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The current mutation

ID: V7380
DNA: 11547C>A
Protein: G3849G
Position: 11812








COV2Var annotation categories







Summary information of mutation (11547C>A)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   11812
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   synonymous_variant
  DNA Level   DNA Mutation: 11547C>A
  Ref Seq: C
  Mut Seq: A
  Protein Level   Protein 1-letter Mutation: G3849G
  Protein 3-letter Mutation: Gly3849Gly

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 (11547C>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 B.1.2 8 5 6.25e-1
2020-10 B.1.1.222 8 1 1.25e-1
2020-10 B.1.36.8 8 1 1.25e-1
2020-11 B.1.1.442 8 2 2.50e-1
2020-11 B.1.351 8 2 2.50e-1
2020-11 B.1.128 8 1 1.25e-1
2020-12 B.1.351 73 28 3.84e-1
2020-12 B.1 73 14 1.92e-1
2020-12 B.1.160 73 13 1.78e-1
2020-03 B.1 1 1 1.00e+0
2020-04 B.39 1 1 1.00e+0
2020-05 B.1.1 5 2 4.00e-1
2020-05 A 5 1 2.00e-1
2020-05 B.1 5 1 2.00e-1
2020-07 B.1 2 1 5.00e-1
2020-07 B.1.369 2 1 5.00e-1
2020-08 B.1.516 1 1 1.00e+0
2020-09 B.1.160 1 1 1.00e+0
2021-01 B.1.351 64 30 4.69e-1
2021-01 B.1.177 64 9 1.41e-1
2021-01 B.1.1.7 64 8 1.25e-1
2021-10 AY.4 86 40 4.65e-1
2021-10 AY.103 86 5 5.81e-2
2021-10 AY.106 86 5 5.81e-2
2021-11 AY.4 99 43 4.34e-1
2021-11 AY.99.2 99 6 6.06e-2
2021-11 AY.103 99 5 5.05e-2
2021-12 AY.103 49 8 1.63e-1
2021-12 AY.4 49 7 1.43e-1
2021-12 AY.113 49 6 1.22e-1
2021-02 B.1.351 123 101 8.21e-1
2021-02 R.1 123 9 7.32e-2
2021-02 B.1.1.7 123 3 2.44e-2
2021-03 B.1.351 909 846 9.31e-1
2021-03 B.1.1.7 909 43 4.73e-2
2021-03 R.1 909 10 1.10e-2
2021-04 B.1.351 804 700 8.71e-1
2021-04 B.1.1.7 804 92 1.14e-1
2021-04 B.1 804 2 2.49e-3
2021-05 B.1.351 528 467 8.84e-1
2021-05 B.1.1.7 528 50 9.47e-2
2021-05 P.1 528 5 9.47e-3
2021-06 B.1.351 794 752 9.47e-1
2021-06 B.1.1.7 794 33 4.16e-2
2021-06 AY.44 794 2 2.52e-3
2021-07 B.1.351 591 561 9.49e-1
2021-07 B.1.1.7 591 12 2.03e-2
2021-07 AY.103 591 2 3.38e-3
2021-08 B.1.351 175 98 5.60e-1
2021-08 AY.29 175 29 1.66e-1
2021-08 AY.103 175 8 4.57e-2
2021-09 AY.4 64 15 2.34e-1
2021-09 AY.25 64 8 1.25e-1
2021-09 AY.34.1 64 8 1.25e-1
2022-01 BA.1.1 37 12 3.24e-1
2022-01 BA.1.17.2 37 5 1.35e-1
2022-01 AY.122 37 4 1.08e-1
2022-10 BF.7.6 46 25 5.43e-1
2022-10 BQ.1.6 46 15 3.26e-1
2022-10 BA.5.2.20 46 3 6.52e-2
2022-11 BF.7.6 36 16 4.44e-1
2022-11 BQ.1.6 36 8 2.22e-1
2022-11 XBB.2 36 6 1.67e-1
2022-12 BF.7.6 57 14 2.46e-1
2022-12 BQ.1.6 57 14 2.46e-1
2022-12 XBB.2 57 9 1.58e-1
2022-02 BA.1.1 67 53 7.91e-1
2022-02 BA.2 67 5 7.46e-2
2022-02 BA.2.3 67 4 5.97e-2
2022-03 BA.1.1 77 41 5.32e-1
2022-03 BA.2 77 21 2.73e-1
2022-03 BA.2.3 77 13 1.69e-1
2022-04 BA.2 59 44 7.46e-1
2022-04 BA.1.1 59 8 1.36e-1
2022-04 BA.2.3 59 5 8.47e-2
2022-05 BA.2 25 13 5.20e-1
2022-05 BA.2.9 25 5 2.00e-1
2022-05 BA.2.24 25 3 1.20e-1
2022-06 BA.2 14 6 4.29e-1
2022-06 BA.4.1 14 5 3.57e-1
2022-06 BA.2.13 14 1 7.14e-2
2022-07 BA.2 9 5 5.56e-1
2022-07 BA.4.1 9 2 2.22e-1
2022-07 BA.4.8 9 1 1.11e-1
2022-08 BA.4.6.4 8 2 2.50e-1
2022-08 BA.5.2.26 8 2 2.50e-1
2022-08 BA.2.75.3 8 1 1.25e-1
2022-09 BQ.1.6 17 8 4.71e-1
2022-09 BA.5.6 17 3 1.76e-1
2022-09 BF.7.6 17 3 1.76e-1
2023-01 BF.7.6 25 5 2.00e-1
2023-01 BQ.1.1 25 3 1.20e-1
2023-01 CH.1.1.3 25 3 1.20e-1
2023-02 BN.3.1 4 1 2.50e-1
2023-02 BQ.1.1.19 4 1 2.50e-1
2023-02 XBB.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
V7380 B.1.351 1.15e-1 3593 2020-2-18 2022-10-26
V7380 BF.7.6 1.90e-2 63 2022-2-21 2023-2-18
V7380 BQ.1.6 4.45e-2 47 2022-7-25 2023-2-13
V7380 B.1.1.442 3.85e-2 2 2020-5-16 2021-4-13






Examining mutation (11547C>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 (11547C>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 -5.14e+0 1.03e+0 -4.98e+0 6.33e-7 Decrease
Deceased 1.35e+0 3.06e-1 4.42e+0 1.01e-5 Increase
Homebound -2.11e+1 6.51e+3 -3.25e-3 9.97e-1 Decrease
Hospitalized -5.06e+0 2.24e-1 -2.26e+1 9.57e-113 Decrease
Mild -5.15e+0 1.02e+0 -5.04e+0 4.57e-7 Decrease
Recovered 3.15e+0 2.29e-1 1.38e+1 4.89e-43 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 -3.89e-1 9.50e-2 -4.09e+0 4.35e-5 Decrease
18-39 4.36e-1 4.37e-2 9.98e+0 1.87e-23 Increase
40-64 -7.54e-2 4.51e-2 -1.67e+0 9.46e-2 Decrease
65-84 -3.19e-1 6.82e-2 -4.68e+0 2.88e-6 Decrease
>=85 -1.15e+0 1.57e-1 -7.33e+0 2.34e-13 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 -3.22e-2 4.32e-2 -7.44e-1 4.57e-1 Decrease





Investigating natural selection at mutation (11547C>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 (11547C>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 (11547C>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 (11547C>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 (11547C>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 (11547C>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 (11547C>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 (11547C>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.

        Show as:

        Show interface residues:





Impact of mutation (11547C>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 (11547C>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
V8851 1746T>C synonymous_variant S L582L 6.43e-1 BA.1.1
V3798 794A>G missense_variant S Y265C 6.01e-1 AY.4
V1086 3741G>T missense_variant ORF1ab_pp1a K1247N 1.00e+0 BA.1.1.18
V1087 3743T>C missense_variant ORF1ab_pp1a F1248S 1.00e+0 BA.1.1.18
V5589 1043A>G missense_variant N D348G 7.61e-1 BA.2.3
V6674 5922C>T synonymous_variant ORF1ab_pp1a H1974H 7.07e-1 AY.4.2
V9121 3720C>T synonymous_variant S C1240C 7.07e-1 AY.47
V2088 10628C>T missense_variant ORF1ab_pp1a T3543I 7.53e-1 B.1
V5103 91T>C missense_variant ORF8 Y31H 7.36e-1 B.1
V7156 9705A>G synonymous_variant ORF1ab_pp1a A3235A 7.53e-1 B.1
V7624 13383C>T synonymous_variant ORF1ab_pp1ab Y4461Y 6.85e-1 B.1
V2026 10075C>T missense_variant ORF1ab_pp1a P3359S 6.12e-1 BA.5.6
V4676 121G>T missense_variant E A41S 7.07e-1 AY.106
V5886 264G>T synonymous_variant ORF1ab_pp1a L88L 1.00e+0 AY.106
V5990 885C>T synonymous_variant ORF1ab_pp1a G295G 8.94e-1 AY.106
V6869 7500C>T synonymous_variant ORF1ab_pp1a S2500S 8.16e-1 AY.106
V6054 1344C>T synonymous_variant ORF1ab_pp1a D448D 1.00e+0 AY.116.1
V4504 385C>T missense_variant ORF3a L129F 1.00e+0 AY.117
V7266 10537C>T synonymous_variant ORF1ab_pp1a L3513L 1.00e+0 AY.117
V2676 15063G>T missense_variant ORF1ab_pp1ab M5021I 1.00e+0 AY.120.2
V4096 2515G>T missense_variant S D839Y 1.00e+0 AY.120
V1726 7844C>T missense_variant ORF1ab_pp1a T2615I 1.00e+0 AY.122.6
V1921 9173C>T missense_variant ORF1ab_pp1a T3058I 1.00e+0 AY.122.6
V2808 16423A>G missense_variant ORF1ab_pp1ab I5475V 1.00e+0 AY.122.6
V4675 89C>T missense_variant E T30I 1.00e+0 AY.122.6
V4775 373C>T missense_variant M H125Y 7.07e-1 AY.122.6
V4781 463C>T missense_variant M H155Y 1.00e+0 AY.122.6
V5555 867G>T missense_variant N Q289H 1.00e+0 AY.122.6
V3742 644A>G missense_variant S D215G 7.07e-1 AY.124
V4399 161C>T missense_variant ORF3a A54V 7.07e-1 AY.124
V5630 1154G>A missense_variant N R385K 7.07e-1 AY.124
V8130 17277C>T synonymous_variant ORF1ab_pp1ab D5759D 7.07e-1 AY.124
V8184 17706T>C synonymous_variant ORF1ab_pp1ab D5902D 1.00e+0 AY.124
V2770 15983C>T missense_variant ORF1ab_pp1ab A5328V 6.12e-1 AY.23
V5999 930T>C synonymous_variant ORF1ab_pp1a N310N 1.00e+0 AY.36
V8964 2568C>T synonymous_variant S N856N 6.45e-1 AY.4.2.2
V3994 1958C>T missense_variant S A653V 1.00e+0 AY.43.3
V4785 524C>T missense_variant M T175M 1.00e+0 AY.43.3
V5357 268G>T missense_variant N A90S 1.00e+0 AY.43.3
V5960 669C>T synonymous_variant ORF1ab_pp1a D223D 7.07e-1 AY.43.3
V638 1902G>T missense_variant ORF1ab_pp1a K634N 1.00e+0 AY.43.3
V6849 7329C>T synonymous_variant ORF1ab_pp1a G2443G 1.00e+0 AY.43.3
V9783 1080C>T synonymous_variant N Y360Y 1.00e+0 AY.43.3
V3392 20347C>T missense_variant ORF1ab_pp1ab L6783F 6.02e-1 AY.5.3
V6106 1732C>T synonymous_variant ORF1ab_pp1a L578L 1.00e+0 AY.54
V7782 14544T>C synonymous_variant ORF1ab_pp1ab Y4848Y 1.00e+0 AY.54
V9436 114A>G synonymous_variant ORF7a G38G 1.00e+0 AY.54
V3372 20219C>T missense_variant ORF1ab_pp1ab S6740F 7.07e-1 AY.59
V3666 459G>A missense_variant S M153I 1.00e+0 AY.59
V8734 789A>G synonymous_variant S A263A 1.00e+0 AY.59
V1316 5363C>T missense_variant ORF1ab_pp1a T1788M 6.39e-1 AY.99.2
V1333 5459C>T missense_variant ORF1ab_pp1a T1820I 7.07e-1 B.1.1.529
V719 2262G>T missense_variant ORF1ab_pp1a E754D 1.00e+0 B.1.1.529
V8836 1629C>T synonymous_variant S F543F 7.07e-1 B.1.1.529
V2740 15661C>T missense_variant ORF1ab_pp1ab L5221F 9.75e-1 B.1.351
V3555 79G>T missense_variant S A27S 9.80e-1 B.1.351
V8184 17706T>C synonymous_variant ORF1ab_pp1ab D5902D 9.73e-1 B.1.351
V2325 12145A>G missense_variant ORF1ab_pp1a I4049V 7.54e-1 B.1.36.29
V4633 775G>T missense_variant ORF3a V259L 9.25e-1 B.1.36.29
V6064 1419C>T synonymous_variant ORF1ab_pp1a I473I 6.52e-1 B.1.36.29
V6921 7875C>T synonymous_variant ORF1ab_pp1a S2625S 7.05e-1 B.1.36.29
V7304 10908C>T synonymous_variant ORF1ab_pp1a L3636L 7.05e-1 B.1.36.29
V8927 2334C>T synonymous_variant S T778T 1.00e+0 B.1.36.29
V9741 894C>T synonymous_variant N Y298Y 7.73e-1 B.1.36.29
V1967 9595_9597delTTA conservative_inframe_deletion ORF1ab_pp1a L3199del 7.07e-1 B.1.36.8
V3442 20770C>T missense_variant ORF1ab_pp1ab L6924F 1.00e+0 B.1.36.8
V4012 2027C>T missense_variant S T676I 7.07e-1 B.1.36.8
V4200 3352G>T missense_variant S D1118Y 1.00e+0 B.1.36.8
V4485 328G>T missense_variant ORF3a A110S 7.07e-1 B.1.36.8
V4918 184C>T stop_gained ORF7a Q62* 7.07e-1 B.1.36.8
V5023 40_42delTTA conservative_inframe_deletion ORF7b L14del 1.00e+0 B.1.36.8
V647 1958C>T missense_variant ORF1ab_pp1a S653L 1.00e+0 B.1.36.8
V6874 7551T>C synonymous_variant ORF1ab_pp1a S2517S 7.07e-1 B.1.36.8
V71 -59C>T upstream_gene_variant ORF1ab_pp1a None 8.16e-1 B.1.369
V8006 16362C>T synonymous_variant ORF1ab_pp1ab L5454L 1.00e+0 B.1.427
V2740 15661C>T missense_variant ORF1ab_pp1ab L5221F 7.07e-1 B.1.620
V3555 79G>T missense_variant S A27S 7.07e-1 B.1.620
V4310 35C>T missense_variant ORF3a T12I 7.07e-1 B.1.620
V4888 110C>T missense_variant ORF7a S37F 7.07e-1 B.1.620
V7766 14460C>T synonymous_variant ORF1ab_pp1ab F4820F 7.07e-1 B.1.620
V7966 16059C>T synonymous_variant ORF1ab_pp1ab C5353C 7.07e-1 B.1.620
V8184 17706T>C synonymous_variant ORF1ab_pp1ab D5902D 7.07e-1 B.1.620
V1863 8672C>T missense_variant ORF1ab_pp1a A2891V 6.12e-1 BA.2.24
V4091 2485G>A missense_variant S A829T 1.00e+0 BA.2.75.3
V5559 898C>T missense_variant N H300Y 1.00e+0 BA.2.75.3
V9233 666C>T synonymous_variant ORF3a D222D 6.45e-1 BA.5.2.20
V948 3218G>T missense_variant ORF1ab_pp1a G1073V 1.00e+0 BE.1.1.2
V1406 6020C>T missense_variant ORF1ab_pp1a T2007I 7.07e-1 BE.1.4
V2808 16423A>G missense_variant ORF1ab_pp1ab I5475V 7.07e-1 BE.1.4
V5850 99C>T synonymous_variant ORF1ab_pp1a D33D 1.00e+0 BE.1.4
V1438 6115C>T missense_variant ORF1ab_pp1a L2039F 7.07e-1 BF.26
V2211 11256G>T missense_variant ORF1ab_pp1a M3752I 1.00e+0 BF.26
V4608 717G>T missense_variant ORF3a E239D 7.07e-1 BF.26
V536 1567A>G missense_variant ORF1ab_pp1a I523V 7.07e-1 BF.26
V6214 2427A>T synonymous_variant ORF1ab_pp1a T809T 1.00e+0 BF.26
V9353 405A>G synonymous_variant M E135E 1.00e+0 BF.26
V4048 2147C>T missense_variant S T716I 7.07e-1 BF.7.14
V1873 8729C>T missense_variant ORF1ab_pp1a T2910I 1.00e+0 BF.7.5
V1936 9268A>G missense_variant ORF1ab_pp1a T3090A 7.07e-1 BF.7.5
V3397 20413C>T missense_variant ORF1ab_pp1ab P6805S 1.00e+0 BF.7.5
V6176 2184C>T synonymous_variant ORF1ab_pp1a G728G 7.07e-1 BF.7.5
V7918 15675T>C synonymous_variant ORF1ab_pp1ab D5225D 7.07e-1 BF.7.5
V6817 7002C>T synonymous_variant ORF1ab_pp1a F2334F 7.07e-1 BM.4.1.1
V3368 20201A>G missense_variant ORF1ab_pp1ab D6734G 7.07e-1 BN.3.1
V3969 1841A>G missense_variant S D614G -7.07e-1 BN.3.1
V3997 1963C>T missense_variant S H655Y -7.07e-1 BN.3.1
V4701 -32T>C upstream_gene_variant M None 7.07e-1 BN.3.1
V4702 -31A>T upstream_gene_variant M None 7.07e-1 BN.3.1
V4703 -25delT upstream_gene_variant M None 7.07e-1 BN.3.1
V4704 -26T>C upstream_gene_variant M None 7.07e-1 BN.3.1
V7347 11322T>C synonymous_variant ORF1ab_pp1a N3774N 7.07e-1 BN.3.1
V7892 15474C>T synonymous_variant ORF1ab_pp1ab F5158F 7.07e-1 BN.3.1
V798 2645C>T missense_variant ORF1ab_pp1a T882I 7.07e-1 BN.3.1
V9773 1011C>T synonymous_variant N I337I 7.07e-1 BN.3.1
V1844 8590T>C missense_variant ORF1ab_pp1a F2864L 1.00e+0 BQ.1.1.11
V3693 541G>A missense_variant S G181R 1.00e+0 BQ.1.1.11
V5073 22G>T stop_gained ORF8 G8* 7.07e-1 BQ.1.1.11
V5658 -23C>T upstream_gene_variant ORF10 None 1.00e+0 BQ.1.1.11
V6463 4321C>T synonymous_variant ORF1ab_pp1a L1441L 7.07e-1 BQ.1.1.11
V6716 6156G>T synonymous_variant ORF1ab_pp1a V2052V 1.00e+0 BQ.1.1.11
V9200 390C>T synonymous_variant ORF3a C130C 8.16e-1 BQ.1.1.11
V7423 11811C>T synonymous_variant ORF1ab_pp1a N3937N 7.07e-1 BQ.1.1.19
V2924 17210C>T missense_variant ORF1ab_pp1ab T5737I 7.81e-1 BQ.1.6
V8903 2076C>T synonymous_variant S I692I 7.61e-1 BQ.1.6
V499 1358T>C missense_variant ORF1ab_pp1a I453T 7.07e-1 P.1.7
V6782 6732C>T synonymous_variant ORF1ab_pp1a I2244I 1.00e+0 P.1.7
V1268 4965G>T missense_variant ORF1ab_pp1a K1655N 1.00e+0 P.3
V2163 11023_11031delTCTGGTTTT conservative_inframe_deletion ORF1ab_pp1a S3675_F3677del 7.06e-1 P.3
V2415 12853G>T missense_variant ORF1ab_pp1a A4285S 1.00e+0 P.3
V2740 15661C>T missense_variant ORF1ab_pp1ab L5221F 1.00e+0 P.3
V342 794C>T missense_variant ORF1ab_pp1a T265I 1.00e+0 P.3
V3555 79G>T missense_variant S A27S 7.06e-1 P.3
V3599 239A>C missense_variant S D80A 7.06e-1 P.3
V3751 725_733delTTGCTTTAC disruptive_inframe_deletion S L242_L244del 7.06e-1 P.3
V48 -92G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 P.3
V5965 690C>T synonymous_variant ORF1ab_pp1a C230C 1.00e+0 P.3
V8184 17706T>C synonymous_variant ORF1ab_pp1ab D5902D 1.00e+0 P.3
V9585 111A>T synonymous_variant N S37S 1.00e+0 P.3
V1348 5561C>T missense_variant ORF1ab_pp1a T1854I 8.04e-1 R.1
V2172 11057C>T missense_variant ORF1ab_pp1a A3686V 9.77e-1 R.1
V4759 244A>G missense_variant M I82V 8.70e-1 R.1
V6633 5577C>T synonymous_variant ORF1ab_pp1a Y1859Y 1.00e+0 R.1
V9200 390C>T synonymous_variant ORF3a C130C 9.38e-1 R.1
V6523 4755C>T synonymous_variant ORF1ab_pp1a D1585D 1.00e+0 XBB.1
V1316 5363C>T missense_variant ORF1ab_pp1a T1788M 1.00e+0 AY.75.2
V2021 10058A>G missense_variant ORF1ab_pp1a K3353R 7.06e-1 AY.75.2
V2163 11023_11031delTCTGGTTTT conservative_inframe_deletion ORF1ab_pp1a S3675_F3677del 1.00e+0 AY.75.2
V2267 11743C>T missense_variant ORF1ab_pp1a L3915F 1.00e+0 AY.75.2
V2897 16995G>T missense_variant ORF1ab_pp1ab E5665D 1.00e+0 AY.75.2
V342 794C>T missense_variant ORF1ab_pp1a T265I 1.00e+0 AY.75.2
V3742 644A>G missense_variant S D215G 7.06e-1 AY.75.2
V3751 725_733delTTGCTTTAC disruptive_inframe_deletion S L242_L244del 7.06e-1 AY.75.2
V7337 11241A>G synonymous_variant ORF1ab_pp1a V3747V 1.00e+0 AY.75.2
V8449 19719C>T synonymous_variant ORF1ab_pp1ab V6573V 7.06e-1 AY.75.2
V8518 20406G>A synonymous_variant ORF1ab_pp1ab A6802A 1.00e+0 AY.75.2
V1426 6087G>T missense_variant ORF1ab_pp1a K2029N 7.00e-1 B.1.1.442
V3373 20223G>T missense_variant ORF1ab_pp1ab K6741N 7.00e-1 B.1.1.442
V3697 542G>T missense_variant S G181V 7.00e-1 B.1.1.442
V3998 1972A>G missense_variant S N658D 7.00e-1 B.1.1.442
V4524 463G>T missense_variant ORF3a D155Y 7.00e-1 B.1.1.442
V5513 702G>T missense_variant N M234I 7.00e-1 B.1.1.442
V7273 10605G>T synonymous_variant ORF1ab_pp1a L3535L 7.00e-1 B.1.1.442
V7881 15390C>T synonymous_variant ORF1ab_pp1ab D5130D 1.00e+0 B.1.1.442
V8591 20991G>C synonymous_variant ORF1ab_pp1ab A6997A 7.00e-1 B.1.1.442
V8820 1497C>T synonymous_variant S P499P 1.00e+0 B.1.1.442
V968 3287C>T missense_variant ORF1ab_pp1a P1096L 7.00e-1 B.1.1.442
V2447 13166C>T missense_variant ORF1ab_pp1a P4389L 1.00e+0 B.1.177.33
V6045 1284C>T synonymous_variant ORF1ab_pp1a S428S 1.00e+0 B.1.177.33
V7044 8868C>T synonymous_variant ORF1ab_pp1a L2956L 1.00e+0 B.1.177.33
V7159 9717T>C synonymous_variant ORF1ab_pp1a N3239N 7.06e-1 B.1.177.33
V9490 36C>T synonymous_variant ORF7b C12C 1.00e+0 B.1.177.33
V975 3304A>G missense_variant ORF1ab_pp1a S1102G 7.06e-1 B.1.177.33
V7227 10221A>G synonymous_variant ORF1ab_pp1a S3407S 1.00e+0 B.1.516
V1192 4586A>G missense_variant ORF1ab_pp1a K1529R 1.00e+0 B.1.530
V2240 11478G>T missense_variant ORF1ab_pp1a Q3826H 1.00e+0 B.1.530
V2740 15661C>T missense_variant ORF1ab_pp1ab L5221F 1.00e+0 B.1.530
V2840 16671G>T missense_variant ORF1ab_pp1ab M5557I -1.00e+0 B.1.530
V3525 26C>T missense_variant S P9L 1.00e+0 B.1.530
V3599 239A>C missense_variant S D80A 1.00e+0 B.1.530
V3742 644A>G missense_variant S D215G 1.00e+0 B.1.530
V3909 1450G>A missense_variant S E484K 1.00e+0 B.1.530
V3927 1501A>T missense_variant S N501Y 1.00e+0 B.1.530
V4187 3301C>T missense_variant S H1101Y 1.00e+0 B.1.530
V4232 3526G>T missense_variant S V1176F 1.00e+0 B.1.530
V4535 512C>T missense_variant ORF3a S171L 1.00e+0 B.1.530
V4692 212C>T missense_variant E P71L 1.00e+0 B.1.530
V5237 1delA frameshift_variant&start_lost N M1fs 1.00e+0 B.1.530
V5635 1172C>T missense_variant N T391I 1.00e+0 B.1.530
V5749 *4340C>T downstream_gene_variant S None 1.00e+0 B.1.530
V608 1796C>T missense_variant ORF1ab_pp1a A599V 1.00e+0 B.1.530
V895 3026A>G missense_variant ORF1ab_pp1a Q1009R -1.00e+0 B.1.530
V2513 13598C>T missense_variant ORF1ab_pp1ab T4533I 1.00e+0 BA.4.8
V4775 373C>T missense_variant M H125Y 1.00e+0 BA.4.8
V893 3011C>T missense_variant ORF1ab_pp1a T1004I 1.00e+0 BA.4.8





Manual curation of mutation (11547C>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