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The current mutation

ID: V1664
DNA: 7478G>T
Protein: S2493I
Position: 7743








COV2Var annotation categories







Summary information of mutation (7478G>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   7743
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 7478G>T
  Ref Seq: G
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: S2493I
  Protein 3-letter Mutation: Ser2493Ile

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 (7478G>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.1.234 125 78 6.24e-1
2020-10 B.1 125 16 1.28e-1
2020-10 B.1.417 125 13 1.04e-1
2020-11 B.1.234 355 299 8.42e-1
2020-11 B.1.177 355 11 3.10e-2
2020-11 B.1.362 355 11 3.10e-2
2020-12 B.1.234 190 58 3.05e-1
2020-12 B.1.1.222 190 53 2.79e-1
2020-12 B.1.177 190 48 2.53e-1
2020-03 B.1 9 7 7.78e-1
2020-03 B 9 2 2.22e-1
2020-04 B.1 14 6 4.29e-1
2020-04 B.1.1 14 4 2.86e-1
2020-04 B 14 3 2.14e-1
2020-05 B.1.142 6 2 3.33e-1
2020-05 A 6 1 1.67e-1
2020-05 A.1 6 1 1.67e-1
2020-06 B.1.1.228 6 2 3.33e-1
2020-06 B.1 6 1 1.67e-1
2020-06 B.1.1 6 1 1.67e-1
2020-07 B.1.1.464 17 7 4.12e-1
2020-07 B.1.417 17 3 1.76e-1
2020-07 B.1.1.135 17 2 1.18e-1
2020-08 B.1.1.464 23 11 4.78e-1
2020-08 B.1 23 3 1.30e-1
2020-08 B.1.1.171 23 2 8.70e-2
2020-09 B.1.1.464 43 17 3.95e-1
2020-09 B.1.234 43 12 2.79e-1
2020-09 B.1 43 6 1.40e-1
2021-01 B.1.177 317 172 5.43e-1
2021-01 B.1.1.222 317 46 1.45e-1
2021-01 B.1.234 317 31 9.78e-2
2021-10 AY.4 787 378 4.80e-1
2021-10 AY.126 787 206 2.62e-1
2021-10 AY.98 787 131 1.66e-1
2021-11 AY.4 1043 471 4.52e-1
2021-11 AY.98 1043 295 2.83e-1
2021-11 AY.126 1043 183 1.75e-1
2021-12 AY.98 605 226 3.74e-1
2021-12 AY.4 605 214 3.54e-1
2021-12 AY.126 605 78 1.29e-1
2021-02 B.1.177 180 97 5.39e-1
2021-02 B.1.1.222 180 20 1.11e-1
2021-02 B.1.1 180 14 7.78e-2
2021-03 B.1.177 184 45 2.45e-1
2021-03 B.1.1.318 184 27 1.47e-1
2021-03 B.1.1.7 184 27 1.47e-1
2021-04 B.1.1.7 83 22 2.65e-1
2021-04 B.1.351 83 17 2.05e-1
2021-04 P.1 83 8 9.64e-2
2021-05 B.1.1.7 67 38 5.67e-1
2021-05 B.1.351 67 10 1.49e-1
2021-05 P.1 67 9 1.34e-1
2021-06 P.1 64 14 2.19e-1
2021-06 B.1.1.318 64 11 1.72e-1
2021-06 B.1.1.7 64 10 1.56e-1
2021-07 AY.4 87 22 2.53e-1
2021-07 P.1 87 8 9.20e-2
2021-07 B.1.1.318 87 7 8.05e-2
2021-08 AY.4 176 88 5.00e-1
2021-08 B.1 176 10 5.68e-2
2021-08 AY.4.7 176 8 4.55e-2
2021-09 AY.4 433 312 7.21e-1
2021-09 AY.98 433 26 6.00e-2
2021-09 B.1.617.2 433 14 3.23e-2
2022-01 AY.98 116 37 3.19e-1
2022-01 AY.126 116 17 1.47e-1
2022-01 BA.1.1 116 15 1.29e-1
2022-10 BA.5.2.13 93 77 8.28e-1
2022-10 BE.1.4 93 11 1.18e-1
2022-10 BF.7 93 3 3.23e-2
2022-11 BA.5.2.13 147 67 4.56e-1
2022-11 BQ.1.2 147 37 2.52e-1
2022-11 BQ.1.1.18 147 9 6.12e-2
2022-12 BA.5.2.13 124 53 4.27e-1
2022-12 BQ.1.2 124 42 3.39e-1
2022-12 BQ.1.1.18 124 20 1.61e-1
2022-02 BA.1.17 54 17 3.15e-1
2022-02 BA.2 54 12 2.22e-1
2022-02 BA.1.1 54 9 1.67e-1
2022-03 BA.2 47 28 5.96e-1
2022-03 BA.1.1 47 6 1.28e-1
2022-03 BA.1.17 47 4 8.51e-2
2022-04 BA.2 23 7 3.04e-1
2022-04 BA.2.34 23 7 3.04e-1
2022-04 BA.2.9 23 5 2.17e-1
2022-05 BA.2 38 27 7.11e-1
2022-05 BA.2.34 38 4 1.05e-1
2022-05 BA.2.36 38 2 5.26e-2
2022-06 BA.2 33 13 3.94e-1
2022-06 BA.5.5 33 7 2.12e-1
2022-06 BA.5.3.2 33 5 1.52e-1
2022-07 BF.13 9 2 2.22e-1
2022-07 BA.2.34 9 1 1.11e-1
2022-07 BA.2.75.3 9 1 1.11e-1
2022-08 BE.1.4 13 4 3.08e-1
2022-08 BA.2 13 2 1.54e-1
2022-08 BA.5.2.13 13 2 1.54e-1
2022-09 BA.5.2.13 108 48 4.44e-1
2022-09 BE.1.4 108 47 4.35e-1
2022-09 BF.7 108 4 3.70e-2
2023-01 BQ.1.2 60 26 4.33e-1
2023-01 BQ.1.1.18 60 20 3.33e-1
2023-01 BQ.1.1 60 3 5.00e-2
2023-02 BQ.1.1.18 13 7 5.38e-1
2023-02 BQ.1.2 13 6 4.62e-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
V1664 A.28 2.22e-2 6 2020-7-28 2021-5-28
V1664 AN.1 4.00e-2 2 2020-7-7 2021-3-29
V1664 AY.126 1.15e-2 498 2020-10-14 2022-5-9
V1664 AY.98 1.76e-2 722 2020-10-14 2022-6-29
V1664 B.1.1.222 2.43e-2 135 2020-4-4 2022-3-2
V1664 B.1.1.318 1.32e-2 47 2020-5-14 2021-11-27
V1664 B.1.1.464 6.26e-2 62 2020-4-1 2021-7-7
V1664 B.1.234 6.13e-2 493 2020-5-22 2022-3-24
V1664 B.1.362 1.93e-2 13 2020-4-3 2021-5-5
V1664 B.1.415.1 3.33e-2 4 2021-5-7 2021-8-2
V1664 B.1.417 9.13e-1 21 2020-4-2 2021-7-1
V1664 BA.2.34 3.51e-2 17 2022-1-5 2022-8-30
V1664 BA.5.2.13 7.51e-2 248 2022-6-23 2023-2-13
V1664 BE.1.4 2.02e-2 71 2022-2-17 2023-2-17
V1664 BQ.1.2 1.05e-2 111 2022-1-4 2023-2-21






Examining mutation (7478G>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 (7478G>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 -1.25e+1 3.59e+2 -3.49e-2 9.72e-1 Decrease
Deceased -1.45e+1 8.79e+2 -1.65e-2 9.87e-1 Decrease
Homebound -2.54e+0 2.55e+3 -9.94e-4 9.99e-1 Decrease
Hospitalized 1.36e+1 3.77e+2 3.60e-2 9.71e-1 Increase
Mild -1.07e+1 6.13e+2 -1.75e-2 9.86e-1 Decrease
Recovered -1.15e+1 3.79e+2 -3.03e-2 9.76e-1 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 1.55e-1 1.33e-1 1.16e+0 2.46e-1 Increase
18-39 -3.09e-1 7.77e-2 -3.98e+0 6.94e-5 Decrease
40-64 -8.93e-3 7.59e-2 -1.18e-1 9.06e-1 Decrease
65-84 4.32e-1 9.54e-2 4.53e+0 6.01e-6 Increase
>=85 3.83e-2 2.04e-1 1.87e-1 8.51e-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 -4.56e-2 7.33e-2 -6.22e-1 5.34e-1 Decrease





Investigating natural selection at mutation (7478G>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
nsp3 2720 8554 1945 1675 3.00e-2 AY.85 MEME

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 (7478G>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_pp1a 490015 6.04 543550 89.08 -0.022
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (7478G>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
S2493I ORF1ab_pp1a Point 2493 -0.7 Decrease 7 25 Environment
S2493I ORF1ab_pp1a Point 2493 -0.59 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (7478G>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
S2493I ORF1ab_pp1a Point 0.318 Loss of Relative_solvent_accessibility (Pr = 0.41 | P = 7.0e-04)
Altered PPI_residue (Pr = 0.34 | P = 6.4e-03)
Altered Cytoplasmic_loop (Pr = 0.27 | P = 6.0e-04)
Loss of Sodium_binding at K2497 (Pr = 0.16 | P = 0.07)
Loss of Proteolytic_cleavage at D2492 (Pr = 0.13 | P = 0.02)
Loss of N-linked_glycosylation at N2498 (Pr = 0.10 | P = 0.01)
Gain of Copper_binding at D2492 (Pr = 0.03 | P = 0.08)




Exploring mutation (7478G>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 (7478G>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
S2493I ORF1ab_pp1a 7743 Proteinase K IVDIVTVKNG (pos: 2493)
 NA




Impact of spike protein mutation (7478G>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 (7478G>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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        Show interface residues:





Impact of mutation (7478G>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 (7478G>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
V7195 9942C>T synonymous_variant ORF1ab_pp1a N3314N 6.70e-1 B.1.177
V7472 12174C>T synonymous_variant ORF1ab_pp1a P4058P 7.49e-1 B.1.177
V7607 13251C>T synonymous_variant ORF1ab_pp1ab G4417G 9.68e-1 B.1.177
V9138 21C>T synonymous_variant ORF3a I7I 8.63e-1 B.1.177
V4677 122C>T missense_variant E A41V 6.14e-1 AY.4
V6739 6363C>T synonymous_variant ORF1ab_pp1a T2121T 7.66e-1 AY.4
V7677 13854G>T synonymous_variant ORF1ab_pp1ab T4618T 6.92e-1 AY.4
V9088 3507C>T synonymous_variant S I1169I 6.23e-1 AY.100
V1259 4913C>A missense_variant ORF1ab_pp1a T1638N 8.16e-1 BE.1.1
V6340 3327T>C synonymous_variant ORF1ab_pp1a N1109N 7.52e-1 AY.126
V8659 240T>C synonymous_variant S D80D 6.30e-1 AY.126
V2298 11902G>T missense_variant ORF1ab_pp1a V3968F 1.00e+0 AY.20
V6920 7872G>T synonymous_variant ORF1ab_pp1a V2624V 7.07e-1 AY.20
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 9.69e-1 AY.98
V3072 18188C>T missense_variant ORF1ab_pp1ab A6063V 7.07e-1 A.1
V8628 66T>C synonymous_variant S T22T 7.74e-1 A.2.5
V8903 2076C>T synonymous_variant S I692I 7.07e-1 A
V2467 13307G>T missense_variant ORF1ab_pp1ab G4436V 1.00e+0 AY.110
V9224 618C>T synonymous_variant ORF3a Y206Y 7.07e-1 AY.110
V4107 2567A>G missense_variant S N856S 8.45e-1 AY.113
V4506 392G>C missense_variant ORF3a W131S 8.45e-1 AY.113
V8171 17583G>A synonymous_variant ORF1ab_pp1ab Q5861Q 1.00e+0 AY.116
V4122 2695G>T missense_variant S A899S 7.07e-1 AY.119.1
V2623 14477C>T missense_variant ORF1ab_pp1ab S4826F 6.25e-1 AY.121
V2689 15143C>T missense_variant ORF1ab_pp1ab A5048V 1.00e+0 AY.122.1
V979 3322C>T missense_variant ORF1ab_pp1a H1108Y 7.07e-1 AY.124
V9629 348G>A synonymous_variant N G116G 7.07e-1 AY.33
V2422 12923T>C missense_variant ORF1ab_pp1a I4308T 8.94e-1 AY.34
V3395 20365C>T missense_variant ORF1ab_pp1ab H6789Y 1.00e+0 AY.34
V7479 12231T>C synonymous_variant ORF1ab_pp1a Y4077Y 1.00e+0 AY.34
V8133 17298G>T synonymous_variant ORF1ab_pp1ab R5766R 8.16e-1 AY.34
V8711 624G>T synonymous_variant S T208T 1.00e+0 AY.34
V6716 6156G>T synonymous_variant ORF1ab_pp1a V2052V 1.00e+0 AY.4.2.1
V1569 6662C>T missense_variant ORF1ab_pp1a P2221L 8.66e-1 AY.4.7
V5762 *4350G>T downstream_gene_variant S None 7.63e-1 AY.4.7
V5337 163G>T missense_variant N A55S 1.00e+0 AY.5.3
V1169 4418C>T missense_variant ORF1ab_pp1a A1473V 7.07e-1 AY.53
V240 360G>T missense_variant ORF1ab_pp1a K120N 7.07e-1 AY.59
V4248 3604G>C missense_variant S E1202Q 1.00e+0 AY.59
V6683 5997T>C synonymous_variant ORF1ab_pp1a N1999N 7.07e-1 AY.59
V5653 1240G>T missense_variant N A414S 7.07e-1 AY.7.1
V9594 150G>A synonymous_variant N A50A 7.07e-1 AY.7.1
V9345 372C>T synonymous_variant M L124L 8.66e-1 AY.72
V8214 17919C>T synonymous_variant ORF1ab_pp1ab D5973D 1.00e+0 AY.91
V1891 8902T>C missense_variant ORF1ab_pp1a Y2968H 1.00e+0 AZ.2
V3474 20956G>A missense_variant ORF1ab_pp1ab A6986T 1.00e+0 AZ.2
V48 -92G>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 AZ.2
V5514 704C>T missense_variant N S235F 7.07e-1 AZ.2
V5748 *4338C>T downstream_gene_variant S None 7.07e-1 AZ.2
V1502 6317C>T missense_variant ORF1ab_pp1a T2106I 6.26e-1 B.1.110.3
V7269 10569C>T synonymous_variant ORF1ab_pp1a A3523A 8.42e-1 B.1.110.3
V7795 14661C>T synonymous_variant ORF1ab_pp1ab V4887V 6.26e-1 B.1.110.3
V8915 2196C>T synonymous_variant S T732T 8.42e-1 B.1.110.3
V3413 20498C>T missense_variant ORF1ab_pp1ab T6833I 1.00e+0 B.1.1.189
V7930 15717C>T synonymous_variant ORF1ab_pp1ab I5239I 1.00e+0 B.1.1.189
V2730 15593C>T missense_variant ORF1ab_pp1ab T5198I 9.69e-1 B.1.1.222
V5443 581C>T missense_variant N S194L 8.67e-1 B.1.1.222
V6630 5547C>T synonymous_variant ORF1ab_pp1a D1849D 9.61e-1 B.1.1.222
V6984 8418C>T synonymous_variant ORF1ab_pp1a I2806I 8.75e-1 B.1.1.222
V7135 9591G>T synonymous_variant ORF1ab_pp1a V3197V 8.58e-1 B.1.1.222
V7814 14844C>T synonymous_variant ORF1ab_pp1ab T4948T 8.71e-1 B.1.1.222
V9095 3534C>T synonymous_variant S N1178N 9.70e-1 B.1.1.222
V9747 924C>T synonymous_variant N A308A 8.34e-1 B.1.1.222
V2048 10361C>T missense_variant ORF1ab_pp1a A3454V 7.07e-1 B.1.1.25
V5594 1075G>T missense_variant N A359S 1.00e+0 B.1.1.25
V6690 6045C>T synonymous_variant ORF1ab_pp1a S2015S 9.48e-1 B.1.1.277
V1773 8143G>A missense_variant ORF1ab_pp1a V2715I 7.74e-1 B.1.1.28
V2348 12346A>G missense_variant ORF1ab_pp1a M4116V 6.32e-1 B.1.1.28
V2873 16858G>T missense_variant ORF1ab_pp1ab A5620S 6.70e-1 B.1.1.28
V3257 19561G>A missense_variant ORF1ab_pp1ab V6521M 7.74e-1 B.1.1.28
V3678 488C>T missense_variant S A163V 6.32e-1 B.1.1.28
V6722 6180C>T synonymous_variant ORF1ab_pp1a D2060D 6.32e-1 B.1.1.28
V3483 21038C>T missense_variant ORF1ab_pp1ab P7013L 7.07e-1 B.1.1.306
V3484 21040C>A missense_variant ORF1ab_pp1ab R7014S 7.07e-1 B.1.1.306
V9813 1245C>T synonymous_variant N D415D 7.07e-1 B.1.1.306
V3283 19735G>T missense_variant ORF1ab_pp1ab V6579F 7.07e-1 B.1.1.372
V3682 526C>T missense_variant S L176F 1.00e+0 B.1.1.39
V3308 19868C>T missense_variant ORF1ab_pp1ab A6623V 9.13e-1 B.1.1.416
V4454 280C>T missense_variant ORF3a L94F 8.94e-1 B.1.1.416
V8391 19224C>T synonymous_variant ORF1ab_pp1ab V6408V 8.94e-1 B.1.1.416
V1626 7034C>T missense_variant ORF1ab_pp1a A2345V 6.95e-1 B.1.1.464
V379 926C>T missense_variant ORF1ab_pp1a P309L 9.83e-1 B.1.1.464
V9467 256C>T synonymous_variant ORF7a L86L 8.25e-1 B.1.1.464
V3099 18383C>T missense_variant ORF1ab_pp1ab P6128L 1.00e+0 B.1.1.486
V619 1841C>T missense_variant ORF1ab_pp1a T614I 1.00e+0 B.1.1.486
V9718 804C>T synonymous_variant N Y268Y 1.00e+0 B.1.1.486
V203 261G>T missense_variant ORF1ab_pp1a E87D 8.71e-1 B.1.1.519
V3523 24G>T missense_variant S L8F 1.00e+0 B.1.177.44
V5946 588C>T synonymous_variant ORF1ab_pp1a Y196Y 1.00e+0 B.1.177.75
V2513 13598C>T missense_variant ORF1ab_pp1ab T4533I 7.07e-1 B.1.177.81
V7331 11190C>T synonymous_variant ORF1ab_pp1a A3730A 1.00e+0 B.1.177.81
V899 3039G>T missense_variant ORF1ab_pp1a E1013D 7.07e-1 B.1.177.82
V4509 393G>T missense_variant ORF3a W131C 9.18e-1 B.1.234
V6585 5214T>C synonymous_variant ORF1ab_pp1a H1738H 9.80e-1 B.1.234
V8302 18549T>C synonymous_variant ORF1ab_pp1ab D6183D 9.80e-1 B.1.234
V9310 184T>C synonymous_variant M L62L 9.32e-1 B.1.234
V8469 19935C>T synonymous_variant ORF1ab_pp1ab Y6645Y 7.07e-1 B.1.240
V680 2069C>T missense_variant ORF1ab_pp1a A690V 6.12e-1 B.1.258.11
V9357 429G>C synonymous_variant M V143V 8.66e-1 B.1.351.2
V1099 3840G>T missense_variant ORF1ab_pp1a K1280N 1.00e+0 B.1.362
V1783 8237C>T missense_variant ORF1ab_pp1a T2746I 9.60e-1 B.1.362
V5853 105G>T synonymous_variant ORF1ab_pp1a V35V 9.18e-1 B.1.362
V9719 810A>G synonymous_variant N V270V 9.18e-1 B.1.362
V1081 3722C>T missense_variant ORF1ab_pp1a T1241I 7.07e-1 B.1.369
V2563 13925C>T missense_variant ORF1ab_pp1ab A4642V 7.07e-1 B.1.369
V2738 15644G>T missense_variant ORF1ab_pp1ab G5215V 7.07e-1 B.1.369
V6511 4695G>T synonymous_variant ORF1ab_pp1a V1565V 7.07e-1 B.1.369
V8974 2640T>C synonymous_variant S G880G 7.07e-1 B.1.369
V3235 19402G>T missense_variant ORF1ab_pp1ab D6468Y 1.00e+0 B.1.36
V6563 5025T>C synonymous_variant ORF1ab_pp1a Y1675Y 1.00e+0 B.1.36
V8469 19935C>T synonymous_variant ORF1ab_pp1ab Y6645Y 7.07e-1 B.1.427
V3524 25C>T missense_variant S P9S 8.16e-1 B.1.466.2
V3527 38G>T missense_variant S S13I 8.16e-1 B.1.466.2
V5038 92C>T missense_variant ORF7b S31L 7.07e-1 B.1.525
V1799 8347G>T missense_variant ORF1ab_pp1a V2783F 8.66e-1 B.1.582
V8127 17238C>T synonymous_variant ORF1ab_pp1ab F5746F 7.74e-1 B.1.582
V7575 13005T>C synonymous_variant ORF1ab_pp1a D4335D 1.00e+0 B.1.617.1
V1309 5307G>T missense_variant ORF1ab_pp1a M1769I 7.64e-1 B.1.637
V8963 2565T>C synonymous_variant S F855F 7.71e-1 B.1.637
V1249 4850C>T missense_variant ORF1ab_pp1a T1617I 1.00e+0 BA.2.3.1
V9296 84C>T synonymous_variant M F28F 1.00e+0 BA.2.3.1
V4903 139C>T missense_variant ORF7a H47Y 1.00e+0 BA.2.50
V260 421_429delAAGTCATTT conservative_inframe_deletion ORF1ab_pp1a K141_F143del 1.00e+0 BA.2.75.3
V9463 237C>T synonymous_variant ORF7a A79A 1.00e+0 BA.2.75.3
V2127 10863G>A missense_variant ORF1ab_pp1a M3621I 1.00e+0 BA.4
V6760 6516C>T synonymous_variant ORF1ab_pp1a F2172F 7.07e-1 BA.5.10
V8823 1524C>T synonymous_variant S Y508Y 6.32e-1 BA.5.10
V3824 1037G>C missense_variant S R346T 7.07e-1 BA.5.1.15
V8466 19884C>T synonymous_variant ORF1ab_pp1ab F6628F 1.00e+0 BA.5.1.15
V8624 33C>T synonymous_variant S V11V 1.00e+0 BA.5.1.15
V7717 14139C>T synonymous_variant ORF1ab_pp1ab F4713F 6.20e-1 BA.5.2.13
V6102 1708C>T synonymous_variant ORF1ab_pp1a L570L 9.13e-1 BA.5.3.2
V8994 2820C>T synonymous_variant S S940S 9.26e-1 BA.5.3.2
V2807 16394C>T missense_variant ORF1ab_pp1ab T5465I 1.00e+0 BA.5
V2368 12482C>T missense_variant ORF1ab_pp1a T4161I 9.59e-1 BE.1.4
V8831 1608C>T synonymous_variant S N536N 6.22e-1 BE.1.4
V9521 108G>A synonymous_variant ORF8 P36P 8.95e-1 BE.1.4
V6428 4066C>T synonymous_variant ORF1ab_pp1a L1356L 1.00e+0 BF.13
V2901 17024C>T missense_variant ORF1ab_pp1ab T5675I 7.07e-1 BF.21
V709 2218A>G missense_variant ORF1ab_pp1a I740V 7.07e-1 BN.1.3
V6963 8208T>C synonymous_variant ORF1ab_pp1a N2736N 1.00e+0 BN.3.1
V9260 12C>T synonymous_variant E F4F 7.07e-1 BQ.1.1.10
V7963 16029C>T synonymous_variant ORF1ab_pp1ab C5343C 6.32e-1 BQ.1.1.1
V3871 1331A>T missense_variant S K444M 7.07e-1 BQ.1.11
V4214 3428C>T missense_variant S P1143L 1.00e+0 BQ.1.11
V3871 1331A>T missense_variant S K444M 7.07e-1 BQ.1.12
V7222 10191C>T synonymous_variant ORF1ab_pp1a F3397F 6.12e-1 BQ.1.12
V4003 1996A>G missense_variant S I666V 1.00e+0 BQ.1.18
V7222 10191C>T synonymous_variant ORF1ab_pp1a F3397F 7.07e-1 BQ.1.18
V8127 17238C>T synonymous_variant ORF1ab_pp1ab F5746F 1.00e+0 BQ.1.18
V2485 13448A>G missense_variant ORF1ab_pp1ab K4483R 9.91e-1 BQ.1.2
V3871 1331A>T missense_variant S K444M 8.35e-1 BQ.1.2
V7222 10191C>T synonymous_variant ORF1ab_pp1a F3397F 9.87e-1 BQ.1.2
V8127 17238C>T synonymous_variant ORF1ab_pp1ab F5746F 9.87e-1 BQ.1.2
V1661 7471G>A missense_variant ORF1ab_pp1a V2491I 7.07e-1 BT.2
V2045 10340C>T missense_variant ORF1ab_pp1a P3447L 1.00e+0 C.36
V310 619C>T missense_variant ORF1ab_pp1a R207C 1.00e+0 C.36
V4971 283G>C missense_variant ORF7a E95Q 1.00e+0 C.36
V9503 126C>T synonymous_variant ORF7b H42H 1.00e+0 C.36
V8771 1110T>C synonymous_variant S N370N 7.07e-1 C.37
V6443 4173C>T synonymous_variant ORF1ab_pp1a V1391V 7.07e-1 CQ.2
V9641 426A>G synonymous_variant N P142P 7.07e-1 CQ.2
V2489 13456C>T missense_variant ORF1ab_pp1ab P4486S 6.31e-1 DF.1
V7867 15276C>T synonymous_variant ORF1ab_pp1ab V5092V 1.00e+0 DF.1
V9135 3816C>T synonymous_variant S Y1272Y 7.07e-1 P.1.15
V3344 20125C>T missense_variant ORF1ab_pp1ab R6709C 7.07e-1 P.1.17
V890 2999C>T missense_variant ORF1ab_pp1a T1000I 7.07e-1 P.1.17
V1520 6394A>G missense_variant ORF1ab_pp1a S2132G 6.71e-1 R.1
V2582 14029C>T missense_variant ORF1ab_pp1ab R4677C 7.03e-1 A.28
V4014 2031G>C missense_variant S Q677H 7.03e-1 A.28
V4610 719C>T missense_variant ORF3a P240L 7.03e-1 A.28
V6574 5100C>T synonymous_variant ORF1ab_pp1a Y1700Y 6.70e-1 A.28
V4061 2240C>T missense_variant S T747I 1.00e+0 AY.4.1
V5417 533G>T missense_variant N G178V 1.00e+0 AY.4.1
V2143 10957G>T missense_variant ORF1ab_pp1a V3653F 1.00e+0 B.1.1.135
V4690 203C>T missense_variant E S68F 1.00e+0 B.1.1.135
V5060 -5C>T upstream_gene_variant ORF8 None 1.00e+0 B.1.1.135
V2930 17269G>A missense_variant ORF1ab_pp1ab G5757S 7.06e-1 B.1.1.171
V5807 *4385C>T downstream_gene_variant S None 8.15e-1 B.1.1.171
V460 1249C>T missense_variant ORF1ab_pp1a H417Y 1.00e+0 B.1.1.228
V9294 78C>T synonymous_variant M F26F 1.00e+0 B.1.1.302
V2990 17735C>T missense_variant ORF1ab_pp1ab T5912I 7.06e-1 B.1.1.312
V4462 295G>T missense_variant ORF3a A99S 1.00e+0 B.1.1.312
V1234 4766C>T missense_variant ORF1ab_pp1a T1589I 1.00e+0 B.1.142
V3296 19792G>A missense_variant ORF1ab_pp1ab G6598S 1.00e+0 B.1.195
V1898 8939A>G missense_variant ORF1ab_pp1a D2980G 1.00e+0 B.1.210
V4509 393G>T missense_variant ORF3a W131C 1.00e+0 B.1.210
V5635 1172C>T missense_variant N T391I 1.00e+0 B.1.210
V6585 5214T>C synonymous_variant ORF1ab_pp1a H1738H 1.00e+0 B.1.210
V661 1993G>A missense_variant ORF1ab_pp1a V665I 1.00e+0 B.1.210
V6921 7875C>T synonymous_variant ORF1ab_pp1a S2625S 1.00e+0 B.1.210
V8302 18549T>C synonymous_variant ORF1ab_pp1ab D6183D 1.00e+0 B.1.210
V9310 184T>C synonymous_variant M L62L 1.00e+0 B.1.210
V3342 20110A>G missense_variant ORF1ab_pp1ab I6704V 1.00e+0 B.1.390
V3847 1151C>T missense_variant S P384L 1.00e+0 B.1.390
V5614 1129G>T missense_variant N D377Y 1.00e+0 B.1.390
V3732 637G>T missense_variant S V213L 1.00e+0 B.1.411
V3837 1099G>T missense_variant S V367F 1.00e+0 B.1.411
V1823 8483C>T missense_variant ORF1ab_pp1a A2828V 8.62e-1 B.1.415.1
V2021 10058A>G missense_variant ORF1ab_pp1a K3353R 1.00e+0 B.1.415.1
V306 607G>A missense_variant ORF1ab_pp1a D203N -6.91e-1 B.1.417
V5848 90C>T synonymous_variant ORF1ab_pp1a G30G -6.91e-1 B.1.417
V6580 5157T>C synonymous_variant ORF1ab_pp1a N1719N 1.00e+0 B.1.417
V6789 6786C>T synonymous_variant ORF1ab_pp1a Y2262Y 1.00e+0 B.1.417
V7682 13914C>T synonymous_variant ORF1ab_pp1ab T4638T -6.91e-1 B.1.417
V9066 3366G>T synonymous_variant S V1122V -6.91e-1 B.1.417
V372 913C>T missense_variant ORF1ab_pp1a P305S 1.00e+0 Q.8
V8604 21093T>C synonymous_variant ORF1ab_pp1ab N7031N 1.00e+0 Q.8
V9388 606C>T synonymous_variant M G202G 8.15e-1 Q.8





Manual curation of mutation (7478G>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