 BQ.1.1.32
V4564 578G>T missense_variant ORF3a W193L 7.07e-1 BQ.1.1.32
V8034 16605C>T synonymous_variant ORF1ab_pp1ab Y5535Y 1.00e+0 BQ.1.1.32
V4366 119C>T missense_variant ORF3a S40L 8.66e-1 XBF
V5369 337C>A missense_variant N L113I 9.68e-1 XBF
V7993 16257T>C synonymous_variant ORF1ab_pp1ab N5419N 9.68e-1 XBF
V8001 16311C>T synonymous_variant ORF1ab_pp1ab D5437D 1.00e+0 AY.25.1.1
V3508 21204G>T missense_variant ORF1ab_pp1ab M7068I 1.00e+0 B.1.1.521
V3748 665C>T missense_variant S A222V 7.05e-1 B.1.1.521
V5505 659C>T missense_variant N A220V 7.05e-1 B.1.1.521
V5600 1093C>T missense_variant N P365S 1.00e+0 B.1.1.521
V5713 88G>T missense_variant ORF10 V30L 7.05e-1 B.1.1.521
V5866 180T>C synonymous_variant ORF1ab_pp1a V60V 7.05e-1 B.1.1.521
V6170 2151C>T synonymous_variant ORF1ab_pp1a Y717Y 1.00e+0 B.1.1.521
V6689 6021C>T synonymous_variant ORF1ab_pp1a T2007T 7.05e-1 B.1.1.521
V8429 19575T>C synonymous_variant ORF1ab_pp1ab N6525N -7.05e-1 B.1.1.521
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.521
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 1.00e+0 B.1.1.521
V9322 279C>G synonymous_variant M L93L 7.05e-1 B.1.1.521
V9790 1113C>T synonymous_variant N D371D 1.00e+0 B.1.1.521
V1935 9261G>T missense_variant ORF1ab_pp1a M3087I -6.24e-1 B.1.160.10
V2182 11114C>T missense_variant ORF1ab_pp1a A3705V 1.00e+0 B.1.160.10
V2329 12194C>T missense_variant ORF1ab_pp1a T4065I -7.01e-1 B.1.160.10
V2536 13729G>T missense_variant ORF1ab_pp1ab A4577S -8.13e-1 B.1.160.10
V2723 15502G>T missense_variant ORF1ab_pp1ab V5168L -8.13e-1 B.1.160.10
V2836 16625A>G missense_variant ORF1ab_pp1ab K5542R -8.13e-1 B.1.160.10
V2857 16755G>T missense_variant ORF1ab_pp1ab E5585D -8.13e-1 B.1.160.10
V2990 17735C>T missense_variant ORF1ab_pp1ab T5912I -8.13e-1 B.1.160.10
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 1.00e+0 B.1.160.10
V3748 665C>T missense_variant S A222V 1.00e+0 B.1.160.10
V3896 1430G>A missense_variant S S477N -6.24e-1 B.1.160.10
V4390 148G>A missense_variant ORF3a V50I 1.00e+0 B.1.160.10
V4406 171G>T missense_variant ORF3a Q57H -1.00e+0 B.1.160.10
V460 1249C>T missense_variant ORF1ab_pp1a H417Y -6.24e-1 B.1.160.10
V5505 659C>T missense_variant N A220V 1.00e+0 B.1.160.10
V5512 702G>C missense_variant N M234I -6.24e-1 B.1.160.10
V5600 1093C>T missense_variant N P365S 1.00e+0 B.1.160.10
V5713 88G>T missense_variant ORF10 V30L 1.00e+0 B.1.160.10
V5866 180T>C synonymous_variant ORF1ab_pp1a V60V 1.00e+0 B.1.160.10
V6454 4278C>T synonymous_variant ORF1ab_pp1a T1426T -7.01e-1 B.1.160.10
V6689 6021C>T synonymous_variant ORF1ab_pp1a T2007T 1.00e+0 B.1.160.10
V7336 11232C>T synonymous_variant ORF1ab_pp1a Y3744Y -8.13e-1 B.1.160.10
V8300 18540C>T synonymous_variant ORF1ab_pp1ab S6180S 1.00e+0 B.1.160.10
V8315 18613C>T synonymous_variant ORF1ab_pp1ab L6205L -8.13e-1 B.1.160.10
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.160.10
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 1.00e+0 B.1.160.10
V9195 318C>T synonymous_variant ORF3a L106L -7.01e-1 B.1.160.10
V9314 213C>T synonymous_variant M Y71Y -1.00e+0 B.1.160.10
V9322 279C>G synonymous_variant M L93L 1.00e+0 B.1.160.10
V9339 354T>C synonymous_variant M I118I -8.13e-1 B.1.160.10
V9790 1113C>T synonymous_variant N D371D 1.00e+0 B.1.160.10
V3508 21204G>T missense_variant ORF1ab_pp1ab M7068I 1.00e+0 B.1.160.30
V5505 659C>T missense_variant N A220V 7.05e-1 B.1.160.30
V5600 1093C>T missense_variant N P365S 1.00e+0 B.1.160.30
V6170 2151C>T synonymous_variant ORF1ab_pp1a Y717Y 1.00e+0 B.1.160.30
V9790 1113C>T synonymous_variant N D371D 1.00e+0 B.1.160.30
V2182 11114C>T missense_variant ORF1ab_pp1a A3705V 1.00e+0 B.1.160.32
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 1.00e+0 B.1.160.32
V3748 665C>T missense_variant S A222V 8.14e-1 B.1.160.32
V4796 3G>T start_lost ORF6 M1? 1.00e+0 B.1.160.32
V5505 659C>T missense_variant N A220V 1.00e+0 B.1.160.32
V5600 1093C>T missense_variant N P365S 1.00e+0 B.1.160.32
V5627 1147C>T missense_variant N P383S 1.00e+0 B.1.160.32
V5713 88G>T missense_variant ORF10 V30L 7.03e-1 B.1.160.32
V5866 180T>C synonymous_variant ORF1ab_pp1a V60V 8.14e-1 B.1.160.32
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 8.14e-1 B.1.160.32
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 1.00e+0 B.1.160.32
V9322 279C>G synonymous_variant M L93L 7.03e-1 B.1.160.32
V9790 1113C>T synonymous_variant N D371D 1.00e+0 B.1.160.32
V3508 21204G>T missense_variant ORF1ab_pp1ab M7068I 1.00e+0 B.1.177.23
V5600 1093C>T missense_variant N P365S 1.00e+0 B.1.177.23
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.177.23
V9790 1113C>T synonymous_variant N D371D 1.00e+0 B.1.177.23
V53 -80C>T upstream_gene_variant ORF1ab_pp1a None -7.05e-1 B.1.177.40
V531 1555G>A missense_variant ORF1ab_pp1a G519S -7.05e-1 B.1.177.40
V4011 2025G>T missense_variant S Q675H 1.00e+0 B.1.177.89
V5281 53G>T missense_variant N G18V 1.00e+0 B.1.177.89
V6170 2151C>T synonymous_variant ORF1ab_pp1a Y717Y 1.00e+0 B.1.177.89
V6265 2772C>T synonymous_variant ORF1ab_pp1a F924F -1.00e+0 B.1.177.89
V1571 6689T>C missense_variant ORF1ab_pp1a I2230T 1.00e+0 B.1.1.83
V2536 13729G>T missense_variant ORF1ab_pp1ab A4577S 1.00e+0 B.1.1.83
V3950 1709C>A missense_variant S A570D 1.00e+0 B.1.1.83
V5248 7G>C missense_variant N D3H 1.00e+0 B.1.1.83
V5250 8A>T missense_variant N D3V 1.00e+0 B.1.1.83
V5251 9T>A missense_variant N D3E 1.00e+0 B.1.1.83
V5514 704C>T missense_variant N S235F 7.06e-1 B.1.1.83
V5954 648C>T synonymous_variant ORF1ab_pp1a S216S 1.00e+0 B.1.1.83
V7758 14412C>T synonymous_variant ORF1ab_pp1ab P4804P 7.06e-1 B.1.1.83
V7836 15015C>T synonymous_variant ORF1ab_pp1ab H5005H 1.00e+0 B.1.1.83
V7948 15912T>C synonymous_variant ORF1ab_pp1ab T5304T 7.06e-1 B.1.1.83
V3104 18410G>A missense_variant ORF1ab_pp1ab R6137K 1.00e+0 B.1.36.9





Manual curation of mutation (20397T>C)-related literature from PubMed

The pubmed.mineR and pubmed-mapper were utilized for extracting literature from PubMed, followed by manual filtering.
Note: PubMed: (COVID-19 [Title/Abstract] OR SARS-COV-2 [Title/Abstract]) AND (DNA mutation [Title/Abstract] OR Protein mutation-1 letter [Title/Abstract] OR Protein mutation-3 letter [Title/Abstract]).

DNA level Protein level Paper title Journal name Publication year Pubmed ID