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The current mutation

ID: V6512
DNA: 4710G>A
Protein: V1570V
Position: 4975








COV2Var annotation categories







Summary information of mutation (4710G>A)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   4975
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   synonymous_variant
  DNA Level   DNA Mutation: 4710G>A
  Ref Seq: G
  Mut Seq: A
  Protein Level   Protein 1-letter Mutation: V1570V
  Protein 3-letter Mutation: Val1570Val

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 (4710G>A) 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 AY.46.6 2 1 5.00e-1
2020-10 B.1.1.294 2 1 5.00e-1
2020-11 B.1.1 1 1 1.00e+0
2020-12 B.1.2 7 4 5.71e-1
2020-12 B.1.1.7 7 1 1.43e-1
2020-12 B.1.177.21 7 1 1.43e-1
2020-05 B 1 1 1.00e+0
2021-01 AY.46.6 11 4 3.64e-1
2021-01 B.1.2 11 4 3.64e-1
2021-01 B.1.1.7 11 2 1.82e-1
2021-10 AY.46.6 2094 1999 9.55e-1
2021-10 AY.122 2094 20 9.55e-3
2021-10 AY.103 2094 17 8.12e-3
2021-11 AY.46.6 3134 2898 9.25e-1
2021-11 AY.46.6.1 3134 112 3.57e-2
2021-11 AY.122 3134 24 7.66e-3
2021-12 AY.46.6 2444 2075 8.49e-1
2021-12 AY.46.6.1 2444 224 9.17e-2
2021-12 B.1.617.2 2444 60 2.45e-2
2021-02 B.1.2 21 8 3.81e-1
2021-02 B.1.258.17 21 6 2.86e-1
2021-02 B.1.1.7 21 5 2.38e-1
2021-03 B.1.1.7 60 55 9.17e-1
2021-03 B.1.2 60 2 3.33e-2
2021-03 AY.46.6 60 1 1.67e-2
2021-04 B.1.1.7 54 51 9.44e-1
2021-04 B.1.617.2 54 2 3.70e-2
2021-04 B.1.1.519 54 1 1.85e-2
2021-05 B.1.1.7 18 18 1.00e+0
2021-06 B.1.1.7 11 5 4.55e-1
2021-06 B.1.617.2 11 3 2.73e-1
2021-06 AY.112 11 1 9.09e-2
2021-07 AY.46.6 63 33 5.24e-1
2021-07 B.1.617.2 63 12 1.90e-1
2021-07 AY.44 63 4 6.35e-2
2021-08 AY.46.6 1530 1492 9.75e-1
2021-08 AY.44 1530 15 9.80e-3
2021-08 AY.103 1530 4 2.61e-3
2021-09 AY.46.6 2212 2145 9.70e-1
2021-09 AY.4 2212 16 7.23e-3
2021-09 AY.44 2212 14 6.33e-3
2022-01 AY.46.6 371 257 6.93e-1
2022-01 BA.2 371 44 1.19e-1
2022-01 AY.46.6.1 371 24 6.47e-2
2022-10 BA.5.2.22 58 27 4.66e-1
2022-10 BA.5.6 58 12 2.07e-1
2022-10 BF.7 58 9 1.55e-1
2022-11 BF.7 26 11 4.23e-1
2022-11 BA.5.6 26 5 1.92e-1
2022-11 BA.5.2.22 26 1 3.85e-2
2022-12 BQ.1.1 30 9 3.00e-1
2022-12 BF.26 30 6 2.00e-1
2022-12 BQ.1.2 30 6 2.00e-1
2022-02 BA.2 365 314 8.60e-1
2022-02 BA.1.1 365 20 5.48e-2
2022-02 BA.1.17.2 365 8 2.19e-2
2022-03 BA.2 898 855 9.52e-1
2022-03 XAE 898 24 2.67e-2
2022-03 BA.1.1 898 5 5.57e-3
2022-04 BA.2 1032 1002 9.71e-1
2022-04 XAE 1032 21 2.03e-2
2022-04 BA.2.31 1032 3 2.91e-3
2022-05 BA.2 740 677 9.15e-1
2022-05 XAE 740 52 7.03e-2
2022-05 BA.2.35 740 4 5.41e-3
2022-06 BA.2 236 197 8.35e-1
2022-06 XAE 236 30 1.27e-1
2022-06 BA.2.35 236 7 2.97e-2
2022-07 BA.2 88 67 7.61e-1
2022-07 BA.2.56 88 14 1.59e-1
2022-07 BE.1.1 88 2 2.27e-2
2022-08 BA.2 32 14 4.38e-1
2022-08 BA.5.2.22 32 7 2.19e-1
2022-08 BA.4.6 32 2 6.25e-2
2022-09 BA.5.2.22 36 15 4.17e-1
2022-09 BA.5.6 36 8 2.22e-1
2022-09 BA.4.6 36 3 8.33e-2
2023-01 BF.7 52 41 7.88e-1
2023-01 BN.1.2 52 3 5.77e-2
2023-01 BQ.1.1 52 3 5.77e-2
2023-02 XBB.1.9 4 3 7.50e-1
2023-02 BQ.1.1 4 1 2.50e-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
V6512 AY.30 1.31e-2 47 2021-3-6 2022-5-2
V6512 BA.5.2.22 1.08e-2 50 2022-5-17 2023-2-1
V6512 AY.46.6 4.19e-1 10914 2020-8-11 2022-11-9
V6512 AY.46.6.1 1.00e+0 185 2021-10-17 2022-2-17
V6512 BA.2.35 2.89e-2 11 2022-3-1 2022-10-3
V6512 XAE 1.00e+0 130 2022-2-26 2022-11-19






Examining mutation (4710G>A) 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 (4710G>A) 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 -1.61e+0 1.06e+0 -1.52e+0 1.29e-1 Decrease
Deceased 1.30e-1 5.47e-1 2.38e-1 8.12e-1 Increase
Homebound -4.53e-15 3.93e+4 -1.15e-19 1.00e+0 Decrease
Hospitalized -8.10e-2 2.50e-1 -3.24e-1 7.46e-1 Decrease
Mild 3.56e-1 2.76e-1 1.29e+0 1.97e-1 Increase
Recovered 5.25e-2 2.41e-1 2.18e-1 8.28e-1 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 4.67e-1 7.24e-2 6.45e+0 1.14e-10 Increase
18-39 -1.01e-1 4.64e-2 -2.18e+0 2.90e-2 Decrease
40-64 -1.91e-2 4.44e-2 -4.29e-1 6.68e-1 Decrease
65-84 -1.23e-3 5.96e-2 -2.06e-2 9.84e-1 Decrease
>=85 -3.14e-1 1.21e-1 -2.61e+0 9.10e-3 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 -3.59e-2 4.33e-2 -8.29e-1 4.07e-1 Decrease





Investigating natural selection at mutation (4710G>A) 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 (4710G>A)

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 (4710G>A)

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 (4710G>A)

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 (4710G>A) 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 (4710G>A)

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 (4710G>A) 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 (4710G>A) 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 (4710G>A) 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 (4710G>A) 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
V6542 4905C>T synonymous_variant ORF1ab_pp1a Y1635Y 6.57e-1 AY.43
V6302 3075G>T synonymous_variant ORF1ab_pp1a V1025V 7.07e-1 BA.1.1.2
V881 2977G>A missense_variant ORF1ab_pp1a G993S 7.07e-1 BA.1.18
V4482 322C>G missense_variant ORF3a L108V 8.16e-1 BA.4.6
V8538 20601T>C synonymous_variant ORF1ab_pp1ab H6867H 7.75e-1 BE.1.1
V1932 9256C>T missense_variant ORF1ab_pp1a L3086F 7.12e-1 AY.122
V9441 129T>C synonymous_variant ORF7a N43N 6.71e-1 AY.122
V1619 6959C>T missense_variant ORF1ab_pp1a A2320V 8.54e-1 BA.5.6
V1057 3637C>T missense_variant ORF1ab_pp1a P1213S 6.76e-1 BF.7
V5526 727G>T missense_variant N G243C 7.16e-1 BF.7
V1955 9449C>T missense_variant ORF1ab_pp1a T3150I 7.07e-1 AY.112.2
V3681 520C>T missense_variant S P174S 7.07e-1 AY.112.2
V4535 512C>T missense_variant ORF3a S171L 7.07e-1 AY.112.2
V53 -80C>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 AY.112.2
V1356 5638G>T missense_variant ORF1ab_pp1a V1880F 6.71e-1 AY.112
V4524 463G>T missense_variant ORF3a D155Y 8.49e-1 AY.119.2
V8584 20955C>T synonymous_variant ORF1ab_pp1ab F6985F 8.81e-1 AY.119.2
V1517 6386C>T missense_variant ORF1ab_pp1a A2129V 1.00e+0 AY.132
V2302 11923G>T missense_variant ORF1ab_pp1a V3975F 1.00e+0 AY.132
V6080 1560C>T synonymous_variant ORF1ab_pp1a A520A 1.00e+0 AY.132
V9531 186G>T synonymous_variant ORF8 V62V 1.00e+0 AY.132
V345 803G>A missense_variant ORF1ab_pp1a G268E 1.00e+0 AY.27
V669 2016G>T missense_variant ORF1ab_pp1a K672N 7.27e-1 AY.30
V7163 9729C>T synonymous_variant ORF1ab_pp1a N3243N 6.50e-1 AY.30
V7073 9054C>T synonymous_variant ORF1ab_pp1a F3018F 7.07e-1 AY.34.1
V8694 447C>T synonymous_variant S N149N 1.00e+0 AY.34.1
V7864 15228T>C synonymous_variant ORF1ab_pp1ab D5076D 1.00e+0 AY.34
V424 1112C>T missense_variant ORF1ab_pp1a P371L 7.07e-1 AY.36.1
V5054 124C>T missense_variant ORF7b H42Y 6.68e-1 AY.36
V3074 18199C>T missense_variant ORF1ab_pp1ab P6067S 8.16e-1 AY.4.2.2
V3694 541G>C missense_variant S G181R 1.00e+0 AY.42
V3773 752C>T missense_variant S P251L 1.00e+0 AY.42
V2094 10712C>T missense_variant ORF1ab_pp1a A3571V 1.00e+0 AY.43.4
V2611 14320G>A missense_variant ORF1ab_pp1ab A4774T 1.00e+0 AY.43.4
V3036 17991G>T missense_variant ORF1ab_pp1ab M5997I 9.13e-1 AY.43.4
V3152 18743C>T missense_variant ORF1ab_pp1ab A6248V 8.94e-1 AY.43.4
V6095 1647C>T synonymous_variant ORF1ab_pp1a S549S 9.13e-1 AY.43.4
V6690 6045C>T synonymous_variant ORF1ab_pp1a S2015S 7.90e-1 AY.43.4
V6945 8061C>T synonymous_variant ORF1ab_pp1a D2687D 1.00e+0 AY.43.4
V9357 429G>C synonymous_variant M V143V 1.00e+0 AY.43.4
V4341 85G>A missense_variant ORF3a V29I 7.07e-1 AY.45
V4376 128T>C missense_variant ORF3a F43S 7.07e-1 AY.45
V4905 148G>T missense_variant ORF7a A50S 7.07e-1 AY.45
V6830 7128G>T synonymous_variant ORF1ab_pp1a P2376P 6.71e-1 AY.74
V6997 8520G>A synonymous_variant ORF1ab_pp1a Q2840Q 8.66e-1 AY.74
V4032 2062G>A missense_variant S A688T 1.00e+0 AY.85
V947 3218G>A missense_variant ORF1ab_pp1a G1073E 7.07e-1 AY.85
V1670 7499C>T missense_variant ORF1ab_pp1a S2500F 1.00e+0 AY.88
V3540 62G>T missense_variant S R21I 1.00e+0 AY.88
V6221 2451C>T synonymous_variant ORF1ab_pp1a G817G 1.00e+0 AY.88
V6830 7128G>T synonymous_variant ORF1ab_pp1a P2376P 1.00e+0 AY.88
V3442 20770C>T missense_variant ORF1ab_pp1ab L6924F 1.00e+0 B.1.1.294
V3556 80C>T missense_variant S A27V 1.00e+0 B.1.1.294
V359 876G>T missense_variant ORF1ab_pp1a K292N 1.00e+0 B.1.1.294
V4067 2306G>T missense_variant S G769V 7.07e-1 B.1.1.294
V4068 2311G>T missense_variant S A771S 1.00e+0 B.1.1.294
V7426 11835C>T synonymous_variant ORF1ab_pp1a A3945A 1.00e+0 B.1.1.294
V5853 105G>T synonymous_variant ORF1ab_pp1a V35V 7.07e-1 B.1.1.519
V7194 9939T>C synonymous_variant ORF1ab_pp1a L3313L 7.07e-1 B.1.1.519
V3528 42G>T missense_variant S Q14H 7.07e-1 B.1.243
V195 253_255delATG conservative_inframe_deletion ORF1ab_pp1a M85del 7.06e-1 B.1.640.1
V2366 12476C>T missense_variant ORF1ab_pp1a T4159I 6.32e-1 B.1.640.1
V3171 18845G>T missense_variant ORF1ab_pp1ab S6282I 1.00e+0 B.1.640.1
V4134 2816C>T missense_variant S S939F 8.16e-1 B.1.640.1
V3372 20219C>T missense_variant ORF1ab_pp1ab S6740F 6.12e-1 BA.2.23
V4531 494C>T missense_variant ORF3a S165F 1.00e+0 BA.2.31
V534 1559C>T missense_variant ORF1ab_pp1a A520V 9.00e-1 BA.2.56
V1203 4628C>T missense_variant ORF1ab_pp1a T1543I 1.00e+0 BA.2.75.2
V3275 19697C>T missense_variant ORF1ab_pp1ab T6566M 6.12e-1 BA.5.2.21
V2901 17024C>T missense_variant ORF1ab_pp1ab T5675I 9.80e-1 BA.5.2.22
V5914 411C>T synonymous_variant ORF1ab_pp1a G137G 6.46e-1 BA.5.2.22
V1561 6600G>T missense_variant ORF1ab_pp1a K2200N 7.07e-1 BA.5.2.31
V5376 378C>A missense_variant N N126K 7.07e-1 BA.5.2.31
V6589 5232C>T synonymous_variant ORF1ab_pp1a C1744C 1.00e+0 BA.5.3.2
V6243 2607T>C synonymous_variant ORF1ab_pp1a N869N 6.03e-1 BF.26
V7918 15675T>C synonymous_variant ORF1ab_pp1ab D5225D 7.07e-1 B
V4190 3310G>C missense_variant S V1104L 1.00e+0 BN.1.9
V7654 13701C>T synonymous_variant ORF1ab_pp1ab Y4567Y 1.00e+0 BN.1.9
V4311 37G>C missense_variant ORF3a V13L 1.00e+0 BQ.1.1.15
V8063 16803T>C synonymous_variant ORF1ab_pp1ab Y5601Y 1.00e+0 BQ.1.1.32
V4405 171G>C missense_variant ORF3a Q57H 1.00e+0 BQ.1.1.4
V7067 9015A>G synonymous_variant ORF1ab_pp1a V3005V 1.00e+0 BQ.1.1.4
V7265 10533C>T synonymous_variant ORF1ab_pp1a D3511D 1.00e+0 BQ.1.1.4
V8211 17898C>T synonymous_variant ORF1ab_pp1ab D5966D 7.07e-1 BQ.1.1.4
V9115 3672G>A synonymous_variant S L1224L 6.32e-1 BQ.1.1.4
V3658 448A>G missense_variant S K150E 1.00e+0 BQ.1.1.6
V5807 *4385C>T downstream_gene_variant S None 7.56e-1 BQ.1.2
V6244 2613C>T synonymous_variant ORF1ab_pp1a F871F 7.14e-1 BQ.1.2
V4272 3711G>C missense_variant S M1237I 7.07e-1 P.1.15
V9511 51C>T synonymous_variant ORF8 H17H 7.74e-1 P.1.15
V9780 1062T>C synonymous_variant N N354N 7.07e-1 XBB.2
V75 -53G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 AY.103.1
V1175 4498C>T missense_variant ORF1ab_pp1a H1500Y 7.06e-1 BA.2.17
V1332 5455G>A missense_variant ORF1ab_pp1a G1819S 1.00e+0 BA.2.17
V1431 6097G>A missense_variant ORF1ab_pp1a A2033T 1.00e+0 BA.2.17
V1665 7484C>T missense_variant ORF1ab_pp1a T2495I 1.00e+0 BA.2.17
V1921 9173C>T missense_variant ORF1ab_pp1a T3058I 1.00e+0 BA.2.17
V1932 9256C>T missense_variant ORF1ab_pp1a L3086F 1.00e+0 BA.2.17
V2271 11765A>G missense_variant ORF1ab_pp1a Q3922R 1.00e+0 BA.2.17
V2343 12275C>T missense_variant ORF1ab_pp1a A4092V 7.06e-1 BA.2.17
V2653 14762C>T missense_variant ORF1ab_pp1ab A4921V 7.06e-1 BA.2.17
V345 803G>A missense_variant ORF1ab_pp1a G268E 7.06e-1 BA.2.17
V3870 1331A>G missense_variant S K444R 1.00e+0 BA.2.17
V3877 1336G>A missense_variant S G446S 7.06e-1 BA.2.17
V3884 1354C>A missense_variant S L452M 1.00e+0 BA.2.17
V3904 1442A>G missense_variant S N481S 7.06e-1 BA.2.17
V4078 2386G>C missense_variant S D796H 7.06e-1 BA.2.17
V4094 2500A>G missense_variant S I834V 7.06e-1 BA.2.17
V4387 145G>A missense_variant ORF3a G49S 7.06e-1 BA.2.17
V4640 784C>T missense_variant ORF3a P262S 7.06e-1 BA.2.17
V4647 803C>T missense_variant ORF3a T268M 7.06e-1 BA.2.17
V4837 170C>T missense_variant ORF6 P57L 7.06e-1 BA.2.17
V5380 401C>T missense_variant N A134V 7.06e-1 BA.2.17
V5997 921G>A synonymous_variant ORF1ab_pp1a A307A 1.00e+0 BA.2.17
V6009 999G>A synonymous_variant ORF1ab_pp1a T333T 1.00e+0 BA.2.17
V6035 1206C>T synonymous_variant ORF1ab_pp1a R402R 7.06e-1 BA.2.17
V6444 4179G>A synonymous_variant ORF1ab_pp1a V1393V 1.00e+0 BA.2.17
V6655 5766C>T synonymous_variant ORF1ab_pp1a N1922N 1.00e+0 BA.2.17
V6745 6396T>C synonymous_variant ORF1ab_pp1a S2132S 1.00e+0 BA.2.17
V6846 7299C>T synonymous_variant ORF1ab_pp1a S2433S 1.00e+0 BA.2.17
V7046 8883T>C synonymous_variant ORF1ab_pp1a I2961I 1.00e+0 BA.2.17
V7081 9144A>G synonymous_variant ORF1ab_pp1a V3048V 7.06e-1 BA.2.17
V7166 9750C>T synonymous_variant ORF1ab_pp1a Y3250Y 7.06e-1 BA.2.17
V7750 14358G>A synonymous_variant ORF1ab_pp1ab T4786T 7.06e-1 BA.2.17
V8025 16503C>T synonymous_variant ORF1ab_pp1ab N5501N 7.06e-1 BA.2.17
V8317 18624C>T synonymous_variant ORF1ab_pp1ab H6208H 1.00e+0 BA.2.17
V8994 2820C>T synonymous_variant S S940S 1.00e+0 BA.2.17
V9210 480C>T synonymous_variant ORF3a Y160Y 7.06e-1 BA.2.17
V9272 91C>T synonymous_variant E L31L 7.06e-1 BA.2.17
V9371 492G>A synonymous_variant M L164L 7.06e-1 BA.2.17
V9619 294C>T synonymous_variant N D98D 7.06e-1 BA.2.17
V9648 447C>T synonymous_variant N R149R 7.06e-1 BA.2.17
V3494 21103A>G missense_variant ORF1ab_pp1ab I7035V 1.00e+0 BA.2.35
V3891 1380T>G missense_variant S N460K -7.05e-1 BN.1.4.1
V3896 1430G>A missense_variant S S477N -7.05e-1 BN.1.4.1
V3900 1433C>A missense_variant S T478K -7.05e-1 BN.1.4.1
V3911 1451A>C missense_variant S E484A -1.00e+0 BN.1.4.1
V3921 1469T>C missense_variant S F490S -7.05e-1 BN.1.4.1
V3926 1493A>G missense_variant S Q498R -1.00e+0 BN.1.4.1
V3927 1501A>T missense_variant S N501Y -1.00e+0 BN.1.4.1
V3930 1513T>C missense_variant S Y505H -1.00e+0 BN.1.4.1
V3957 1721A>T missense_variant S D574V 1.00e+0 BN.1.4.1
V6823 7053C>T synonymous_variant ORF1ab_pp1a F2351F 1.00e+0 BN.1.4.1
V7780 14538C>T synonymous_variant ORF1ab_pp1ab D4846D 1.00e+0 BN.1.4.1
V9590 126C>T synonymous_variant N P42P 1.00e+0 BN.1.4.1





Manual curation of mutation (4710G>A)-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