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The current mutation

ID: V5700
DNA: 47T>C
Protein: L16P
Position: 29604








COV2Var annotation categories







Summary information of mutation (47T>C)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp11
  Gene Name   ORF10
  Gene Type   protein_coding
  Genome position   29604
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 47T>C
  Ref Seq: T
  Mut Seq: C
  Protein Level   Protein 1-letter Mutation: L16P
  Protein 3-letter Mutation: Leu16Pro

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 (47T>C) across geographic regions, temporal trends, and lineages

The count of genome sequences harboring this mutation and its distribution across global regions offer insights into regional variations.
Note: The distribution of mutation across 218 geographical regions. Color representation of genome sequence counts. The data is obtained from GISAID's metadata, specifically capturing the regional distribution of genomic sequences.



The dynamic count of genome sequences containing this mutation over time.
Note: Clicking the "Count" or "Cumulative Count" button toggles the view. Count represents the number of genome sequences per month. Cumulative count represents the accumulated total count up to the respective month. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.



For every time point represented in the graph above, identifying the top 3 lineages with the highest count of genome sequences carrying this mutation aids in pinpointing noteworthy lineages for further analysis.
Note: Users can filter the lineages by entering a "Year-Month" term in the search box. For example, entering 2020-01 will display lineages that appeared in January 2020. The data is obtained from GISAID's metadata, specifically capturing the collection date of genomic sequences.

Collection date Lineage Total lineage monthly counts Lineage-specific monthly counts Lineage-specific monthly frequency
2020-10 B.1.1.10 3 1 3.33e-1
2020-10 B.1.177.15 3 1 3.33e-1
2020-10 B.1.337 3 1 3.33e-1
2020-11 B.1.177 4 4 1.00e+0
2020-12 B.1.177.57 6 3 5.00e-1
2020-12 B.1.177.82 6 2 3.33e-1
2020-12 B.1.298 6 1 1.67e-1
2020-08 B.1.509 1 1 1.00e+0
2020-09 B.1.177.15 4 3 7.50e-1
2020-09 B.1.2 4 1 2.50e-1
2021-01 B.1.1 16 11 6.88e-1
2021-01 B.1.2 16 2 1.25e-1
2021-01 B.1.243 16 1 6.25e-2
2021-10 AY.4 2241 1960 8.75e-1
2021-10 AY.5 2241 180 8.03e-2
2021-10 B.1.617.2 2241 51 2.28e-2
2021-11 AY.4 2343 2089 8.92e-1
2021-11 AY.5 2343 193 8.24e-2
2021-11 B.1.617.2 2343 30 1.28e-2
2021-12 AY.4 1163 1034 8.89e-1
2021-12 AY.5 1163 47 4.04e-2
2021-12 B.1.617.2 1163 29 2.49e-2
2021-02 B.1.369 4 3 7.50e-1
2021-02 AY.33 4 1 2.50e-1
2021-03 B.1.177.81 11 4 3.64e-1
2021-03 B.1.1.7 11 3 2.73e-1
2021-03 B.1.369 11 2 1.82e-1
2021-04 B.1.1.7 27 20 7.41e-1
2021-04 B.1.617.2 27 3 1.11e-1
2021-04 B.1 27 1 3.70e-2
2021-05 B.1.1.7 20 18 9.00e-1
2021-05 P.1.7 20 1 5.00e-2
2021-05 XB 20 1 5.00e-2
2021-06 AY.4 128 103 8.05e-1
2021-06 AY.5 128 12 9.38e-2
2021-06 B.1.617.2 128 7 5.47e-2
2021-07 AY.4 1031 955 9.26e-1
2021-07 B.1.617.2 1031 36 3.49e-2
2021-07 AY.5 1031 27 2.62e-2
2021-08 AY.4 1840 1728 9.39e-1
2021-08 AY.5 1840 84 4.57e-2
2021-08 AY.43 1840 5 2.72e-3
2021-09 AY.4 2184 1853 8.48e-1
2021-09 AY.5 2184 286 1.31e-1
2021-09 B.1.617.2 2184 25 1.14e-2
2022-01 AY.4 69 28 4.06e-1
2022-01 AY.42 69 11 1.59e-1
2022-01 BA.1.1 69 10 1.45e-1
2022-10 CA.3 5 3 6.00e-1
2022-10 BQ.1.1 5 2 4.00e-1
2022-11 BQ.1.2 23 8 3.48e-1
2022-11 BN.1.2 23 5 2.17e-1
2022-11 BQ.1.1 23 5 2.17e-1
2022-12 BQ.1.1.32 76 26 3.42e-1
2022-12 BQ.1.1 76 19 2.50e-1
2022-12 BQ.1.2 76 13 1.71e-1
2022-02 BA.1.1 22 6 2.73e-1
2022-02 BA.2.9 22 5 2.27e-1
2022-02 BA.2 22 4 1.82e-1
2022-03 BA.2 40 20 5.00e-1
2022-03 BA.1.1 40 14 3.50e-1
2022-03 BA.2.9 40 3 7.50e-2
2022-04 BA.2 33 14 4.24e-1
2022-04 BA.2.9 33 9 2.73e-1
2022-04 BA.2.48 33 4 1.21e-1
2022-05 BA.2 29 14 4.83e-1
2022-05 BA.2.9 29 11 3.79e-1
2022-05 BA.2.48 29 2 6.90e-2
2022-06 BA.2 8 3 3.75e-1
2022-06 BA.2.48 8 2 2.50e-1
2022-06 BA.4.1 8 1 1.25e-1
2022-07 BE.1 6 3 5.00e-1
2022-07 BA.2 6 1 1.67e-1
2022-07 BA.2.56 6 1 1.67e-1
2022-08 BA.2.56 9 4 4.44e-1
2022-08 BA.4 9 2 2.22e-1
2022-08 BA.2.38 9 1 1.11e-1
2022-09 BA.5.2.44 1 1 1.00e+0
2023-01 BQ.1.1.32 65 20 3.08e-1
2023-01 BQ.1.1 65 18 2.77e-1
2023-01 BQ.1.2 65 10 1.54e-1
2023-02 BN.1.2 3 1 3.33e-1
2023-02 BQ.1.1 3 1 3.33e-1
2023-02 BQ.1.1.32 3 1 3.33e-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
V5700 AY.4 1.19e-2 9750 2020-8-3 2022-10-18
V5700 AY.4.9 1.79e-2 44 2020-8-11 2022-6-7
V5700 AY.5 1.35e-2 829 2020-9-8 2022-7-26






Examining mutation (47T>C) 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 (47T>C) 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 -1.15e+1 6.20e+2 -1.85e-2 9.85e-1 Decrease
Deceased -1.26e+1 6.23e+2 -2.02e-2 9.84e-1 Decrease
Homebound -9.81e+0 1.66e+3 -5.92e-3 9.95e-1 Decrease
Hospitalized 1.33e+1 3.59e+2 3.72e-2 9.70e-1 Increase
Mild -1.09e+1 6.23e+2 -1.75e-2 9.86e-1 Decrease
Recovered -1.24e+1 3.68e+2 -3.37e-2 9.73e-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 2.93e-1 2.17e-1 1.35e+0 1.77e-1 Increase
18-39 -6.90e-1 1.67e-1 -4.12e+0 3.80e-5 Decrease
40-64 2.68e-1 1.38e-1 1.94e+0 5.23e-2 Increase
65-84 3.01e-1 1.76e-1 1.70e+0 8.82e-2 Increase
>=85 1.99e-1 3.42e-1 5.81e-1 5.61e-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 3.64e-1 1.38e-1 2.63e+0 8.49e-3 Increase





Investigating natural selection at mutation (47T>C) 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 (47T>C)

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 ORF10 4433.18 7.93 4470 97.37 0.495
Reference ORF10 4449.23 7.93 4470 107.63 0.637




Alterations in protein stability induced by mutation (47T>C)

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
L16P ORF10 Point 16 -1.32 Decrease 7 25 Environment
L16P ORF10 Point 16 -1.34 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (47T>C)

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
L16P ORF10 Point 0.131 Altered PPI_residue (Pr = 0.40 | P = 9.3e-04)
Loss of Helix (Pr = 0.35 | P = 4.1e-04)
Gain of Strand (Pr = 0.30 | P = 2.9e-03)
Altered Cytoplasmic_loop (Pr = 0.29 | P = 3.8e-04)
Altered PPI_hotspot (Pr = 0.27 | P = 8.1e-03)
Altered Stability (Pr = 0.08 | P = 0.06)
Gain of Sulfation at Y14 (Pr = 0.02 | P = 0.03)




Exploring mutation (47T>C) 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 (47T>C)

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
L16P ORF10 29604 Pepsin (pH1.3) NA
 YSLLLCRMNS (pos: 17)
TIYSLLLCRM (pos: 15)
L16P ORF10 29604 Proteinase K NA
 IYSLLLCRMN (pos: 16)
L16P ORF10 29604 Thermolysin NA
 TIYSLLLCRM (pos: 15)
L16P ORF10 29604 Chymotrypsin-low specificity NA
 IYSLLLCRMN (pos: 16)
L16P ORF10 29604 Pepsin (pH>2) NA
 YSLLLCRMNS (pos: 17)
TIYSLLLCRM (pos: 15)
FTIYSLLLCR (pos: 14)




Impact of spike protein mutation (47T>C) 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 (47T>C) 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 (47T>C) 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 (47T>C) 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
V7273 10605G>T synonymous_variant ORF1ab_pp1a L3535L 6.37e-1 AY.4
V3300 19804G>T missense_variant ORF1ab_pp1ab G6602C 8.21e-1 AY.5
V6094 1644C>T synonymous_variant ORF1ab_pp1a F548F 9.65e-1 AY.5
V679 2060C>T missense_variant ORF1ab_pp1a A687V 6.18e-1 AY.5
V6904 7776T>C synonymous_variant ORF1ab_pp1a D2592D 9.51e-1 AY.5
V4371 124C>T missense_variant ORF3a P42S 6.67e-1 BA.1.18
V8723 684T>C synonymous_variant S D228D 7.07e-1 BA.4.1
V7912 15645T>C synonymous_variant ORF1ab_pp1ab G5215G 9.06e-1 BQ.1.1
V4511 401G>A missense_variant ORF3a R134H 6.50e-1 B.1.1
V9681 603C>T synonymous_variant N S201S 6.16e-1 B.1.1
V154 145G>T missense_variant ORF1ab_pp1a G49C 6.66e-1 AY.109
V4269 3704G>T missense_variant S C1235F 1.00e+0 AY.109
V8061 16776T>C synonymous_variant ORF1ab_pp1ab N5592N 8.66e-1 AY.109
V9776 1023C>T synonymous_variant N D341D 6.54e-1 AY.109
V6144 1962C>T synonymous_variant ORF1ab_pp1a T654T 7.75e-1 AY.111
V7273 10605G>T synonymous_variant ORF1ab_pp1a L3535L 6.71e-1 AY.111
V7914 15660C>T synonymous_variant ORF1ab_pp1ab Y5220Y 7.75e-1 AY.111
V7989 16206C>T synonymous_variant ORF1ab_pp1ab P5402P 7.75e-1 AY.111
V8738 819G>A synonymous_variant S R273R 7.75e-1 AY.111
V631 1879G>T missense_variant ORF1ab_pp1a V627F 1.00e+0 AY.116.1
V8256 18207T>C synonymous_variant ORF1ab_pp1ab D6069D 6.54e-1 AY.116.1
V6311 3156A>G synonymous_variant ORF1ab_pp1a V1052V 8.16e-1 AY.119
V6895 7719T>C synonymous_variant ORF1ab_pp1a D2573D 6.67e-1 AY.33
V2130 10879A>G missense_variant ORF1ab_pp1a M3627V 6.49e-1 AY.42
V3691 539A>T missense_variant S E180V 7.07e-1 AY.45
V7466 12141C>T synonymous_variant ORF1ab_pp1a N4047N 7.07e-1 AY.45
V9525 117T>C synonymous_variant ORF8 I39I 7.07e-1 AY.45
V5843 72C>T synonymous_variant ORF1ab_pp1a R24R 8.54e-1 AY.4.9
V5955 655C>T synonymous_variant ORF1ab_pp1a L219L 8.15e-1 AY.4.9
V6237 2577C>T synonymous_variant ORF1ab_pp1a A859A 7.09e-1 AY.4.9
V3300 19804G>T missense_variant ORF1ab_pp1ab G6602C 1.00e+0 AY.5.3
V5101 88C>T missense_variant ORF8 P30S 1.00e+0 AY.5.3
V6094 1644C>T synonymous_variant ORF1ab_pp1a F548F 1.00e+0 AY.5.3
V6904 7776T>C synonymous_variant ORF1ab_pp1a D2592D 1.00e+0 AY.5.3
V8296 18492G>T synonymous_variant ORF1ab_pp1ab P6164P 1.00e+0 AY.5.3
V2996 17765C>T missense_variant ORF1ab_pp1ab A5922V 1.00e+0 AY.5.4
V3300 19804G>T missense_variant ORF1ab_pp1ab G6602C 1.00e+0 AY.5.4
V3564 152C>T missense_variant S T51I 1.00e+0 AY.5.4
V6094 1644C>T synonymous_variant ORF1ab_pp1a F548F 8.16e-1 AY.5.4
V679 2060C>T missense_variant ORF1ab_pp1a A687V 1.00e+0 AY.5.4
V6904 7776T>C synonymous_variant ORF1ab_pp1a D2592D 1.00e+0 AY.5.4
V7423 11811C>T synonymous_variant ORF1ab_pp1a N3937N 8.16e-1 AY.5.4
V7795 14661C>T synonymous_variant ORF1ab_pp1ab V4887V 6.32e-1 AY.5.4
V7797 14667C>T synonymous_variant ORF1ab_pp1ab N4889N 1.00e+0 AY.5.4
V6516 4728C>T synonymous_variant ORF1ab_pp1a N1576N 1.00e+0 AY.71
V9095 3534C>T synonymous_variant S N1178N 1.00e+0 AY.71
V2516 13633G>T missense_variant ORF1ab_pp1ab D4545Y 1.00e+0 B.1.1.10
V2795 16264G>T missense_variant ORF1ab_pp1ab V5422F 7.07e-1 B.1.1.10
V6591 5247C>T synonymous_variant ORF1ab_pp1a N1749N 1.00e+0 B.1.1.10
V66 -63C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 B.1.1.10
V7785 14574C>T synonymous_variant ORF1ab_pp1ab I4858I 1.00e+0 B.1.1.10
V9665 519A>T synonymous_variant N A173A 1.00e+0 B.1.1.10
V2266 11726A>G missense_variant ORF1ab_pp1a E3909G 1.00e+0 B.1.177.82
V9755 945C>T synonymous_variant N F315F 8.16e-1 B.1.177.82
V2164 11022G>T missense_variant ORF1ab_pp1a L3674F 1.00e+0 B.1.243
V3364 20197A>G missense_variant ORF1ab_pp1ab T6733A 7.07e-1 B.1.243
V1169 4418C>T missense_variant ORF1ab_pp1a A1473V 7.17e-1 B.1.369
V2267 11743C>T missense_variant ORF1ab_pp1a L3915F 9.35e-1 B.1.369
V2349 12347T>C missense_variant ORF1ab_pp1a M4116T 9.35e-1 B.1.369
V2658 14890C>T missense_variant ORF1ab_pp1ab H4964Y 9.35e-1 B.1.369
V2694 15187G>A missense_variant ORF1ab_pp1ab G5063S 8.82e-1 B.1.369
V4775 373C>T missense_variant M H125Y 8.36e-1 B.1.369
V5068 13G>A missense_variant ORF8 V5I 9.35e-1 B.1.369
V7066 8994A>G synonymous_variant ORF1ab_pp1a V2998V 8.01e-1 B.1.369
V9438 120C>T synonymous_variant ORF7a Y40Y 7.97e-1 B.1.369
V9582 105G>T synonymous_variant N A35A 6.05e-1 B.1.369
V2922 17180C>T missense_variant ORF1ab_pp1ab A5727V 1.00e+0 B.1.509
V3027 17922G>T missense_variant ORF1ab_pp1ab M5974I 7.07e-1 B.1.637
V3781 761C>T missense_variant S S254F 1.00e+0 BA.1.1.8
V5254 16C>A missense_variant N P6T 1.00e+0 BA.2.18
V3967 1839G>T missense_variant S Q613H 1.00e+0 BA.2.3.1
V1843 8584G>T missense_variant ORF1ab_pp1a V2862L 1.00e+0 BA.2.38
V6028 1161C>T synonymous_variant ORF1ab_pp1a Y387Y 7.07e-1 BA.2.38
V5453 598G>A missense_variant N G200S 8.94e-1 BA.2.48
V4332 68C>T missense_variant ORF3a A23V 7.30e-1 BA.2.56
V2848 16715G>A missense_variant ORF1ab_pp1ab R5572K 7.07e-1 BA.4.6.5
V2981 17680G>T missense_variant ORF1ab_pp1ab V5894L 7.07e-1 BA.4.6.5
V4105 2555C>T missense_variant S A852V 7.07e-1 BA.4
V6840 7206C>T synonymous_variant ORF1ab_pp1a D2402D 1.00e+0 BA.5.2.36
V6984 8418C>T synonymous_variant ORF1ab_pp1a I2806I 1.00e+0 BA.5.2.36
V8396 19260C>T synonymous_variant ORF1ab_pp1ab L6420L 1.00e+0 BA.5.2.36
V1018 3473C>T missense_variant ORF1ab_pp1a P1158L 7.07e-1 BA.5.2.48
V4517 428C>T missense_variant ORF3a A143V 7.07e-1 BA.5
V8295 18492G>A synonymous_variant ORF1ab_pp1ab P6164P 9.39e-1 BN.1.2
V204 269C>T missense_variant ORF1ab_pp1a A90V 9.43e-1 BQ.1.1.15
V3329 20020A>T missense_variant ORF1ab_pp1ab I6674F 7.07e-1 BQ.1.15
V3330 20021T>C missense_variant ORF1ab_pp1ab I6674T 7.07e-1 BQ.1.15
V7498 12489C>T synonymous_variant ORF1ab_pp1a C4163C 7.07e-1 BQ.1.15
V7912 15645T>C synonymous_variant ORF1ab_pp1ab G5215G 1.00e+0 BQ.1.1.8
V7912 15645T>C synonymous_variant ORF1ab_pp1ab G5215G 7.07e-1 BQ.1.18
V4337 77C>T missense_variant ORF3a S26L 7.74e-1 CA.3
V7972 16110T>C synonymous_variant ORF1ab_pp1ab N5370N 1.00e+0 CH.1.1.3
V60 -73C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 XB
V6387 3768T>C synonymous_variant ORF1ab_pp1a Y1256Y 1.00e+0 XB
V1652 7283A>G missense_variant ORF1ab_pp1a N2428S 1.00e+0 B.1.298
V4263 3682G>T missense_variant S V1228L 1.00e+0 B.1.337
V9631 378C>T synonymous_variant N N126N 1.00e+0 B.1.337
V2410 12794C>T missense_variant ORF1ab_pp1a T4265I 1.00e+0 B.1.627
V4839 181G>C missense_variant ORF6 D61H 1.00e+0 B.1.627
V4841 182A>T missense_variant ORF6 D61V 1.00e+0 B.1.627
V4979 296C>T missense_variant ORF7a P99L 1.00e+0 B.1.627
V7452 12030C>T synonymous_variant ORF1ab_pp1a T4010T 1.00e+0 B.1.627
V8449 19719C>T synonymous_variant ORF1ab_pp1ab V6573V 7.06e-1 B.1.627





Manual curation of mutation (47T>C)-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