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The current mutation

ID: V2240
DNA: 11478G>T
Protein: Q3826H
Position: 11743








COV2Var annotation categories







Summary information of mutation (11478G>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   11743
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 11478G>T
  Ref Seq: G
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: Q3826H
  Protein 3-letter Mutation: Gln3826His

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 (11478G>T) across geographic regions, temporal trends, and lineages

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



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



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

Collection date Lineage Total lineage monthly counts Lineage-specific monthly counts Lineage-specific monthly frequency
2020-10 B.1.1.33 14 4 2.86e-1
2020-10 K.3 14 4 2.86e-1
2020-10 B.1.1.93 14 2 1.43e-1
2020-11 B.1.1.121 26 16 6.15e-1
2020-11 B.1.177 26 3 1.15e-1
2020-11 B.1.351 26 2 7.69e-2
2020-12 B.1.561 40 21 5.25e-1
2020-12 B.1.160 40 5 1.25e-1
2020-12 B.1.1.201 40 2 5.00e-2
2020-04 B.1.1.137 4 2 5.00e-1
2020-04 B.29 4 1 2.50e-1
2020-04 B.6 4 1 2.50e-1
2020-05 B.1 2 1 5.00e-1
2020-05 B.1.1 2 1 5.00e-1
2020-06 B.1.1.93 9 6 6.67e-1
2020-06 B.1.1.299 9 2 2.22e-1
2020-06 B.1 9 1 1.11e-1
2020-07 B.1.1.93 38 27 7.11e-1
2020-07 B.1 38 7 1.84e-1
2020-07 B.1.590 38 3 7.89e-2
2020-08 B.1.590 8 5 6.25e-1
2020-08 B.1.1.93 8 2 2.50e-1
2020-08 B.1.1 8 1 1.25e-1
2020-09 B.1.590 12 6 5.00e-1
2020-09 B.1.1.93 12 3 2.50e-1
2020-09 B.1.1.284 12 1 8.33e-2
2021-01 B.1.2 26 5 1.92e-1
2021-01 B.1.1.7 26 3 1.15e-1
2021-01 B.1.561 26 3 1.15e-1
2021-10 AY.39 291 65 2.23e-1
2021-10 AY.9.2 291 60 2.06e-1
2021-10 AY.3 291 33 1.13e-1
2021-11 AY.4 357 100 2.80e-1
2021-11 AY.9.2 357 81 2.27e-1
2021-11 AY.39 357 48 1.34e-1
2021-12 AY.103 195 32 1.64e-1
2021-12 AY.3 195 26 1.33e-1
2021-12 AY.9.2 195 26 1.33e-1
2021-02 B.1.1.280 24 4 1.67e-1
2021-02 B.1.1.7 24 4 1.67e-1
2021-02 B.1.160 24 4 1.67e-1
2021-03 B.1.526 74 29 3.92e-1
2021-03 B.1.1.7 74 24 3.24e-1
2021-03 B.1.2 74 7 9.46e-2
2021-04 B.1.1.7 124 53 4.27e-1
2021-04 B.1.526 124 42 3.39e-1
2021-04 P.1 124 11 8.87e-2
2021-05 B.1.1.7 88 49 5.57e-1
2021-05 P.1 88 23 2.61e-1
2021-05 B.1.438.1 88 4 4.55e-2
2021-06 B.1.1.7 52 18 3.46e-1
2021-06 P.1 52 13 2.50e-1
2021-06 A.2.5 52 3 5.77e-2
2021-07 AY.7 151 27 1.79e-1
2021-07 AY.25 151 21 1.39e-1
2021-07 AY.4 151 21 1.39e-1
2021-08 AY.4 282 35 1.24e-1
2021-08 AY.44 282 35 1.24e-1
2021-08 AY.25 282 33 1.17e-1
2021-09 AY.9.2 313 51 1.63e-1
2021-09 AY.3 313 35 1.12e-1
2021-09 AY.39 313 35 1.12e-1
2022-01 AY.9.2 15 4 2.67e-1
2022-01 BA.1.18 15 3 2.00e-1
2022-01 AY.26 15 2 1.33e-1
2022-10 BF.7 34 16 4.71e-1
2022-10 BA.5.1.3 34 5 1.47e-1
2022-10 BF.5 34 5 1.47e-1
2022-11 BF.7 23 5 2.17e-1
2022-11 BQ.1.1 23 5 2.17e-1
2022-11 BF.5 23 2 8.70e-2
2022-12 BN.1.2 32 7 2.19e-1
2022-12 BQ.1.1.5 32 4 1.25e-1
2022-12 BQ.1.1 32 3 9.38e-2
2022-02 BA.2 25 14 5.60e-1
2022-02 BA.2.9 25 4 1.60e-1
2022-02 BA.1.18 25 2 8.00e-2
2022-03 BA.2 84 70 8.33e-1
2022-03 BA.2.9 84 8 9.52e-2
2022-03 BA.1 84 1 1.19e-2
2022-04 BA.2 86 58 6.74e-1
2022-04 BA.2.9 86 18 2.09e-1
2022-04 BA.2.44 86 4 4.65e-2
2022-05 BA.2 51 32 6.27e-1
2022-05 BA.2.9 51 8 1.57e-1
2022-05 BA.2.3.8 51 3 5.88e-2
2022-06 BA.2 25 11 4.40e-1
2022-06 BA.2.40.1 25 3 1.20e-1
2022-06 BA.2.35 25 2 8.00e-2
2022-07 BA.5.2.8 23 11 4.78e-1
2022-07 BA.5.5 23 2 8.70e-2
2022-07 BA.2.35 23 1 4.35e-2
2022-08 BA.5.1.3 27 3 1.11e-1
2022-08 BE.1.1 27 3 1.11e-1
2022-08 BE.1.1.2 27 3 1.11e-1
2022-09 BF.7 19 6 3.16e-1
2022-09 BA.5.1.3 19 3 1.58e-1
2022-09 BA.4.6 19 1 5.26e-2
2023-01 XBB.1.5 31 8 2.58e-1
2023-01 BQ.1.1 31 5 1.61e-1
2023-01 BN.1.2.1 31 3 9.68e-2
2023-02 XBB.1.5 3 3 1.00e+0

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
V2240 B.1.1.121 2.56e-2 8 2020-3-31 2021-1-30
V2240 B.1.1.93 1.00e+0 40 2020-6-16 2020-10-19
V2240 B.1.406 2.31e-2 4 2020-7-6 2021-3-26
V2240 B.1.590 7.18e-2 14 2020-3-15 2020-11-20
V2240 BA.2.3.8 1.42e-2 4 2022-2-8 2022-8-19
V2240 K.3 3.09e-2 5 2020-8-29 2020-12-9
V2240 XBB.6.1 2.00e-2 3 2022-10-22 2023-2-13






Examining mutation (11478G>T) found in abundant sequences of non-human animal hosts

Exploring mutation presence across 35 non-human animal hosts for cross-species transmission.
Note: We retained the mutation that appear in at least three non-human animal hosts' sequences. The data is obtained from GISAID's metadata, specifically capturing the host of genomic sequences.

Animal host Lineage Source region Collection date Accession ID




Association between mutation (11478G>T) and patients of different ages, genders, and statuses

Note: The logistic regression model was employed to examine changes in patient data before and after the mutation. The logistic regression model was conducted using the glm function in R. The data is obtained from GISAID's metadata, specifically capturing the patient status, gender, and age of genomic sequences.

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient status Ambulatory NA NA NA NA NA
Deceased NA NA NA NA NA
Homebound NA NA NA NA NA
Hospitalized NA NA NA NA NA
Mild NA NA NA NA NA
Recovered NA NA NA NA NA

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 -1.49e+1 8.40e+2 -1.77e-2 9.86e-1 Decrease
18-39 -1.71e+0 6.33e-1 -2.70e+0 6.93e-3 Decrease
40-64 -1.04e-1 4.72e-1 -2.20e-1 8.26e-1 Decrease
65-84 1.37e+0 4.92e-1 2.77e+0 5.55e-3 Increase
>=85 2.38e+0 6.10e-1 3.91e+0 9.42e-5 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 -8.84e-1 5.26e-1 -1.68e+0 9.31e-2 Decrease





Investigating natural selection at mutation (11478G>T) site for genetic adaptation and diversity

Note: Investigating the occurrence of positive selection or negative selection at this mutation site reveals implications for genetic adaptation and diversity.

The MEME method within the HyPhy software was employed to analyze positive selection. MEME: episodic selection.
Note: List of sites found to be under episodic selection by MEME (p < 0.05). "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site P-value Lineage Method

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
nsp6 10973 11842 290 257 22.09 3.05 4.00e-2 BA.2.75.2 FEL
nsp6 10973 11842 290 257 11.37 0.00 4.00e-2 BQ.1.11 FEL
nsp6 10973 11842 290 257 43.80 0.00 2.00e-2 A.27 FEL
nsp6 10973 11842 290 257 8.12 0.00 4.00e-2 BE.1.1 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
nsp6 10973 11842 290 257 9.80e-1 0.00e+0 BA.2.75.2 FUBAR
nsp6 10973 11842 290 257 9.80e-1 1.00e-2 BQ.1.11 FUBAR
nsp6 10973 11842 290 257 9.90e-1 0.00e+0 A.27 FUBAR
nsp6 10973 11842 290 257 9.70e-1 2.00e-2 BE.1.1 FUBAR
nsp6 10973 11842 290 257 0.00e+0 9.80e-1 AY.9.2 FUBAR




Alterations in protein physicochemical properties induced by mutation (11478G>T)

Understanding the alterations in protein physicochemical properties can reveal the evolutionary processes and adaptive changes of viruses
Note: ProtParam software was used for the analysis of physicochemical properties. Significant change threshold: A change exceeding 10% compared to the reference is considered a significant change. "GRAVY" is an abbreviation for "grand average of hydropathicity".

Group Protein name Molecular weight Theoretical PI Extinction coefficients Aliphatic index GRAVY
Mutation ORF1ab_pp1a 489997.92 6.04 543550 88.99 -0.023
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (11478G>T)

The impact of mutations on protein stability directly or indirectly affects the biological characteristics, adaptability, and transmission capacity of the virus
Note: iMutant 2.0 was utilized to analyze the effects of mutations on protein stability. pH 7 and a temperature of 25°C are employed to replicate the in vitro environment. pH 7.4 and a temperature of 37°C are utilized to simulate the in vivo environment.

Mutation Protein name Mutation type Position ΔDDG Stability pH Temperature Condition
Q3826H ORF1ab_pp1a Point 3826 -0.77 Decrease 7 25 Environment
Q3826H ORF1ab_pp1a Point 3826 -0.67 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (11478G>T)

The impact of mutations on protein function
Note: The MutPred2 software was used to predict the pathogenicity of a mutation and gives the molecular mechanism of pathogenicity. A score above 0.5 indicates an increased likelihood of pathogenicity. "Pr" is the abbreviation for "proportion. P" is the abbreviation for "p-value.

Mutation Protein name Mutation type Score Molecular mechanisms
Q3826H ORF1ab_pp1a Point 0.154 Loss of Relative_solvent_accessibility (Pr = 0.27 | P = 0.02)
Altered PPI_hotspot (Pr = 0.25 | P = 0.02)
Altered MoRF (Pr = 0.23 | P = 0.09)
Altered Cytoplasmic_loop (Pr = 0.22 | P = 2.8e-03)
Gain of Allosteric_site at Y3822 (Pr = 0.21 | P = 0.03)
Altered DNA_binding (Pr = 0.14 | P = 0.05)
Gain of Nickel_binding at Q3826 (Pr = 0.10 | P = 0.10)
Gain of Copper_binding at Y3822 (Pr = 0.04 | P = 0.05)




Exploring mutation (11478G>T) distribution within intrinsically disordered protein regions

Intrinsically Disordered Proteins (IDPs) which refers to protein regions that have no unique 3D structure. In viral proteins, mutations in the disordered regions s are critical for immune evasion and antibody escape, suggesting potential additional implications for vaccines and monoclonal therapeutic strategies.
Note: The iupred3 software was utilized for analyzing IDPs. A score greater than 0.5 is considered indicative of an IDP. In the plot, "POS" represents the position of the mutation.





Alterations in enzyme cleavage sites induced by mutation (11478G>T)

Exploring the impact of mutations on the cleavage sites of 28 enzymes.
Note: The PeptideCutter software was used for detecting enzymes cleavage sites. The increased enzymes cleavage sites refer to the cleavage sites in the mutated protein that are added compared to the reference protein. Conversely, the decreased enzymes cleavage sites indicate the cleavage sites in the mutated protein that are reduced compared to the reference protein.

Mutation Protein name Genome position Enzyme name Increased cleavage sites Decreased cleavage sites
Q3826H ORF1ab_pp1a 11743 Chymotrypsin-low specificity MNSHGLLPPK (pos: 3826)
 NA




Impact of spike protein mutation (11478G>T) on antigenicity and immunogenicity

Investigating the impact of mutations on antigenicity and immunogenicity carries important implications for vaccine design and our understanding of immune responses.
Note: An absolute change greater than 0.0102 (three times the median across sites) in antigenicity score is considered significant. An absolute changegreater than 0.2754 (three times the median across sites) in immunogenicity score is considered significant. The VaxiJen tool was utilized for antigenicity analysis. The IEDB tool was used for immunogenicity analysis. Antigens with a prediction score of more than 0.4 for this tool are considered candidate antigens. MHC I immunogenicity score >0, indicating a higher probability to stimulate an immune response.

Group Protein name Protein region Antigenicity score Immunogenicity score




Impact of mutation (11478G>T) on viral transmissibility by the affinity between RBD and ACE2 receptor

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

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


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

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Impact of mutation (11478G>T) on immune escape by the affinity between RBD and antibody/serum

By utilizing experimental data from deep mutational scanning (DMS), we can uncover how mutations affect the interaction between the receptor binding domain (RBD) and antibodies/serum. This approach provides valuable insights into strategies for evading the host immune response.
Note: We considered a mutation to mediate strong escape if the escape score exceeded 0.1 (10% of the maximum score of 1). A total of 1,504 antibodies/serum data were collected for this analysis. "Condition name" refers to the name of the antibodies/serum. "Mut escape score" represents the escape score of the mutation in that specific condition. "Avg mut escape score" indicates the average escape score of the mutation site in that condition, considering the occurrence of this mutation and other mutations. Class 1 antibodies bind to an epitope only in the RBD “up” conformation, and are the most abundant. Class 2 antibodies bind to the RBD both in “up” and “down” conformations. Class 3 and class 4 antibodies both bind outside the ACE2 binding site. Class 3 antibodies bind the RBD in both the open and closed conformation, while class 4 antibodies bind only in the open conformation.

Mutation Condition name Condition type Condition subtype Condition year Mut escape score Avg mut escape score




Investigating the co-mutation patterns of mutation (11478G>T) across 2,735 viral lineages

Investigating the co-mutation patterns of SARS-CoV-2 across 2,735 viral lineages to unravel the cooperative effects of different mutations. In biological research, correlation analysis of mutation sites helps us understand whether there is a close relationship or interaction between certain mutations.
Note: The Spearman correlation coefficient is used to calculate the correlation between two mutations within each Pango lineage. Holm–Bonferroni method was used for multiple test adjustment. We retained mutation pairs with correlation values greater than 0.6 or less than -0.6 and Holm–Bonferroni corrected p-values less than 0.05.

Associated mutation ID DNA mutation Mutation type Protein name Protein mutation correlation coefficient Lineage
V2841 16679G>T missense_variant ORF1ab_pp1ab S5560I 7.46e-1 AY.25
V890 2999C>T missense_variant ORF1ab_pp1a T1000I 6.41e-1 AY.3
V8492 20148A>G synonymous_variant ORF1ab_pp1ab E6716E 6.32e-1 AY.5
V2587 14054C>T missense_variant ORF1ab_pp1ab T4685I 6.84e-1 AY.26
V2819 16486C>T missense_variant ORF1ab_pp1ab P5496S 7.66e-1 AY.39
V4517 428C>T missense_variant ORF3a A143V 8.03e-1 AY.39
V5160 200C>T missense_variant ORF8 S67F 7.48e-1 AY.39
V5789 *4367G>C downstream_gene_variant S None 8.00e-1 AY.39
V864 2912C>T missense_variant ORF1ab_pp1a P971L 6.81e-1 AY.39
V9800 1167G>A synonymous_variant N Q389Q 9.42e-1 AY.39
V3936 1565C>T missense_variant S A522V 6.55e-1 AY.47
V889 2996C>T missense_variant ORF1ab_pp1a T999I 6.22e-1 AY.47
V4424 201G>T missense_variant ORF3a K67N 8.70e-1 AY.9.2
V7120 9481C>T synonymous_variant ORF1ab_pp1a L3161L 6.67e-1 BF.5
V6109 1761A>G synonymous_variant ORF1ab_pp1a T587T 6.22e-1 XBB.1.5
V4355 104T>C missense_variant ORF3a I35T 8.66e-1 A.2.5
V4452 277C>T missense_variant ORF3a H93Y 1.00e+0 A
V9332 318G>T synonymous_variant M T106T 6.68e-1 AY.118
V6250 2677C>T synonymous_variant ORF1ab_pp1a L893L 6.32e-1 AY.119.2
V2610 14316G>T missense_variant ORF1ab_pp1ab M4772I 7.74e-1 AY.13
V3047 18034A>G missense_variant ORF1ab_pp1ab I6012V 1.00e+0 AY.16
V3336 20056C>T missense_variant ORF1ab_pp1ab H6686Y 1.00e+0 AY.16
V63 -67G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 AY.16
V981 3337C>T missense_variant ORF1ab_pp1a H1113Y 1.00e+0 AY.16
V3806 865G>A missense_variant S V289I 7.07e-1 AY.24
V7139 9606G>A synonymous_variant ORF1ab_pp1a T3202T 7.07e-1 AY.24
V2841 16679G>T missense_variant ORF1ab_pp1ab S5560I 1.00e+0 AY.25.3
V3734 638T>C missense_variant S V213A 8.16e-1 AY.28
V4500 379C>T missense_variant ORF3a L127F 1.00e+0 AY.28
V7423 11811C>T synonymous_variant ORF1ab_pp1a N3937N 7.74e-1 AY.28
V9459 225T>C synonymous_variant ORF7a Y75Y 1.00e+0 AY.28
V1347 5557C>T missense_variant ORF1ab_pp1a L1853F 6.57e-1 AY.34.1
V7223 10200G>A synonymous_variant ORF1ab_pp1a K3400K 6.03e-1 AY.34.1
V7397 11676C>T synonymous_variant ORF1ab_pp1a V3892V 6.03e-1 AY.34.1
V7587 13113C>T synonymous_variant ORF1ab_pp1a T4371T 6.03e-1 AY.34.1
V8233 18087T>C synonymous_variant ORF1ab_pp1ab N6029N 6.03e-1 AY.34.1
V5162 202A>T stop_gained ORF8 K68* 1.00e+0 AY.39.1.2
V3350 20140C>T missense_variant ORF1ab_pp1ab P6714S 1.00e+0 AY.39.2
V3783 767C>T missense_variant S S256L 7.07e-1 AY.45
V3321 19974G>T missense_variant ORF1ab_pp1ab R6658S 6.32e-1 AY.46.4
V5409 494C>T missense_variant N T165I 8.94e-1 AY.46.4
V9497 60T>C synonymous_variant ORF7b L20L 8.94e-1 AY.46.4
V4726 45G>T missense_variant M K15N 7.07e-1 AY.46.5
V5039 94C>T missense_variant ORF7b L32F 7.07e-1 AY.46
V1823 8483C>T missense_variant ORF1ab_pp1a A2828V 7.07e-1 AY.4.7
V3223 19278G>T missense_variant ORF1ab_pp1ab M6426I 6.54e-1 AY.57
V3608 284C>T missense_variant S T95I 7.07e-1 AY.62
V4517 428C>T missense_variant ORF3a A143V 7.07e-1 AY.62
V4799 13G>A missense_variant ORF6 V5I 7.07e-1 AY.62
V6176 2184C>T synonymous_variant ORF1ab_pp1a G728G 7.07e-1 AY.62
V8850 1734T>C synonymous_variant S D578D 7.07e-1 AY.62
V4069 2314G>A missense_variant S V772I 9.01e-1 AY.75
V2610 14316G>T missense_variant ORF1ab_pp1ab M4772I 1.00e+0 AY.77
V4358 110T>C missense_variant ORF3a I37T 1.00e+0 AY.77
V2736 15643G>T missense_variant ORF1ab_pp1ab G5215C 8.99e-1 AY.7
V504 1405C>T missense_variant ORF1ab_pp1a L469F 6.66e-1 AY.92
V7921 15688C>T synonymous_variant ORF1ab_pp1ab L5230L 6.66e-1 AY.92
V4462 295G>T missense_variant ORF3a A99S 8.65e-1 AY.99
V8401 19299G>A synonymous_variant ORF1ab_pp1ab L6433L 7.07e-1 B.1.1.192
V4332 68C>T missense_variant ORF3a A23V 1.00e+0 B.1.126
V5194 298G>T missense_variant ORF8 V100L 7.07e-1 B.1.126
V5990 885C>T synonymous_variant ORF1ab_pp1a G295G 1.00e+0 B.1.126
V8161 17502C>T synonymous_variant ORF1ab_pp1ab V5834V 7.07e-1 B.1.126
V3584 208G>T missense_variant S V70F 7.07e-1 B.1.1.28
V4892 113G>T missense_variant ORF7a G38V 7.07e-1 B.1.1.28
V5800 *4376T>C downstream_gene_variant S None 7.07e-1 B.1.1.28
V8955 2517T>C synonymous_variant S D839D 7.07e-1 B.1.1.28
V3112 18449C>T missense_variant ORF1ab_pp1ab A6150V 8.94e-1 B.1.1.33
V2244 11496G>T missense_variant ORF1ab_pp1a K3832N 1.00e+0 B.1.1.420
V7282 10704C>T synonymous_variant ORF1ab_pp1a F3568F 8.66e-1 B.1.1.420
V7799 14673C>T synonymous_variant ORF1ab_pp1ab D4891D 1.00e+0 B.1.1.420
V9359 432C>T synonymous_variant M I144I 6.12e-1 B.1.160
V973 3301G>A missense_variant ORF1ab_pp1a G1101S 6.45e-1 B.1.160
V2594 14143C>T missense_variant ORF1ab_pp1ab P4715S 7.07e-1 B.1.177.82
V5337 163G>T missense_variant N A55S 7.07e-1 B.1.177.82
V5782 *4361G>A downstream_gene_variant S None 7.07e-1 B.1.177.82
V9824 30G>T synonymous_variant ORF10 P10P 7.07e-1 B.1.177.82
V1368 5758T>C missense_variant ORF1ab_pp1a Y1920H 9.35e-1 B.1.258
V2889 16943A>G missense_variant ORF1ab_pp1ab Y5648C 7.56e-1 B.1.258
V6413 3942G>T synonymous_variant ORF1ab_pp1a A1314A 7.07e-1 B.1.36.29
V3325 20006C>T missense_variant ORF1ab_pp1ab A6669V 7.07e-1 B.1.36
V8675 328T>C synonymous_variant S L110L 1.00e+0 B.1.36
V4270 3707G>T missense_variant S C1236F 7.07e-1 B.1.438.1
V3599 239A>C missense_variant S D80A 1.00e+0 B.1.466.2
V5957 657G>T synonymous_variant ORF1ab_pp1a L219L 7.07e-1 B.1.466.2
V7314 11049T>C synonymous_variant ORF1ab_pp1a V3683V 1.00e+0 B.1.525
V3615 292T>C missense_variant S S98P 8.72e-1 B.1.526
V7387 11583A>G synonymous_variant ORF1ab_pp1a K3861K 7.69e-1 B.1.561
V7829 14973C>T synonymous_variant ORF1ab_pp1ab H4991H 7.07e-1 B.1.609
V2932 17287G>A missense_variant ORF1ab_pp1ab G5763R 1.00e+0 B.1.617.1
V4251 3621G>T missense_variant S E1207D 7.07e-1 B.1.617.1
V6185 2229G>A synonymous_variant ORF1ab_pp1a E743E 1.00e+0 B.1.617.1
V5553 862G>A missense_variant N D288N 1.00e+0 BA.1.14
V5950 613C>T synonymous_variant ORF1ab_pp1a L205L 1.00e+0 BA.2.19
V6507 4662C>T synonymous_variant ORF1ab_pp1a D1554D 1.00e+0 BA.2.23.1
V4657 -17C>T upstream_gene_variant E None 7.07e-1 BA.2.3.14
V1670 7499C>T missense_variant ORF1ab_pp1a S2500F 7.07e-1 BA.2.32
V5087 52C>T stop_gained ORF8 Q18* 7.07e-1 BA.2.32
V8121 17202A>G synonymous_variant ORF1ab_pp1ab T5734T 7.07e-1 BA.2.32
V3524 25C>T missense_variant S P9S 1.00e+0 BA.2.3.4
V9180 246C>T synonymous_variant ORF3a N82N 1.00e+0 BA.2.3.4
V770 2491A>G missense_variant ORF1ab_pp1a I831V 7.07e-1 BA.2.38
V4400 163G>A missense_variant ORF3a V55I 7.07e-1 BA.2.40.1
V4538 515G>A missense_variant ORF3a G172D 7.07e-1 BA.2.40.1
V5119 133T>C missense_variant ORF8 W45R 7.06e-1 BA.2.44
V4217 3436G>T missense_variant S D1146Y 7.07e-1 BA.2.56
V2670 14996G>T missense_variant ORF1ab_pp1ab S4999I 7.75e-1 BA.5.1.10
V139 103G>T missense_variant ORF1ab_pp1a V35L 7.07e-1 BA.5.1.2
V4263 3682G>T missense_variant S V1228L 9.53e-1 BA.5.1.3
V611 1805C>T missense_variant ORF1ab_pp1a T602I 6.28e-1 BA.5.1.3
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 7.10e-1 BA.5.1.3
V8847 1722T>C synonymous_variant S D574D 8.06e-1 BA.5.1.3
V9423 39T>C synonymous_variant ORF7a A13A 7.31e-1 BA.5.1.3
V254 412G>A missense_variant ORF1ab_pp1a A138T 7.07e-1 BA.5.2.13
V1234 4766C>T missense_variant ORF1ab_pp1a T1589I 1.00e+0 BA.5.2.20
V3120 18562G>A missense_variant ORF1ab_pp1ab V6188I 7.07e-1 BA.5.2.20
V3524 25C>T missense_variant S P9S 7.07e-1 BA.5.2.20
V1496 6293C>T missense_variant ORF1ab_pp1a A2098V 7.07e-1 BA.5.2.24
V2192 11177C>T missense_variant ORF1ab_pp1a A3726V 7.07e-1 BA.5.2.24
V4366 119C>T missense_variant ORF3a S40L 7.07e-1 BA.5.2.24
V5144 184G>T missense_variant ORF8 V62L 8.16e-1 BA.5.2.24
V5516 707G>T missense_variant N G236V 1.00e+0 BA.5.2.24
V6731 6283C>T synonymous_variant ORF1ab_pp1a L2095L 1.00e+0 BA.5.2.24
V3668 460G>C missense_variant S E154Q 1.00e+0 BA.5.2.26
V2650 14753C>T missense_variant ORF1ab_pp1ab A4918V 6.73e-1 BA.5.2.8
V6929 7914G>T synonymous_variant ORF1ab_pp1a R2638R 6.73e-1 BA.5.2.8
V6939 8025C>T synonymous_variant ORF1ab_pp1a L2675L 6.73e-1 BA.5.2.8
V7191 9924C>T synonymous_variant ORF1ab_pp1a T3308T 6.02e-1 BA.5.2.8
V9797 1149G>T synonymous_variant N P383P 8.66e-1 BE.1.1.2
V4920 185A>G missense_variant ORF7a Q62R 1.00e+0 BF.4
V7302 10887C>T synonymous_variant ORF1ab_pp1a V3629V 1.00e+0 BF.4
V4181 3251A>G missense_variant S D1084G 6.32e-1 BF.7.14
V183 245_256delGTCATGTTATGG disruptive_inframe_deletion ORF1ab_pp1a G82_M85del 1.00e+0 BN.1.2.1
V5083 40G>A missense_variant ORF8 A14T 7.74e-1 BN.1.2.1
V5883 258T>G synonymous_variant ORF1ab_pp1a V86V 1.00e+0 BN.1.2.1
V7889 15456C>T synonymous_variant ORF1ab_pp1ab D5152D 8.66e-1 BN.1.2.1
V6552 4953T>C synonymous_variant ORF1ab_pp1a N1651N 7.07e-1 BN.1
V4038 2071T>C missense_variant S S691P 8.16e-1 BQ.1.1.13
V8267 18306C>T synonymous_variant ORF1ab_pp1ab L6102L 6.66e-1 BQ.1.1.5
V2068 10505A>G missense_variant ORF1ab_pp1a Y3502C 1.00e+0 BQ.1
V8247 18177C>T synonymous_variant ORF1ab_pp1ab S6059S 8.16e-1 P.1.14
V4133 2812C>T missense_variant S L938F 6.15e-1 P.1.15
V8439 19635A>G synonymous_variant ORF1ab_pp1ab P6545P 6.74e-1 P.1.15
V862 2911C>T missense_variant ORF1ab_pp1a P971S 6.04e-1 P.1.15
V9748 927C>T synonymous_variant N P309P 6.76e-1 P.1.15
V797 2638A>G missense_variant ORF1ab_pp1a I880V 7.07e-1 P.1.7
V104 -19G>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 AY.19
V5370 355G>T missense_variant N A119S 1.00e+0 AY.19
V5621 1136C>T missense_variant N T379I 1.00e+0 AY.19
V8130 17277C>T synonymous_variant ORF1ab_pp1ab D5759D 1.00e+0 AY.19
V8688 414T>C synonymous_variant S D138D 7.06e-1 AY.19
V1780 8215C>T missense_variant ORF1ab_pp1a P2739S 9.41e-1 B.1.1.121
V7422 11808C>T synonymous_variant ORF1ab_pp1a D3936D 8.63e-1 B.1.1.121
V7507 12550C>T synonymous_variant ORF1ab_pp1a L4184L 8.63e-1 B.1.1.121
V1284 5078C>T missense_variant ORF1ab_pp1a P1693L 1.00e+0 B.1.1.201
V3329 20020A>T missense_variant ORF1ab_pp1ab I6674F 1.00e+0 B.1.1.201
V3330 20021T>C missense_variant ORF1ab_pp1ab I6674T 1.00e+0 B.1.1.201
V3979 1876G>T missense_variant S A626S 1.00e+0 B.1.1.201
V5549 836C>A missense_variant N P279Q 1.00e+0 B.1.1.201
V8632 96C>T synonymous_variant S F32F 1.00e+0 B.1.1.201
V995 3388C>T missense_variant ORF1ab_pp1a L1130F 1.00e+0 B.1.1.201
V1659 7463C>T missense_variant ORF1ab_pp1a S2488F 1.00e+0 B.1.1.280
V1275 5033C>A missense_variant ORF1ab_pp1a T1678N 6.21e-1 B.1.406
V1499 6308C>T missense_variant ORF1ab_pp1a S2103F 6.21e-1 B.1.406
V6890 7671G>T synonymous_variant ORF1ab_pp1a A2557A 6.21e-1 B.1.406
V7193 9933C>T synonymous_variant ORF1ab_pp1a D3311D 6.99e-1 B.1.406
V9407 96C>T synonymous_variant ORF6 I32I 6.99e-1 B.1.406
V1192 4586A>G missense_variant ORF1ab_pp1a K1529R 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
V7380 11547C>A synonymous_variant ORF1ab_pp1a G3849G 1.00e+0 B.1.530
V895 3026A>G missense_variant ORF1ab_pp1a Q1009R -1.00e+0 B.1.530
V2870 16840C>T missense_variant ORF1ab_pp1ab H5614Y -6.28e-1 B.1.590
V2901 17024C>T missense_variant ORF1ab_pp1ab T5675I 6.41e-1 B.1.590
V4011 2025G>T missense_variant S Q675H 8.46e-1 B.1.590
V4329 64G>T missense_variant ORF3a D22Y 9.00e-1 B.1.590
V4678 145G>T missense_variant E V49L -7.61e-1 B.1.590
V5443 581C>T missense_variant N S194L 8.72e-1 B.1.590
V812 2704A>G missense_variant ORF1ab_pp1a M902V -7.42e-1 B.1.590
V8831 1608C>T synonymous_variant S N536N 8.72e-1 B.1.590
V9354 414C>T synonymous_variant M L138L 9.61e-1 B.1.590
V6891 7680C>T synonymous_variant ORF1ab_pp1a Y2560Y 8.65e-1 BA.2.35
V9623 330C>T synonymous_variant N F110F 7.04e-1 BA.2.35
V8362 18951T>C synonymous_variant ORF1ab_pp1ab Y6317Y 1.00e+0 BA.2.9.6
V6126 1854C>T synonymous_variant ORF1ab_pp1a G618G 7.83e-1 K.3
V6397 3828C>T synonymous_variant ORF1ab_pp1a I1276I 1.00e+0 Q.6





Manual curation of mutation (11478G>T)-related literature from PubMed

The pubmed.mineR and pubmed-mapper were utilized for extracting literature from PubMed, followed by manual filtering.
Note: PubMed: (COVID-19 [Title/Abstract] OR SARS-COV-2 [Title/Abstract]) AND (DNA mutation [Title/Abstract] OR Protein mutation-1 letter [Title/Abstract] OR Protein mutation-3 letter [Title/Abstract]).

DNA level Protein level Paper title Journal name Publication year Pubmed ID