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The current mutation

ID: V2525
DNA: 13689A>G
Protein: I4563M
Position: 13953








COV2Var annotation categories







Summary information of mutation (13689A>G)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1ab
  Gene Name   ORF1ab_pp1ab
  Gene Type   protein_coding
  Genome position   13953
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 13689A>G
  Ref Seq: A
  Mut Seq: G
  Protein Level   Protein 1-letter Mutation: I4563M
  Protein 3-letter Mutation: Ile4563Met

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 (13689A>G) 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 C.16 4 2 5.00e-1
2020-10 B.1.1.1 4 1 2.50e-1
2020-10 B.1.429 4 1 2.50e-1
2020-11 C.16 1 1 1.00e+0
2020-12 B.1.177.80 1 1 1.00e+0
2020-03 A.3 3 1 3.33e-1
2020-03 B.1.1.33 3 1 3.33e-1
2020-03 B.31 3 1 3.33e-1
2020-05 B.1.1 10 10 1.00e+0
2020-06 B.1.1 52 51 9.81e-1
2020-06 B.1 52 1 1.92e-2
2020-07 B.1.1 7 7 1.00e+0
2020-08 B.1 2 1 5.00e-1
2020-08 B.1.1 2 1 5.00e-1
2020-09 B.1.1.1 2 1 5.00e-1
2020-09 B.1.1.37 2 1 5.00e-1
2021-01 B.1.575 12 3 2.50e-1
2021-01 B.1.1.1 12 2 1.67e-1
2021-01 B.1.1.343 12 2 1.67e-1
2021-10 AY.126 1315 1090 8.29e-1
2021-10 AY.103 1315 103 7.83e-2
2021-10 AY.4 1315 30 2.28e-2
2021-11 AY.126 2220 1936 8.72e-1
2021-11 AY.103 2220 104 4.68e-2
2021-11 AY.25.1 2220 49 2.21e-2
2021-12 AY.126 1464 1301 8.89e-1
2021-12 AY.25.1 1464 46 3.14e-2
2021-12 AY.103 1464 45 3.07e-2
2021-02 B.1.243 26 17 6.54e-1
2021-02 B.1.575 26 3 1.15e-1
2021-02 B.1.1.1 26 2 7.69e-2
2021-03 B.1.243 39 21 5.38e-1
2021-03 B.1.1.7 39 6 1.54e-1
2021-03 AY.126 39 5 1.28e-1
2021-04 B.1.1.7 15 9 6.00e-1
2021-04 B.1.243 15 5 3.33e-1
2021-04 B.1.617.2 15 1 6.67e-2
2021-06 AY.4 21 7 3.33e-1
2021-06 B.1.1.7 21 6 2.86e-1
2021-06 AY.126 21 3 1.43e-1
2021-07 AY.25 51 29 5.69e-1
2021-07 AY.126 51 8 1.57e-1
2021-07 AY.4 51 3 5.88e-2
2021-08 AY.126 378 288 7.62e-1
2021-08 AY.25 378 29 7.67e-2
2021-08 AY.46.6 378 19 5.03e-2
2021-09 AY.126 503 365 7.26e-1
2021-09 AY.46.6 503 30 5.96e-2
2021-09 AY.103 503 24 4.77e-2
2022-01 AY.126 132 85 6.44e-1
2022-01 BA.1.17.2 132 18 1.36e-1
2022-01 BA.1 132 6 4.55e-2
2022-10 BA.5.2.6 221 214 9.68e-1
2022-10 CP.1.2 221 3 1.36e-2
2022-10 BA.5.2.12 221 1 4.52e-3
2022-11 BA.5.2.6 175 169 9.66e-1
2022-11 BQ.1.1 175 3 1.71e-2
2022-11 BA.5.2.9 175 1 5.71e-3
2022-12 BA.5.2.6 139 127 9.14e-1
2022-12 BQ.1.1 139 7 5.04e-2
2022-12 BE.1.1.1 139 2 1.44e-2
2022-02 BA.2 103 66 6.41e-1
2022-02 BA.1.1 103 19 1.84e-1
2022-02 BA.2.10 103 7 6.80e-2
2022-03 BA.2 314 285 9.08e-1
2022-03 BA.2.10 314 22 7.01e-2
2022-03 BA.2.6 314 4 1.27e-2
2022-04 BA.2 139 127 9.14e-1
2022-04 BA.2.10 139 9 6.47e-2
2022-04 BA.1.1 139 1 7.19e-3
2022-05 BA.2 85 81 9.53e-1
2022-05 BA.2.10 85 1 1.18e-2
2022-05 BA.2.3.4 85 1 1.18e-2
2022-06 BA.2 16 11 6.88e-1
2022-06 BE.1.1 16 4 2.50e-1
2022-06 BA.2.56 16 1 6.25e-2
2022-07 BA.2 14 3 2.14e-1
2022-07 BA.2.56 14 2 1.43e-1
2022-07 BA.5.1.3 14 2 1.43e-1
2022-08 BA.5.2.6 32 21 6.56e-1
2022-08 BF.5 32 4 1.25e-1
2022-08 BA.5.2.8 32 2 6.25e-2
2022-09 BA.5.2.6 97 80 8.25e-1
2022-09 BA.4 97 4 4.12e-2
2022-09 CP.3 97 4 4.12e-2
2023-01 BA.5.2.6 50 40 8.00e-1
2023-01 BF.11 50 3 6.00e-2
2023-01 BF.7 50 2 4.00e-2
2023-02 BA.5.2.6 7 6 8.57e-1
2023-02 BA.5.1.26 7 1 1.43e-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
V2525 AY.126 1.17e-1 5083 2020-10-14 2022-5-9
V2525 B.1.1.343 1.05e-1 2 2020-11-9 2021-4-10
V2525 BA.5.2.6 4.17e-2 658 2022-1-2 2023-2-22
V2525 CP.1.2 7.62e-2 8 2022-9-2 2023-1-3
V2525 CP.3 1.60e-2 4 2022-8-29 2023-2-7






Examining mutation (13689A>G) 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 (13689A>G) 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 -1.49e+1 1.59e+3 -9.35e-3 9.93e-1 Decrease
Deceased -1.48e+1 1.56e+3 -9.45e-3 9.92e-1 Decrease
Homebound 1.68e+1 1.05e+3 1.61e-2 9.87e-1 Increase
Hospitalized 1.99e+0 1.06e+0 1.87e+0 6.10e-2 Increase
Mild -1.47e+1 1.57e+3 -9.35e-3 9.93e-1 Decrease
Recovered -1.54e+1 1.00e+3 -1.54e-2 9.88e-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 -1.40e-2 1.39e-1 -1.01e-1 9.20e-1 Decrease
18-39 -3.13e-1 8.04e-2 -3.89e+0 9.96e-5 Decrease
40-64 4.24e-2 7.54e-2 5.62e-1 5.74e-1 Increase
65-84 2.74e-1 9.10e-2 3.02e+0 2.55e-3 Increase
>=85 4.10e-1 1.53e-1 2.67e+0 7.52e-3 Increase

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient gender Male -1.32e-2 7.31e-2 -1.80e-1 8.57e-1 Decrease





Investigating natural selection at mutation (13689A>G) 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
RdRp 13468 16236 932 171 122.41 0.00 3.00e-2 BF.18 FEL
RdRp 13468 16236 932 171 65.20 0.00 2.00e-2 CM.2 FEL

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 (13689A>G)

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 794075.83 6.32 928150 86.81 -0.071
Reference ORF1ab_pp1ab 794057.79 6.32 928150 86.87 -0.07




Alterations in protein stability induced by mutation (13689A>G)

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
I4563M ORF1ab_pp1ab Point 4563 -2.26 Decrease 7 25 Environment
I4563M ORF1ab_pp1ab Point 4563 -2.25 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (13689A>G)

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
I4563M ORF1ab_pp1ab Point 0.301 Altered Coiled_coil (Pr = 0.35 | P = 0.01)
Altered MoRF (Pr = 0.32 | P = 0.02)
Altered PPI_residue (Pr = 0.29 | P = 0.03)
Gain of Allosteric_site at Y4567 (Pr = 0.27 | P = 4.5e-03)
Altered PPI_hotspot (Pr = 0.27 | P = 8.0e-03)
Loss of Relative_solvent_accessibility (Pr = 0.24 | P = 0.05)
Altered Cytoplasmic_loop (Pr = 0.22 | P = 3.4e-03)
Loss of Zinc_binding at E4559 (Pr = 0.19 | P = 0.07)
Gain of Manganese_binding at E4559 (Pr = 0.17 | P = 0.03)
Loss of Sodium_binding at N4560 (Pr = 0.16 | P = 0.07)
Gain of Potassium_binding at E4559 (Pr = 0.16 | P = 0.02)
Altered DNA_binding (Pr = 0.10 | P = 0.09)




Exploring mutation (13689A>G) 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 (13689A>G)

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
I4563M ORF1ab_pp1ab 13953 Proteinase K NA
 NPDILRVYAN (pos: 4563)
I4563M ORF1ab_pp1ab 13953 Chymotrypsin-low specificity NPDMLRVYAN (pos: 4563)
 NA
I4563M ORF1ab_pp1ab 13953 CNBr NPDMLRVYAN (pos: 4563)
 NA




Impact of spike protein mutation (13689A>G) 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 (13689A>G) on viral transmissibility by the affinity between RBD and ACE2 receptor

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

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


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

        Show as:

        Show interface residues:





Impact of mutation (13689A>G) 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 (13689A>G) 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
V2130 10879A>G missense_variant ORF1ab_pp1a M3627V 7.11e-1 AY.25
V4003 1996A>G missense_variant S I666V 7.07e-1 AY.5
V6260 2727T>C synonymous_variant ORF1ab_pp1a D909D 7.07e-1 BA.1.18
V487 1333G>A missense_variant ORF1ab_pp1a G445S 6.53e-1 AY.103
V1555 6575C>T missense_variant ORF1ab_pp1a A2192V 6.53e-1 AY.126
V2997 17768C>T missense_variant ORF1ab_pp1ab T5923I 8.47e-1 AY.126
V6591 5247C>T synonymous_variant ORF1ab_pp1a N1749N 9.90e-1 AY.126
V8037 16632T>C synonymous_variant ORF1ab_pp1ab N5544N 9.93e-1 AY.126
V4520 447G>T missense_variant ORF3a W149C 6.32e-1 AY.20
V674 2029A>G missense_variant ORF1ab_pp1a T677A 1.00e+0 AY.39
V9663 516C>T synonymous_variant N Y172Y 7.07e-1 AY.39
V5470 617C>T missense_variant N S206F 9.58e-1 B.1.1
V7905 15603T>G synonymous_variant ORF1ab_pp1ab P5201P 7.07e-1 B.1
V5933 540G>A synonymous_variant ORF1ab_pp1a G180G 9.87e-1 BA.2.10
V8840 1668C>T synonymous_variant S N556N 7.07e-1 A.2.5
V3520 13C>T missense_variant S L5F 7.07e-1 A.3
V637 1899G>T missense_variant ORF1ab_pp1a E633D 7.07e-1 AY.102
V7848 15132C>T synonymous_variant ORF1ab_pp1ab F5044F 1.00e+0 AY.102
V6591 5247C>T synonymous_variant ORF1ab_pp1a N1749N 1.00e+0 AY.105
V7795 14661C>T synonymous_variant ORF1ab_pp1ab V4887V 1.00e+0 AY.105
V1629 7069C>T missense_variant ORF1ab_pp1a H2357Y 1.00e+0 AY.117
V9264 42T>C synonymous_variant E V14V 6.67e-1 AY.120
V4541 518A>G missense_variant ORF3a D173G 7.75e-1 AY.27
V8795 1281T>C synonymous_variant S D427D 1.00e+0 AY.30
V9511 51C>T synonymous_variant ORF8 H17H 7.45e-1 AY.32
V1763 8069C>T missense_variant ORF1ab_pp1a A2690V 6.32e-1 AY.34
V8983 2763A>G synonymous_variant S K921K 6.32e-1 AY.34
V9282 220C>T synonymous_variant E L74L 6.03e-1 AY.34
V4823 98T>C missense_variant ORF6 I33T 7.07e-1 AY.4.12
V4973 286C>T missense_variant ORF7a L96F 1.00e+0 AY.4.12
V5729 *4312C>T downstream_gene_variant S None 7.07e-1 AY.4.12
V6638 5619C>T synonymous_variant ORF1ab_pp1a Y1873Y 7.07e-1 AY.4.12
V7094 9237C>T synonymous_variant ORF1ab_pp1a A3079A 1.00e+0 AY.4.12
V7645 13623C>T synonymous_variant ORF1ab_pp1ab Y4541Y 1.00e+0 AY.4.12
V9654 471C>T synonymous_variant N I157I 7.07e-1 AY.4.12
V2082 10609A>G missense_variant ORF1ab_pp1a N3537D 7.19e-1 AY.4.2.1
V3450 20846C>T missense_variant ORF1ab_pp1ab T6949I 9.66e-1 AY.4.2.1
V5196 302G>T missense_variant ORF8 R101L 9.66e-1 AY.4.2.1
V7151 9675C>T synonymous_variant ORF1ab_pp1a S3225S 9.91e-1 AY.4.2.1
V119 35C>T missense_variant ORF1ab_pp1a T12I 6.76e-1 AY.6
V1230 4758G>T missense_variant ORF1ab_pp1a M1586I 6.17e-1 AY.6
V1838 8564C>T missense_variant ORF1ab_pp1a A2855V 7.56e-1 AY.6
V3395 20365C>T missense_variant ORF1ab_pp1ab H6789Y 7.98e-1 AY.6
V7628 13416C>T synonymous_variant ORF1ab_pp1ab Y4472Y 7.56e-1 AY.6
V5123 135G>A stop_gained ORF8 W45* 1.00e+0 AY.91
V2048 10361C>T missense_variant ORF1ab_pp1a A3454V 7.07e-1 AY.98.1
V1118 3941C>T missense_variant ORF1ab_pp1a A1314V 6.70e-1 B.1.1.1
V1532 6436C>T missense_variant ORF1ab_pp1a L2146F 8.01e-1 B.1.1.1
V2927 17254C>T missense_variant ORF1ab_pp1ab L5752F 1.00e+0 B.1.1.1
V3002 17822C>T missense_variant ORF1ab_pp1ab T5941I 6.11e-1 B.1.1.1
V3886 1355T>G missense_variant S L452R 6.85e-1 B.1.1.1
V3927 1501A>T missense_variant S N501Y 7.06e-1 B.1.1.1
V6869 7500C>T synonymous_variant ORF1ab_pp1a S2500S 8.01e-1 B.1.1.1
V6869 7500C>T synonymous_variant ORF1ab_pp1a S2500S 1.00e+0 B.1.1.37
V3678 488C>T missense_variant S A163V 9.55e-1 B.1.243
V3241 19420G>A missense_variant ORF1ab_pp1ab V6474I 7.07e-1 B.1.427
V6002 948C>T synonymous_variant ORF1ab_pp1a C316C 1.00e+0 B.1.575
V6205 2379C>T synonymous_variant ORF1ab_pp1a I793I 6.54e-1 B.1.575
V6417 3981C>T synonymous_variant ORF1ab_pp1a T1327T 6.54e-1 BA.1.21
V7423 11811C>T synonymous_variant ORF1ab_pp1a N3937N 6.54e-1 BA.1.21
V6428 4066C>T synonymous_variant ORF1ab_pp1a L1356L 1.00e+0 BA.2.3.4
V9286 12C>T synonymous_variant M S4S 1.00e+0 BA.2.3.4
V3154 18745G>T missense_variant ORF1ab_pp1ab D6249Y 7.07e-1 BA.2.75.2
V3712 557T>C missense_variant S F186S 1.00e+0 BA.2.75.2
V9628 345T>C synonymous_variant N T115T 1.00e+0 BA.2.75.2
V402 1031G>T missense_variant ORF1ab_pp1a C344F 7.07e-1 BA.5.1.26
V8270 18321A>G synonymous_variant ORF1ab_pp1ab V6107V 7.07e-1 BA.5.1.26
V3785 770G>A missense_variant S G257D 6.32e-1 BA.5.1.3
V665 2006A>G missense_variant ORF1ab_pp1a K669R 7.07e-1 BA.5.1.3
V5807 *4385C>T downstream_gene_variant S None 1.00e+0 BA.5.2.12
V9812 1242T>C synonymous_variant N A414A 1.00e+0 BA.5.2.12
V5807 *4385C>T downstream_gene_variant S None 7.07e-1 BA.5.2.34
V9812 1242T>C synonymous_variant N A414A 7.07e-1 BA.5.2.34
V5311 94C>T missense_variant N R32C 1.00e+0 BA.5.2.44
V8609 21144T>C synonymous_variant ORF1ab_pp1ab F7048F 1.00e+0 BA.5.2.48
V9812 1242T>C synonymous_variant N A414A 9.53e-1 BA.5.2.6
V1589 6777G>T missense_variant ORF1ab_pp1a M2259I 6.11e-1 BA.5.2.8
V4814 62C>T missense_variant ORF6 T21I 7.07e-1 BA.5.2.9
V6961 8173C>T synonymous_variant ORF1ab_pp1a L2725L 1.00e+0 BF.11
V7964 16044C>T synonymous_variant ORF1ab_pp1ab F5348F 6.54e-1 BF.11
V8662 249C>T synonymous_variant S V83V 8.66e-1 BF.11
V3423 20666C>T missense_variant ORF1ab_pp1ab T6889M 7.07e-1 BQ.1.1.23
V565 1654C>T missense_variant ORF1ab_pp1a L552F 1.00e+0 BQ.1.1.23
V2927 17254C>T missense_variant ORF1ab_pp1ab L5752F 1.00e+0 C.16
V6498 4620T>C synonymous_variant ORF1ab_pp1a N1540N 1.00e+0 C.16
V7141 9612T>C synonymous_variant ORF1ab_pp1a Y3204Y 1.00e+0 C.16
V8113 17163G>T synonymous_variant ORF1ab_pp1ab V5721V 6.53e-1 C.16
V8747 888C>T synonymous_variant S L296L 1.00e+0 C.16
V9279 195G>T synonymous_variant E L65L 1.00e+0 C.16
V3614 291G>T missense_variant S K97N 1.00e+0 CN.1
V7235 10302T>C synonymous_variant ORF1ab_pp1a V3434V 1.00e+0 CN.1
V7298 10827T>C synonymous_variant ORF1ab_pp1a N3609N 1.00e+0 CN.1
V2797 16274A>G missense_variant ORF1ab_pp1ab D5425G 6.87e-1 B.1.1.343
V5274 38C>T missense_variant N P13L 1.00e+0 B.1.1.343
V9259 819G>T synonymous_variant ORF3a V273V 1.00e+0 B.1.1.343
V2434 13091C>T missense_variant ORF1ab_pp1a T4364I 1.00e+0 B.1.469
V4262 3682G>C missense_variant S V1228L 1.00e+0 B.1.469
V474 1307C>T missense_variant ORF1ab_pp1a T436I 1.00e+0 B.1.469
V8632 96C>T synonymous_variant S F32F 1.00e+0 B.1.469
V9485 348C>T synonymous_variant ORF7a L116L 7.06e-1 B.1.469
V4735 100C>T missense_variant M L34F 1.00e+0 B.31
V5203 328G>C missense_variant ORF8 E110Q 1.00e+0 BN.1.6
V1291 5162C>T missense_variant ORF1ab_pp1a T1721I 6.93e-1 CP.1.2
V4697 -38_-37delTT upstream_gene_variant M None -6.11e-1 CP.1.2
V5402 466G>T missense_variant N A156S 6.93e-1 CP.1.2
V5807 *4385C>T downstream_gene_variant S None 6.10e-1 CP.1.2
V6066 1458T>C synonymous_variant ORF1ab_pp1a A486A 1.00e+0 CP.1.2
V6752 6438T>C synonymous_variant ORF1ab_pp1a L2146L -8.85e-1 CP.1.2
V8186 17721C>T synonymous_variant ORF1ab_pp1ab D5907D 9.31e-1 CP.1.2
V8761 1029C>T synonymous_variant S N343N 1.00e+0 CP.1.2
V9413 159T>C synonymous_variant ORF6 D53D -8.40e-1 CP.1.2
V9812 1242T>C synonymous_variant N A414A 1.00e+0 CP.1.2
V5860 129T>C synonymous_variant ORF1ab_pp1a R43R 8.64e-1 CP.3
V6426 4056C>T synonymous_variant ORF1ab_pp1a A1352A -6.65e-1 CP.3
V9812 1242T>C synonymous_variant N A414A 8.64e-1 CP.3





Manual curation of mutation (13689A>G)-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