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The current mutation

ID: V3378
DNA: 20291C>T
Protein: S6764F
Position: 20555








COV2Var annotation categories







Summary information of mutation (20291C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1ab
  Gene Name   ORF1ab_pp1ab
  Gene Type   protein_coding
  Genome position   20555
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 20291C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: S6764F
  Protein 3-letter Mutation: Ser6764Phe

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 (20291C>T) 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.1.1.312 22 4 1.82e-1
2020-10 B.1.1.431 22 4 1.82e-1
2020-10 B.1.36 22 4 1.82e-1
2020-11 B.1.1.312 20 4 2.00e-1
2020-11 B.1.177 20 4 2.00e-1
2020-11 B.1.240 20 4 2.00e-1
2020-12 B.1.36.24 39 19 4.87e-1
2020-12 B.1.36.29 39 5 1.28e-1
2020-12 B.1.1.337 39 4 1.03e-1
2020-03 B.1 9 5 5.56e-1
2020-03 A.1 9 2 2.22e-1
2020-03 B.1.1 9 1 1.11e-1
2020-04 B.1 25 11 4.40e-1
2020-04 B.1.1 25 7 2.80e-1
2020-04 B.1.1.164 25 2 8.00e-2
2020-05 B.1.1 23 15 6.52e-1
2020-05 B.1 23 5 2.17e-1
2020-05 B.1.1.266 23 2 8.70e-2
2020-06 B.1.287 61 22 3.61e-1
2020-06 B.1.1 61 21 3.44e-1
2020-06 B.1 61 16 2.62e-1
2020-07 B.1.287 23 7 3.04e-1
2020-07 B.1.1.299 23 6 2.61e-1
2020-07 B.1.36.29 23 3 1.30e-1
2020-08 B.1.36.29 24 7 2.92e-1
2020-08 B.1.280 24 5 2.08e-1
2020-08 B.1 24 3 1.25e-1
2020-09 B.1 26 14 5.38e-1
2020-09 B.1.36 26 4 1.54e-1
2020-09 B.1.1.135 26 2 7.69e-2
2021-01 B.1.36.24 76 19 2.50e-1
2021-01 B.1.2 76 11 1.45e-1
2021-01 B.1.1.519 76 6 7.89e-2
2021-10 AY.4 784 139 1.77e-1
2021-10 AY.44 784 131 1.67e-1
2021-10 AY.103 784 105 1.34e-1
2021-11 AY.44 993 315 3.17e-1
2021-11 AY.103 993 148 1.49e-1
2021-11 AY.4 993 122 1.23e-1
2021-12 AY.44 780 199 2.55e-1
2021-12 B.1.617.2 780 115 1.47e-1
2021-12 AY.103 780 96 1.23e-1
2021-02 B.1.1.7 47 8 1.70e-1
2021-02 B.1.36.29 47 5 1.06e-1
2021-02 B.1.160 47 4 8.51e-2
2021-03 B.1.1.7 72 43 5.97e-1
2021-03 B.1.2 72 6 8.33e-2
2021-03 B.1.429 72 4 5.56e-2
2021-04 B.1.1.7 104 86 8.27e-1
2021-04 B.1.1.519 104 5 4.81e-2
2021-04 B.1.2 104 3 2.88e-2
2021-05 B.1.1.7 45 29 6.44e-1
2021-05 AY.102 45 4 8.89e-2
2021-05 B.1.1.519 45 2 4.44e-2
2021-06 AY.102 50 14 2.80e-1
2021-06 AY.4 50 10 2.00e-1
2021-06 AY.39 50 7 1.40e-1
2021-07 B.1.617.2 254 111 4.37e-1
2021-07 AY.122 254 16 6.30e-2
2021-07 AY.29 254 16 6.30e-2
2021-08 AY.25.1 601 118 1.96e-1
2021-08 AY.9.2 601 72 1.20e-1
2021-08 B.1.617.2 601 72 1.20e-1
2021-09 B.1.617.2 624 124 1.99e-1
2021-09 AY.4 624 87 1.39e-1
2021-09 AY.25.1 624 60 9.62e-2
2022-01 B.1.617.2 154 26 1.69e-1
2022-01 BA.1 154 19 1.23e-1
2022-01 AY.44 154 15 9.74e-2
2022-10 BQ.1.14 17 7 4.12e-1
2022-10 BF.5 17 4 2.35e-1
2022-10 BE.1.1 17 2 1.18e-1
2022-11 BQ.1.14 16 8 5.00e-1
2022-11 BM.2.1 16 3 1.88e-1
2022-11 BQ.1.1.32 16 2 1.25e-1
2022-12 BQ.1.14 16 5 3.12e-1
2022-12 BQ.1.1.18 16 4 2.50e-1
2022-12 BQ.1.1 16 2 1.25e-1
2022-02 BA.1.1 74 39 5.27e-1
2022-02 BA.1.1.12 74 7 9.46e-2
2022-02 BA.1.15 74 6 8.11e-2
2022-03 BA.2 28 13 4.64e-1
2022-03 BA.1.1 28 8 2.86e-1
2022-03 BA.1.15 28 2 7.14e-2
2022-04 BA.2 12 9 7.50e-1
2022-04 BA.2.10 12 1 8.33e-2
2022-04 BA.2.3 12 1 8.33e-2
2022-05 BA.2 9 4 4.44e-1
2022-05 BA.2.3.13 9 3 3.33e-1
2022-05 BA.2.9 9 1 1.11e-1
2022-06 BA.2.3.13 15 3 2.00e-1
2022-06 BA.2 15 2 1.33e-1
2022-06 BA.5.3.4 15 2 1.33e-1
2022-07 BA.2.3.13 11 3 2.73e-1
2022-07 BA.5.3.4 11 2 1.82e-1
2022-07 BA.4.4 11 1 9.09e-2
2022-08 BF.5 13 7 5.38e-1
2022-08 BA.5.2.2 13 1 7.69e-2
2022-08 BA.5.2.28 13 1 7.69e-2
2022-09 BA.5 6 1 1.67e-1
2022-09 BA.5.1.23 6 1 1.67e-1
2022-09 BA.5.1.24 6 1 1.67e-1
2023-01 XBB.1.5 15 3 2.00e-1
2023-01 BQ.1.11 15 2 1.33e-1
2023-01 BR.2.1 15 2 1.33e-1
2023-02 XBF 5 2 4.00e-1
2023-02 BQ.1.1.23 5 1 2.00e-1
2023-02 XBB.1.5 5 1 2.00e-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
V3378 AY.75.3 2.08e-2 10 2021-5-17 2021-9-30
V3378 B.1.1.299 4.00e-2 3 2020-5-22 2020-7-16
V3378 B.1.1.431 3.51e-2 2 2020-6-5 2020-10-20
V3378 B.1.160.18 1.48e-2 2 2020-11-10 2021-3-10
V3378 B.1.177.89 7.69e-2 4 2020-11-21 2021-3-2
V3378 B.1.280 3.94e-2 5 2020-6-27 2021-1-30
V3378 B.1.287 9.67e-1 29 2020-6-2 2020-7-20
V3378 B.1.36.24 2.72e-1 40 2020-6-4 2021-5-27
V3378 B.1.36.29 1.17e-2 28 2020-6-21 2021-11-1
V3378 B.1.478 2.38e-2 3 2020-5-15 2021-3-5
V3378 BM.2.1 4.27e-2 5 2022-7-27 2023-1-31






Examining mutation (20291C>T) 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 (20291C>T) 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 7.49e-17 2.55e+5 2.94e-22 1.00e+0 Increase
Deceased 4.16e-1 5.27e+4 7.89e-6 1.00e+0 Increase
Homebound 7.49e-17 2.55e+5 2.94e-22 1.00e+0 Increase
Hospitalized 1.53e+1 1.66e+3 9.21e-3 9.93e-1 Increase
Mild -1.43e+1 9.78e+2 -1.46e-2 9.88e-1 Decrease
Recovered 6.53e-1 1.22e+4 5.35e-5 1.00e+0 Increase

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 -1.52e+1 5.05e+2 -3.00e-2 9.76e-1 Decrease
18-39 -4.97e-1 2.93e-1 -1.69e+0 9.06e-2 Decrease
40-64 2.54e-1 2.74e-1 9.28e-1 3.53e-1 Increase
65-84 1.32e+0 3.74e-1 3.53e+0 4.12e-4 Increase
>=85 -1.44e+1 8.11e+2 -1.78e-2 9.86e-1 Decrease

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 9.21e-1 3.20e-1 2.88e+0 3.95e-3 Increase





Investigating natural selection at mutation (20291C>T) 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 (20291C>T)

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
Mutation ORF1ab_pp1ab 794117.89 6.32 928150 86.87 -0.07
Reference ORF1ab_pp1ab 794057.79 6.32 928150 86.87 -0.07




Alterations in protein stability induced by mutation (20291C>T)

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
S6764F ORF1ab_pp1ab Point 6764 0.61 Increase 7 25 Environment
S6764F ORF1ab_pp1ab Point 6764 0.59 Increase 7.4 37 Internal




Impact on protein function induced by mutation (20291C>T)

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
S6764F ORF1ab_pp1ab Point 0.281 Loss of Relative_solvent_accessibility (Pr = 0.37 | P = 1.5e-03)
Altered PPI_residue (Pr = 0.34 | P = 6.6e-03)
Altered DNA_binding (Pr = 0.27 | P = 6.5e-03)
Gain of Strand (Pr = 0.26 | P = 0.05)
Loss of Sodium_binding at S6760 (Pr = 0.23 | P = 0.02)
Altered Cytoplasmic_loop (Pr = 0.20 | P = 5.6e-03)
Gain of Manganese_binding at S6767 (Pr = 0.07 | P = 0.09)
Loss of Methylation at K6768 (Pr = 0.07 | P = 0.09)




Exploring mutation (20291C>T) 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 (20291C>T)

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
S6764F ORF1ab_pp1ab 20555 Chymotrypsin-high specificity QDLFVVSKVV (pos: 6764)
 NA
S6764F ORF1ab_pp1ab 20555 Pepsin (pH1.3) QDLFVVSKVV (pos: 6764)
 NA
S6764F ORF1ab_pp1ab 20555 Proteinase K QDLFVVSKVV (pos: 6764)
 NA
S6764F ORF1ab_pp1ab 20555 Thermolysin SQDLFVVSKV (pos: 6763)
 NA
S6764F ORF1ab_pp1ab 20555 Chymotrypsin-low specificity QDLFVVSKVV (pos: 6764)
 NA
S6764F ORF1ab_pp1ab 20555 Pepsin (pH>2) QDLFVVSKVV (pos: 6764)
 NA




Impact of spike protein mutation (20291C>T) 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 (20291C>T) 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.

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Impact of mutation (20291C>T) 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 (20291C>T) 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
V9419 6A>G synonymous_variant ORF7a K2K 6.71e-1 B.1.1.7
V586 1712A>G missense_variant ORF1ab_pp1a D571G 8.96e-1 AY.25.1
V9133 3792G>T synonymous_variant S V1264V 7.31e-1 AY.25.1
V768 2482G>T missense_variant ORF1ab_pp1a D828Y 7.72e-1 AY.39
V4717 5C>T missense_variant M A2V 1.00e+0 BA.1.15.1
V4286 3774A>C missense_variant S E1258D 7.07e-1 A.1
V4426 203G>T missense_variant ORF3a R68I 7.07e-1 A.2.5.2
V6823 7053C>T synonymous_variant ORF1ab_pp1a F2351F 6.53e-1 A.2.5
V8047 16690C>T synonymous_variant ORF1ab_pp1ab L5564L 6.53e-1 A.2.5
V864 2912C>T missense_variant ORF1ab_pp1a P971L 7.55e-1 A.2.5
V4463 296C>T missense_variant ORF3a A99V 7.07e-1 AY.107
V8668 282C>T synonymous_variant S S94S 1.00e+0 AY.107
V1841 8576C>T missense_variant ORF1ab_pp1a T2859I 8.65e-1 AY.108
V329 682G>T missense_variant ORF1ab_pp1a V228L 1.00e+0 AY.108
V5807 *4385C>T downstream_gene_variant S None 8.65e-1 AY.108
V6435 4107A>G synonymous_variant ORF1ab_pp1a G1369G 6.10e-1 AY.108
V7281 10689C>T synonymous_variant ORF1ab_pp1a C3563C 8.65e-1 AY.108
V7551 12861G>A synonymous_variant ORF1ab_pp1a G4287G 1.00e+0 AY.108
V9588 123G>A synonymous_variant N R41R 8.65e-1 AY.108
V1080 3719C>T missense_variant ORF1ab_pp1a T1240I 1.00e+0 AY.109
V4084 2434C>T missense_variant S P812S 7.07e-1 AY.109
V614 1821G>T missense_variant ORF1ab_pp1a Q607H 6.12e-1 AY.109
V2561 13922G>T missense_variant ORF1ab_pp1ab R4641M 6.22e-1 AY.111
V2940 17333C>T missense_variant ORF1ab_pp1ab A5778V 8.81e-1 AY.111
V5200 316G>T stop_gained ORF8 E106* 6.22e-1 AY.111
V644 1937G>T missense_variant ORF1ab_pp1a W646L 6.29e-1 AY.111
V7901 15546C>T synonymous_variant ORF1ab_pp1ab N5182N 6.76e-1 AY.111
V8402 19308C>T synonymous_variant ORF1ab_pp1ab Y6436Y 8.70e-1 AY.111
V8902 2073C>T synonymous_variant S S691S 9.17e-1 AY.111
V9217 582A>G synonymous_variant ORF3a E194E 8.33e-1 AY.111
V9645 435C>T synonymous_variant N H145H 6.22e-1 AY.111
V9696 675C>T synonymous_variant N D225D 8.20e-1 AY.111
V3736 641G>A missense_variant S R214H 8.02e-1 AY.113
V8425 19557A>G synonymous_variant ORF1ab_pp1ab P6519P 8.66e-1 AY.113
V1079 3706G>T missense_variant ORF1ab_pp1a V1236F 1.00e+0 AY.114
V6538 4879C>T synonymous_variant ORF1ab_pp1a L1627L 7.07e-1 AY.114
V4167 3202G>T missense_variant S V1068F 1.00e+0 AY.116.1
V3100 18387G>T missense_variant ORF1ab_pp1ab E6129D 7.07e-1 AY.119
V3001 17819T>C missense_variant ORF1ab_pp1ab I5940T 7.07e-1 AY.123
V804 2672C>T missense_variant ORF1ab_pp1a T891I 7.07e-1 AY.123
V8896 2040T>C synonymous_variant S S680S 7.07e-1 AY.123
V7086 9177C>T synonymous_variant ORF1ab_pp1a C3059C 1.00e+0 AY.124.1
V4839 181G>C missense_variant ORF6 D61H 7.07e-1 AY.124
V1030 3526G>A missense_variant ORF1ab_pp1a A1176T 7.07e-1 AY.127
V9322 279C>G synonymous_variant M L93L 8.56e-1 AY.23
V192 253_258delATGGTT conservative_inframe_deletion ORF1ab_pp1a M85_V86del 7.07e-1 AY.25.2
V4991 332C>T missense_variant ORF7a T111I 7.07e-1 AY.25.2
V5357 268G>T missense_variant N A90S 7.07e-1 AY.25.2
V1689 7609C>T missense_variant ORF1ab_pp1a P2537S 8.16e-1 AY.33.1
V3134 18641G>A missense_variant ORF1ab_pp1ab R6214H 8.16e-1 AY.33.1
V242 370C>T missense_variant ORF1ab_pp1a R124C 6.12e-1 AY.34.1
V4074 2353G>A missense_variant S V785I 8.66e-1 AY.34.1
V3822 1030G>T missense_variant S A344S 1.00e+0 AY.39.1.1
V2061 10456T>C missense_variant ORF1ab_pp1a F3486L 1.00e+0 AY.4.2.3
V3010 17867C>T missense_variant ORF1ab_pp1ab T5956I 7.07e-1 AY.4.2.3
V3722 629_631delTTA disruptive_inframe_deletion S I210del 7.07e-1 AY.4.2.3
V3927 1501A>T missense_variant S N501Y 7.07e-1 AY.4.2.3
V5072 22G>A missense_variant ORF8 G8R 1.00e+0 AY.4.2.3
V8405 19329C>T synonymous_variant ORF1ab_pp1ab N6443N 1.00e+0 AY.4.2.3
V8501 20205G>A synonymous_variant ORF1ab_pp1ab A6735A 1.00e+0 AY.4.2.3
V9199 339C>T synonymous_variant ORF3a Y113Y 1.00e+0 AY.43.2
V5281 53G>T missense_variant N G18V 7.07e-1 AY.4.4
V7471 12171T>C synonymous_variant ORF1ab_pp1a V4057V 7.07e-1 AY.4.4
V1247 4835C>T missense_variant ORF1ab_pp1a S1612L 7.22e-1 AY.4.5
V4191 3310G>T missense_variant S V1104L 8.66e-1 AY.46.2
V4497 375G>T missense_variant ORF3a M125I 9.13e-1 AY.46.2
V560 1646C>T missense_variant ORF1ab_pp1a S549F 9.13e-1 AY.46.2
V6379 3696C>T synonymous_variant ORF1ab_pp1a I1232I 1.00e+0 AY.46.4
V6584 5208T>C synonymous_variant ORF1ab_pp1a F1736F 8.16e-1 AY.4.6
V8284 18423C>T synonymous_variant ORF1ab_pp1ab C6141C 8.16e-1 AY.4.6
V5460 605G>T missense_variant N S202I 7.07e-1 AY.4.7
V5986 843C>T synonymous_variant ORF1ab_pp1a I281I 7.07e-1 AY.4.7
V7034 8805T>C synonymous_variant ORF1ab_pp1a D2935D 7.07e-1 AY.4.7
V9367 474C>T synonymous_variant M R158R 7.07e-1 AY.4.7
V2375 12524C>T missense_variant ORF1ab_pp1a T4175I 7.07e-1 AY.4.8
V5533 755C>T missense_variant N A252V 7.07e-1 AY.4.8
V7922 15693G>A synonymous_variant ORF1ab_pp1ab G5231G 7.07e-1 AY.4.8
V9097 3561T>C synonymous_variant S N1187N 7.07e-1 AY.4.8
V2485 13448A>G missense_variant ORF1ab_pp1ab K4483R 1.00e+0 AY.68
V3897 1430G>T missense_variant S S477I 7.07e-1 AY.68
V4227 3500G>T missense_variant S G1167V 1.00e+0 AY.68
V4498 377G>T missense_variant ORF3a R126M 1.00e+0 AY.68
V4049 2156C>T missense_variant S T719I 7.07e-1 AY.69
V2163 11023_11031delTCTGGTTTT conservative_inframe_deletion ORF1ab_pp1a S3675_F3677del 7.07e-1 AY.71
V3288 19750G>T missense_variant ORF1ab_pp1ab D6584Y 7.07e-1 AY.71
V5813 *4394G>T downstream_gene_variant S None 7.07e-1 AY.71
V3002 17822C>T missense_variant ORF1ab_pp1ab T5941I 8.99e-1 AY.78
V3259 19598C>T missense_variant ORF1ab_pp1ab A6533V 7.16e-1 AY.78
V4273 3711G>T missense_variant S M1237I 7.59e-1 AY.78
V2953 17426C>T missense_variant ORF1ab_pp1ab S5809L 6.32e-1 AY.79
V6656 5772C>T synonymous_variant ORF1ab_pp1a S1924S 6.70e-1 AY.79
V6696 6078T>C synonymous_variant ORF1ab_pp1a D2026D 6.70e-1 AY.79
V2422 12923T>C missense_variant ORF1ab_pp1a I4308T 7.07e-1 AY.90
V3002 17822C>T missense_variant ORF1ab_pp1ab T5941I 1.00e+0 AY.90
V3259 19598C>T missense_variant ORF1ab_pp1ab A6533V 1.00e+0 AY.90
V4273 3711G>T missense_variant S M1237I 1.00e+0 AY.90
V7799 14673C>T synonymous_variant ORF1ab_pp1ab D4891D 1.00e+0 AY.90
V9758 954G>T synonymous_variant N S318S 1.00e+0 AY.90
V3259 19598C>T missense_variant ORF1ab_pp1ab A6533V 7.07e-1 AY.91
V4273 3711G>T missense_variant S M1237I 1.00e+0 AY.91
V6584 5208T>C synonymous_variant ORF1ab_pp1a F1736F 1.00e+0 AY.91
V8284 18423C>T synonymous_variant ORF1ab_pp1ab C6141C 1.00e+0 AY.91
V7872 15315C>T synonymous_variant ORF1ab_pp1ab N5105N 1.00e+0 B.1.1.10
V8053 16740C>T synonymous_variant ORF1ab_pp1ab L5580L 1.00e+0 B.1.1.10
V8161 17502C>T synonymous_variant ORF1ab_pp1ab V5834V 1.00e+0 B.1.1.10
V9133 3792G>T synonymous_variant S V1264V 1.00e+0 B.1.1.10
V3029 17946G>T missense_variant ORF1ab_pp1ab M5982I 1.00e+0 B.1.128
V51 -83C>T upstream_gene_variant ORF1ab_pp1a None 6.64e-1 B.1.1.294
V5457 604A>T missense_variant N S202C 7.28e-1 B.1.1.294
V5459 605G>C missense_variant N S202T 7.28e-1 B.1.1.294
V3104 18410G>A missense_variant ORF1ab_pp1ab R6137K 1.00e+0 B.1.1.317
V5602 1097C>T missense_variant N T366I 1.00e+0 B.1.1.317
V1277 5036C>T missense_variant ORF1ab_pp1a A1679V 7.07e-1 B.1.1.39
V2405 12746C>T missense_variant ORF1ab_pp1a T4249I 7.07e-1 B.1.1.39
V2499 13510C>T missense_variant ORF1ab_pp1ab P4504S 1.00e+0 B.1.1.39
V6349 3369C>T synonymous_variant ORF1ab_pp1a N1123N 7.07e-1 B.1.1.39
V3220 19261G>T missense_variant ORF1ab_pp1ab D6421Y 8.15e-1 B.1.1.432
V813 2708C>T missense_variant ORF1ab_pp1a A903V 1.00e+0 B.1.1.432
V1022 3503C>T missense_variant ORF1ab_pp1a T1168I 7.07e-1 B.1.177.35
V5300 84G>T missense_variant N Q28H 1.00e+0 B.1.177.4
V1725 7841C>T missense_variant ORF1ab_pp1a A2614V 1.00e+0 B.1.177.57
V3267 19631C>T missense_variant ORF1ab_pp1ab A6544V 1.00e+0 B.1.177.57
V708 2215A>G missense_variant ORF1ab_pp1a I739V 1.00e+0 B.1.177.57
V713 2243C>T missense_variant ORF1ab_pp1a P748L 7.07e-1 B.1.177.57
V7711 14098C>T synonymous_variant ORF1ab_pp1ab L4700L 1.00e+0 B.1.177.57
V7419 11803C>T synonymous_variant ORF1ab_pp1a L3935L 1.00e+0 B.1.177.7
V7755 14385C>T synonymous_variant ORF1ab_pp1ab N4795N 1.00e+0 B.1.177.7
V198 257_259delTTG disruptive_inframe_deletion ORF1ab_pp1a V86del 1.00e+0 B.1.177.86
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F 1.00e+0 B.1.177.86
V3493 21101C>T missense_variant ORF1ab_pp1ab P7034L 7.07e-1 B.1.206
V1376 5771G>T missense_variant ORF1ab_pp1a S1924I 1.00e+0 B.1.221
V7097 9255C>T synonymous_variant ORF1ab_pp1a F3085F 1.00e+0 B.1.234
V3931 1522T>C missense_variant S Y508H 7.07e-1 B.1.241
V9430 96A>G synonymous_variant ORF7a K32K 1.00e+0 B.1.241
V2850 16729T>C missense_variant ORF1ab_pp1ab Y5577H 1.00e+0 B.1.265
V5221 357T>G missense_variant ORF8 D119E 7.07e-1 B.1.265
V5919 438C>T synonymous_variant ORF1ab_pp1a G146G 7.07e-1 B.1.265
V6771 6631C>T synonymous_variant ORF1ab_pp1a L2211L 7.07e-1 B.1.265
V7376 11517A>G synonymous_variant ORF1ab_pp1a K3839K 1.00e+0 B.1.265
V9199 339C>T synonymous_variant ORF3a Y113Y 7.07e-1 B.1.265
V953 3232G>A missense_variant ORF1ab_pp1a A1078T 8.16e-1 B.1.265
V9744 906G>T synonymous_variant N P302P 7.06e-1 B.1.265
V3667 459G>T missense_variant S M153I 1.00e+0 B.1.36.1
V3783 767C>T missense_variant S S256L 1.00e+0 B.1.36.1
V4485 328G>T missense_variant ORF3a A110S 1.00e+0 B.1.36.1
V6666 5880C>T synonymous_variant ORF1ab_pp1a F1960F 1.00e+0 B.1.36.1
V9741 894C>T synonymous_variant N Y298Y 6.70e-1 B.1.369
V2220 11292G>T missense_variant ORF1ab_pp1a E3764D 6.66e-1 B.1.36
V5611 1119G>T missense_variant N K373N 6.25e-1 B.1.36
V7846 15108G>T synonymous_variant ORF1ab_pp1ab T5036T 1.00e+0 B.1.561
V7531 12705C>T synonymous_variant ORF1ab_pp1a N4235N 7.07e-1 B.1.595
V3491 21070G>T missense_variant ORF1ab_pp1ab A7024S 8.16e-1 B.1.617.1
V5477 623C>T missense_variant N A208V 6.32e-1 BA.1.1.12
V6833 7155C>T synonymous_variant ORF1ab_pp1a I2385I 7.17e-1 BA.1.1.12
V4048 2147C>T missense_variant S T716I 1.00e+0 BA.1.14.2
V4537 514G>T missense_variant ORF3a G172C 7.01e-1 BA.2.3.13
V7500 12498C>T synonymous_variant ORF1ab_pp1a D4166D 8.77e-1 BA.2.3.13
V8135 17328G>T synonymous_variant ORF1ab_pp1ab V5776V 8.43e-1 BA.2.3.13
V8568 20850C>T synonymous_variant ORF1ab_pp1ab Y6950Y 7.07e-1 BA.2.38
V1515 6382G>A missense_variant ORF1ab_pp1a A2128T 1.00e+0 BA.4.4
V3373 20223G>T missense_variant ORF1ab_pp1ab K6741N 1.00e+0 BA.4.4
V3078 18227C>T missense_variant ORF1ab_pp1ab P6076L 1.00e+0 BA.5.2.2
V3793 782G>T missense_variant S G261V 7.74e-1 BA.5.3.4
V6345 3351T>C synonymous_variant ORF1ab_pp1a V1117V 1.00e+0 BE.3
V7846 15108G>T synonymous_variant ORF1ab_pp1ab T5036T 1.00e+0 BF.3
V4066 2305G>A missense_variant S G769R 7.07e-1 B
V6118 1803T>C synonymous_variant ORF1ab_pp1a I601I 7.07e-1 B
V6737 6351A>G synonymous_variant ORF1ab_pp1a L2117L 7.07e-1 B
V6640 5634A>G synonymous_variant ORF1ab_pp1a K1878K 1.00e+0 BN.1.2
V113 4G>A missense_variant ORF1ab_pp1a E2K 1.00e+0 BQ.1.11
V2755 15812A>G missense_variant ORF1ab_pp1ab D5271G 1.00e+0 BQ.1.1.23
V6939 8025C>T synonymous_variant ORF1ab_pp1a L2675L 1.00e+0 BQ.1.1.25
V7355 11400C>T synonymous_variant ORF1ab_pp1a L3800L 7.07e-1 BQ.1.1.25
V957 3249G>T missense_variant ORF1ab_pp1a M1083I 1.00e+0 BQ.1.1.25
V6676 5931C>T synonymous_variant ORF1ab_pp1a P1977P 7.07e-1 BQ.1.23
V7009 8580A>G synonymous_variant ORF1ab_pp1a R2860R 1.00e+0 BQ.1.8
V307 610C>T missense_variant ORF1ab_pp1a L204F 7.07e-1 BR.2.1
V6064 1419C>T synonymous_variant ORF1ab_pp1a I473I 1.00e+0 A.2.4
V8056 16746C>T synonymous_variant ORF1ab_pp1ab I5582I 1.00e+0 A.2.4
V8094 17016G>T synonymous_variant ORF1ab_pp1ab V5672V 1.00e+0 A.2.4
V79 -48C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 AY.25.1.2
V4427 206G>T missense_variant ORF3a W69L 7.06e-1 B.1.1.135
V5210 343C>T missense_variant ORF8 R115C 7.06e-1 B.1.1.135
V5378 382G>T missense_variant N D128Y 7.06e-1 B.1.1.135
V5929 510C>T synonymous_variant ORF1ab_pp1a T170T 7.06e-1 B.1.1.135
V8601 21042C>T synonymous_variant ORF1ab_pp1ab R7014R 7.06e-1 B.1.1.135
V992 3373G>T missense_variant ORF1ab_pp1a G1125C 7.03e-1 B.1.1.266
V3411 20495C>T missense_variant ORF1ab_pp1ab A6832V 7.06e-1 B.1.1.312
V6982 8397T>C synonymous_variant ORF1ab_pp1a H2799H 7.06e-1 B.1.1.312
V5985 837C>T synonymous_variant ORF1ab_pp1a S279S 1.00e+0 B.1.1.337
V7347 11322T>C synonymous_variant ORF1ab_pp1a N3774N 8.15e-1 B.1.1.337
V6174 2169C>T synonymous_variant ORF1ab_pp1a S723S 1.00e+0 B.1.13
V2981 17680G>T missense_variant ORF1ab_pp1ab V5894L 1.00e+0 B.1.1.431
V784 2602G>T missense_variant ORF1ab_pp1a V868L 1.00e+0 B.1.1.431
V7238 10317C>T synonymous_variant ORF1ab_pp1a D3439D 7.02e-1 B.1.160.18
V9718 804C>T synonymous_variant N Y268Y 7.02e-1 B.1.160.18
V3177 18887C>T missense_variant ORF1ab_pp1ab A6296V 1.00e+0 B.1.177.48
V6921 7875C>T synonymous_variant ORF1ab_pp1a S2625S 8.57e-1 B.1.177.89
V716 2258C>T missense_variant ORF1ab_pp1a T753I 8.57e-1 B.1.177.89
V2116 10818G>T missense_variant ORF1ab_pp1a L3606F 6.27e-1 B.1.280
V419 1084C>A missense_variant ORF1ab_pp1a Q362K 7.68e-1 B.1.280
V1532 6436C>T missense_variant ORF1ab_pp1a L2146F 7.06e-1 B.1.36.24
V1921 9173C>T missense_variant ORF1ab_pp1a T3058I 7.16e-1 B.1.36.24
V2116 10818G>T missense_variant ORF1ab_pp1a L3606F 7.26e-1 B.1.36.24
V3996 1960G>C missense_variant S E654Q 7.16e-1 B.1.36.24
V6125 1848C>T synonymous_variant ORF1ab_pp1a I616I 7.16e-1 B.1.36.24
V6823 7053C>T synonymous_variant ORF1ab_pp1a F2351F 6.85e-1 B.1.36.24
V7295 10809C>T synonymous_variant ORF1ab_pp1a F3603F 6.95e-1 B.1.36.24
V7766 14460C>T synonymous_variant ORF1ab_pp1ab F4820F 6.96e-1 B.1.36.24
V8139 17373A>G synonymous_variant ORF1ab_pp1ab K5791K 7.36e-1 B.1.36.24
V1402 6001G>A missense_variant ORF1ab_pp1a A2001T 1.00e+0 B.1.377
V4655 -18G>T upstream_gene_variant E None 7.04e-1 B.1.377
V3638 432_434delTTA disruptive_inframe_deletion S Y145del 1.00e+0 B.1.382
V6500 4626C>T synonymous_variant ORF1ab_pp1a T1542T 1.00e+0 B.1.382
V1112 3915G>T missense_variant ORF1ab_pp1a K1305N 1.00e+0 B.1.459
V25 -160C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.459
V4024 2042C>T missense_variant S P681L 1.00e+0 B.1.459
V4535 512C>T missense_variant ORF3a S171L 7.06e-1 B.1.459
V4608 717G>T missense_variant ORF3a E239D 1.00e+0 B.1.459
V4609 718C>T missense_variant ORF3a P240S 1.00e+0 B.1.459
V5776 *4358G>A downstream_gene_variant S None 1.00e+0 B.1.459
V7099 9267C>T synonymous_variant ORF1ab_pp1a F3089F 1.00e+0 B.1.459
V8227 18048C>T synonymous_variant ORF1ab_pp1ab V6016V 1.00e+0 B.1.459
V8632 96C>T synonymous_variant S F32F 7.06e-1 B.1.459
V1944 9350C>T missense_variant ORF1ab_pp1a T3117I 8.13e-1 B.1.478
V3433 20723C>T missense_variant ORF1ab_pp1ab T6908I 8.13e-1 B.1.478
V6086 1611A>G synonymous_variant ORF1ab_pp1a A537A 8.13e-1 B.1.478
V195 253_255delATG conservative_inframe_deletion ORF1ab_pp1a M85del 1.00e+0 B.1.595.1
V2036 10183C>T missense_variant ORF1ab_pp1a P3395S 1.00e+0 B.1.595.1
V5643 1201G>T missense_variant N D401Y 1.00e+0 B.23
V5655 1247C>T missense_variant N S416L 6.24e-1 BM.2.1
V6052 1329C>T synonymous_variant ORF1ab_pp1a S443S 1.00e+0 BM.2.1
V7055 8910A>G synonymous_variant ORF1ab_pp1a E2970E 6.56e-1 BM.2.1
V8345 18852A>G synonymous_variant ORF1ab_pp1ab K6284K 1.00e+0 BM.2.1
V5143 184G>C missense_variant ORF8 V62L 1.00e+0 C.1
V4483 322C>T missense_variant ORF3a L108F 1.00e+0 P.6
V7158 9714C>T synonymous_variant ORF1ab_pp1a L3238L 7.06e-1 P.6





Manual curation of mutation (20291C>T)-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