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The current mutation

ID: V8716
DNA: 648C>T
Protein: L216L
Position: 22210








COV2Var annotation categories







Summary information of mutation (648C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp02
  Gene Name   S
  Gene Type   protein_coding
  Genome position   22210
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   synonymous_variant
  DNA Level   DNA Mutation: 648C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: L216L
  Protein 3-letter Mutation: Leu216Leu

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 (648C>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.1.1.58 13 11 8.46e-1
2020-10 B.1.1.398 13 2 1.54e-1
2020-11 B.1.1.58 40 21 5.25e-1
2020-11 B.1.1.398 40 14 3.50e-1
2020-11 B.1.1.298 40 2 5.00e-2
2020-12 B.1.1.58 50 31 6.20e-1
2020-12 B.1.2 50 12 2.40e-1
2020-12 B.1.1.398 50 4 8.00e-2
2020-03 B.1.9 1 1 1.00e+0
2020-04 B.1.1.58 6 5 8.33e-1
2020-04 B.1 6 1 1.67e-1
2020-06 B.1.1.58 2 2 1.00e+0
2020-07 B.1.1.58 15 11 7.33e-1
2020-07 B.1.1.398 15 2 1.33e-1
2020-07 D.2 15 2 1.33e-1
2020-08 B.1.1.58 24 20 8.33e-1
2020-08 B.1 24 2 8.33e-2
2020-08 B.1.1 24 1 4.17e-2
2020-09 B.1.1.58 11 10 9.09e-1
2020-09 B.1.1.33 11 1 9.09e-2
2021-01 B.1.2 54 20 3.70e-1
2021-01 B.1.1.58 54 15 2.78e-1
2021-01 B.1.1.7 54 10 1.85e-1
2021-10 C.1.2 65 25 3.85e-1
2021-10 AY.4 65 13 2.00e-1
2021-10 AY.119 65 9 1.38e-1
2021-11 AY.4 48 18 3.75e-1
2021-11 C.1.2 48 9 1.88e-1
2021-11 AY.44 48 4 8.33e-2
2021-12 AY.4 92 47 5.11e-1
2021-12 AY.44 92 11 1.20e-1
2021-12 AY.9.2 92 6 6.52e-2
2021-02 B.1.1.7 70 24 3.43e-1
2021-02 B.1.1 70 23 3.29e-1
2021-02 B.1.1.58 70 11 1.57e-1
2021-03 B.1.1.7 118 69 5.85e-1
2021-03 B.1.526 118 21 1.78e-1
2021-03 B.1.1 118 10 8.47e-2
2021-04 B.1.526 111 48 4.32e-1
2021-04 B.1.1.7 111 46 4.14e-1
2021-04 P.1 111 5 4.50e-2
2021-05 B.1.1.7 36 25 6.94e-1
2021-05 B.1.526 36 7 1.94e-1
2021-05 B.1 36 1 2.78e-2
2021-06 C.1.2 63 43 6.83e-1
2021-06 P.1 63 14 2.22e-1
2021-06 B.1.1.7 63 3 4.76e-2
2021-07 C.1.2 125 97 7.76e-1
2021-07 P.1 125 6 4.80e-2
2021-07 B.1 125 4 3.20e-2
2021-08 C.1.2 83 48 5.78e-1
2021-08 AY.99.2 83 6 7.23e-2
2021-08 P.1 83 5 6.02e-2
2021-09 C.1.2 79 39 4.94e-1
2021-09 AY.119 79 20 2.53e-1
2021-09 AY.103 79 8 1.01e-1
2022-01 BA.1.1.2 59 32 5.42e-1
2022-01 BA.1.1 59 14 2.37e-1
2022-01 BA.1 59 4 6.78e-2
2022-10 CG.1 5 4 8.00e-1
2022-10 XBB.2 5 1 2.00e-1
2022-11 BA.5.1.1 12 4 3.33e-1
2022-11 BA.5.5 12 2 1.67e-1
2022-11 BF.5 12 2 1.67e-1
2022-12 XBB.1.5 12 3 2.50e-1
2022-12 BF.7.14 12 2 1.67e-1
2022-12 CC.1 12 2 1.67e-1
2022-02 BA.1.1 73 32 4.38e-1
2022-02 BA.1.1.2 73 22 3.01e-1
2022-02 BA.1.1.1 73 3 4.11e-2
2022-03 BA.1.1.2 42 21 5.00e-1
2022-03 BA.1.1 42 13 3.10e-1
2022-03 BA.2 42 5 1.19e-1
2022-04 BA.1.1.2 24 14 5.83e-1
2022-04 BA.2 24 8 3.33e-1
2022-04 BA.1.1 24 1 4.17e-2
2022-05 BA.2 6 3 5.00e-1
2022-05 BA.2.24 6 1 1.67e-1
2022-05 BA.2.3 6 1 1.67e-1
2022-06 BA.2 4 3 7.50e-1
2022-06 BA.2.9 4 1 2.50e-1
2022-07 BA.1.1.2 2 1 5.00e-1
2022-07 BA.5.6 2 1 5.00e-1
2022-08 BA.5.8 2 1 5.00e-1
2022-08 BF.10 2 1 5.00e-1
2022-09 BA.4.6.4 6 2 3.33e-1
2022-09 BA.5.2.26 6 1 1.67e-1
2022-09 BA.5.2.9 6 1 1.67e-1
2023-01 BE.1.1 5 1 2.00e-1
2023-01 BF.7.4.1 5 1 2.00e-1
2023-01 BN.1.2 5 1 2.00e-1
2023-02 XBB.1.5 1 1 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
V8716 B.1.1.398 3.00e-2 11 2020-3-19 2021-8-4
V8716 B.1.1.58 9.93e-1 145 2020-4-8 2021-7-16
V8716 B.1.630 1.08e-2 2 2021-3-17 2022-8-22
V8716 B.1.9 1.22e-2 2 2020-3-4 2021-11-16
V8716 C.1.2 9.28e-1 269 2021-3-18 2022-5-25
V8716 C.40 7.50e-2 3 2021-2-2 2021-10-8
V8716 CG.1 1.21e-2 6 2022-6-27 2023-2-7






Examining mutation (648C>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 (648C>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 -7.23e-15 1.09e+5 -6.62e-20 1.00e+0 Decrease
Deceased -1.54e+1 2.73e+3 -5.65e-3 9.95e-1 Decrease
Homebound -7.23e-15 1.09e+5 -6.62e-20 1.00e+0 Decrease
Hospitalized -2.16e+0 8.22e-1 -2.63e+0 8.54e-3 Decrease
Mild -1.65e+1 1.68e+3 -9.82e-3 9.92e-1 Decrease
Recovered 2.87e+0 8.55e-1 3.36e+0 7.87e-4 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 1.07e-1 2.82e-1 3.81e-1 7.03e-1 Increase
18-39 -2.35e-1 1.42e-1 -1.66e+0 9.73e-2 Decrease
40-64 1.84e-2 1.35e-1 1.36e-1 8.91e-1 Increase
65-84 9.09e-2 1.95e-1 4.67e-1 6.40e-1 Increase
>=85 1.21e+0 3.34e-1 3.63e+0 2.84e-4 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 -6.42e-2 1.33e-1 -4.82e-1 6.30e-1 Decrease





Investigating natural selection at mutation (648C>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

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 (648C>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




Alterations in protein stability induced by mutation (648C>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




Impact on protein function induced by mutation (648C>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




Exploring mutation (648C>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 (648C>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




Impact of spike protein mutation (648C>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 (648C>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.

        Show as:

        Show interface residues:





Impact of mutation (648C>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 (648C>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
V1329 5441A>G missense_variant ORF1ab_pp1a Y1814C 1.00e+0 BA.1.1.18
V1648 7223C>T missense_variant ORF1ab_pp1a T2408I 6.05e-1 BA.1.1.2
V5378 382G>T missense_variant N D128Y 9.12e-1 BA.1.1.2
V7417 11784C>T synonymous_variant ORF1ab_pp1a N3928N 6.84e-1 BA.1.1.2
V8287 18441C>T synonymous_variant ORF1ab_pp1ab D6147D 9.23e-1 BA.1.1.2
V7387 11583A>G synonymous_variant ORF1ab_pp1a K3861K 1.00e+0 BE.1.1
V9311 198G>A synonymous_variant M V66V 1.00e+0 BE.1.1
V494 1348C>A missense_variant ORF1ab_pp1a L450I 7.17e-1 AY.9.2
V641 1924C>T missense_variant ORF1ab_pp1a L642F 7.07e-1 AY.9.2
V5135 163G>A missense_variant ORF8 A55T 9.27e-1 B.1.1
V5294 73G>T missense_variant N G25C 1.00e+0 AY.111
V4081 2425C>T missense_variant S P809S 1.00e+0 AY.119.2
V5081 32C>T missense_variant ORF8 T11I 1.00e+0 AY.30
V7057 8925G>T synonymous_variant ORF1ab_pp1a V2975V 7.07e-1 AY.85
V2368 12482C>T missense_variant ORF1ab_pp1a T4161I 1.00e+0 B.1.1.298
V514 1445C>T missense_variant ORF1ab_pp1a A482V 7.07e-1 B.1.1.298
V5978 798C>T synonymous_variant ORF1ab_pp1a F266F 1.00e+0 B.1.1.298
V8651 210C>T synonymous_variant S V70V 1.00e+0 B.1.1.33
V216 304G>A missense_variant ORF1ab_pp1a E102K 7.07e-1 B.1.1.372
V3525 26C>T missense_variant S P9L 7.07e-1 B.1.1.372
V3550 74C>T missense_variant S P25L 7.07e-1 B.1.1.372
V3662 454T>C missense_variant S W152R 1.00e+0 B.1.1.372
V3717 570G>T missense_variant S R190S 7.07e-1 B.1.1.372
V3755 727_732delGCTTTA conservative_inframe_deletion S A243_L244del 1.00e+0 B.1.1.372
V3881 1345T>C missense_variant S Y449H 7.07e-1 B.1.1.372
V3909 1450G>A missense_variant S E484K 7.07e-1 B.1.1.372
V3997 1963C>T missense_variant S H655Y 7.07e-1 B.1.1.372
V4018 2037T>A missense_variant S N679K 1.00e+0 B.1.1.372
V4048 2147C>T missense_variant S T716I 7.07e-1 B.1.1.372
V4116 2635G>A missense_variant S A879T 1.00e+0 B.1.1.372
V4606 712G>T missense_variant ORF3a D238Y 1.00e+0 B.1.1.372
V4622 766_768delGTT conservative_inframe_deletion ORF3a V256del 7.07e-1 B.1.1.372
V4668 61C>A missense_variant E L21I 7.07e-1 B.1.1.372
V4689 202T>C missense_variant E S68P 1.00e+0 B.1.1.372
V4760 245T>C missense_variant M I82T 7.07e-1 B.1.1.372
V4781 463C>T missense_variant M H155Y 1.00e+0 B.1.1.372
V5085 46T>C missense_variant ORF8 F16L 1.00e+0 B.1.1.372
V5629 1152G>T missense_variant N Q384H 7.07e-1 B.1.1.372
V6862 7434A>G synonymous_variant ORF1ab_pp1a K2478K 7.07e-1 B.1.1.372
V688 2123C>T missense_variant ORF1ab_pp1a T708I 1.00e+0 B.1.1.372
V8293 18483C>T synonymous_variant ORF1ab_pp1ab V6161V 7.07e-1 B.1.1.372
V8338 18789T>C synonymous_variant ORF1ab_pp1ab I6263I 7.07e-1 B.1.1.372
V8671 297C>T synonymous_variant S N99N 1.00e+0 B.1.1.372
V9338 351C>T synonymous_variant M N117N 1.00e+0 B.1.1.372
V9612 243T>C synonymous_variant N D81D 7.07e-1 B.1.1.372
V3742 644A>G missense_variant S D215G 7.07e-1 B.1.1.529
V3881 1345T>C missense_variant S Y449H 1.00e+0 B.1.1.529
V3577 200C>T missense_variant S A67V 7.07e-1 B.1.177.21
V3036 17991G>T missense_variant ORF1ab_pp1ab M5997I 6.54e-1 B.1.177.87
V5921 444G>A synonymous_variant ORF1ab_pp1a E148E 7.07e-1 B.1.243
V291 544T>C missense_variant ORF1ab_pp1a Y182H 1.00e+0 B.1.258
V1570 6671C>T missense_variant ORF1ab_pp1a S2224F 1.00e+0 B.1.466.2
V1537 6455C>T missense_variant ORF1ab_pp1a T2152I 8.96e-1 B.1.526
V1395 5933C>T missense_variant ORF1ab_pp1a S1978F 1.00e+0 BA.1.14.1
V242 370C>T missense_variant ORF1ab_pp1a R124C 1.00e+0 BA.1.14.1
V4773 327G>T missense_variant M M109I 1.00e+0 BA.1.14.1
V8024 16500T>C synonymous_variant ORF1ab_pp1ab L5500L 1.00e+0 BA.2.37
V8344 18849C>T synonymous_variant ORF1ab_pp1ab D6283D 1.00e+0 BA.2.37
V1520 6394A>G missense_variant ORF1ab_pp1a S2132G 1.00e+0 BA.4.6.4
V8327 18696G>A synonymous_variant ORF1ab_pp1ab A6232A 8.94e-1 BA.5.1.1
V4396 157C>T missense_variant ORF3a L53F 7.07e-1 BA.5.2.26
V5386 422C>T missense_variant N T141I 1.00e+0 BA.5.2.26
V600 1766A>G missense_variant ORF1ab_pp1a D589G 7.07e-1 BN.1.2
V2980 17675C>T missense_variant ORF1ab_pp1ab A5892V 1.00e+0 BN.1.9
V4502 383G>T missense_variant ORF3a W128L 1.00e+0 BN.1.9
V4581 637C>A missense_variant ORF3a Q213K 1.00e+0 BN.1.9
V794 2630A>G missense_variant ORF1ab_pp1a D877G 1.00e+0 BQ.1.1.3
V7238 10317C>T synonymous_variant ORF1ab_pp1a D3439D 7.07e-1 BQ.1.14
V1263 4919C>T missense_variant ORF1ab_pp1a P1640L 1.00e+0 P.1.17
V936 3166G>T missense_variant ORF1ab_pp1a V1056L 7.71e-1 P.1.7
V4426 203G>T missense_variant ORF3a R68I 1.00e+0 XAY.2
V8132 17286C>T synonymous_variant ORF1ab_pp1ab L5762L 1.00e+0 XAY.2
V3355 20155G>A missense_variant ORF1ab_pp1ab D6719N 1.00e+0 XBB.2
V3627 412G>C missense_variant S D138H 1.00e+0 XBB.2
V350 820G>T missense_variant ORF1ab_pp1a V274L 1.00e+0 AY.112.3
V3520 13C>T missense_variant S L5F 7.06e-1 AY.112.3
V6174 2169C>T synonymous_variant ORF1ab_pp1a S723S 1.00e+0 AY.112.3
V8508 20289A>G synonymous_variant ORF1ab_pp1ab L6763L 1.00e+0 AY.112.3
V281 496A>G missense_variant ORF1ab_pp1a S166G 7.33e-1 B.1.1.398
V8899 2046G>T synonymous_variant S R682R 8.83e-1 B.1.1.398
V9508 27C>T synonymous_variant ORF8 I9I 7.33e-1 B.1.1.398
V2027 10076C>T missense_variant ORF1ab_pp1a P3359L -1.00e+0 B.1.1.58
V2122 10849G>A missense_variant ORF1ab_pp1a G3617S -1.00e+0 B.1.1.58
V2193 11185C>A missense_variant ORF1ab_pp1a Q3729K -1.00e+0 B.1.1.58
V3520 13C>T missense_variant S L5F -7.05e-1 B.1.1.58
V3638 432_434delTTA disruptive_inframe_deletion S Y145del -7.05e-1 B.1.1.58
V3674 470T>C missense_variant S F157S -1.00e+0 B.1.1.58
V3784 769G>A missense_variant S G257S -1.00e+0 B.1.1.58
V3928 1502A>C missense_variant S N501T -1.00e+0 B.1.1.58
V4068 2311G>T missense_variant S A771S -1.00e+0 B.1.1.58
V4111 2576C>A missense_variant S T859N -1.00e+0 B.1.1.58
V4122 2695G>T missense_variant S A899S -1.00e+0 B.1.1.58
V4770 311C>T missense_variant M A104V -1.00e+0 B.1.1.58
V4797 5T>C missense_variant ORF6 F2S -1.00e+0 B.1.1.58
V5237 1delA frameshift_variant&start_lost N M1fs -1.00e+0 B.1.1.58
V5354 250A>G missense_variant N I84V -1.00e+0 B.1.1.58
V8094 17016G>T synonymous_variant ORF1ab_pp1ab V5672V -1.00e+0 B.1.1.58
V8419 19515A>G synonymous_variant ORF1ab_pp1ab V6505V -1.00e+0 B.1.1.58
V2257 11651C>T missense_variant ORF1ab_pp1a S3884L 1.00e+0 B.1.167
V3150 18734C>T missense_variant ORF1ab_pp1ab A6245V 1.00e+0 B.1.167
V3421 20626G>A missense_variant ORF1ab_pp1ab V6876I 1.00e+0 B.1.167
V3569 184G>A missense_variant S V62I 1.00e+0 B.1.167
V5374 365C>T missense_variant N P122L 1.00e+0 B.1.167
V5901 333G>T synonymous_variant ORF1ab_pp1a V111V 1.00e+0 B.1.167
V5982 828C>T synonymous_variant ORF1ab_pp1a P276P 1.00e+0 B.1.167
V5983 829T>C synonymous_variant ORF1ab_pp1a L277L 1.00e+0 B.1.167
V6047 1290C>T synonymous_variant ORF1ab_pp1a N430N 1.00e+0 B.1.167
V8742 852C>T synonymous_variant S T284T 1.00e+0 B.1.167
V9478 303T>C synonymous_variant ORF7a F101F 1.00e+0 B.1.167
V1085 3737C>T missense_variant ORF1ab_pp1a T1246I 1.00e+0 B.1.630
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 8.14e-1 B.1.630
V1319 5383A>C missense_variant ORF1ab_pp1a K1795Q -7.03e-1 B.1.630
V1346 5552C>T missense_variant ORF1ab_pp1a A1851V 7.05e-1 B.1.630
V1970 9602T>C missense_variant ORF1ab_pp1a L3201P 1.00e+0 B.1.630
V1972 9626C>T missense_variant ORF1ab_pp1a A3209V -8.14e-1 B.1.630
V1986 9832G>A missense_variant ORF1ab_pp1a G3278S 1.00e+0 B.1.630
V216 304G>A missense_variant ORF1ab_pp1a E102K 1.00e+0 B.1.630
V241 364C>T missense_variant ORF1ab_pp1a L122F -7.03e-1 B.1.630
V2806 16372G>T missense_variant ORF1ab_pp1ab A5458S 7.05e-1 B.1.630
V3309 19870G>A missense_variant ORF1ab_pp1ab V6624I 7.05e-1 B.1.630
V342 794C>T missense_variant ORF1ab_pp1a T265I -6.27e-1 B.1.630
V3550 74C>T missense_variant S P25L 1.00e+0 B.1.630
V3717 570G>T missense_variant S R190S 1.00e+0 B.1.630
V3742 644A>G missense_variant S D215G 1.00e+0 B.1.630
V3881 1345T>C missense_variant S Y449H 1.00e+0 B.1.630
V3900 1433C>A missense_variant S T478K 7.03e-1 B.1.630
V3909 1450G>A missense_variant S E484K 8.14e-1 B.1.630
V3927 1501A>T missense_variant S N501Y 1.00e+0 B.1.630
V4018 2037T>A missense_variant S N679K 1.00e+0 B.1.630
V4048 2147C>T missense_variant S T716I 1.00e+0 B.1.630
V4111 2576C>A missense_variant S T859N 8.14e-1 B.1.630
V4188 3303C>A missense_variant S H1101Q 1.00e+0 B.1.630
V4603 686C>A missense_variant ORF3a T229N 1.00e+0 B.1.630
V4622 766_768delGTT conservative_inframe_deletion ORF3a V256del 1.00e+0 B.1.630
V4668 61C>A missense_variant E L21I 1.00e+0 B.1.630
V4732 85C>T missense_variant M L29F 1.00e+0 B.1.630
V4760 245T>C missense_variant M I82T 8.14e-1 B.1.630
V4860 32C>T missense_variant ORF7a T11I 1.00e+0 B.1.630
V5020 40_41delTT frameshift_variant ORF7b L14fs 1.00e+0 B.1.630
V5242 -2A>G upstream_gene_variant N None -1.00e+0 B.1.630
V5243 -2A>T upstream_gene_variant N None 1.00e+0 B.1.630
V5274 38C>T missense_variant N P13L 1.00e+0 B.1.630
V5629 1152G>T missense_variant N Q384H 1.00e+0 B.1.630
V616 1826C>T missense_variant ORF1ab_pp1a T609I 1.00e+0 B.1.630
V6182 2220C>T synonymous_variant ORF1ab_pp1a I740I 1.00e+0 B.1.630
V6862 7434A>G synonymous_variant ORF1ab_pp1a K2478K 1.00e+0 B.1.630
V6869 7500C>T synonymous_variant ORF1ab_pp1a S2500S 1.00e+0 B.1.630
V7069 9021C>T synonymous_variant ORF1ab_pp1a N3007N 7.05e-1 B.1.630
V7610 13272C>T synonymous_variant ORF1ab_pp1ab Y4424Y 1.00e+0 B.1.630
V7814 14844C>T synonymous_variant ORF1ab_pp1ab T4948T 7.05e-1 B.1.630
V8128 17241T>C synonymous_variant ORF1ab_pp1ab N5747N -7.03e-1 B.1.630
V8195 17820C>T synonymous_variant ORF1ab_pp1ab I5940I 7.05e-1 B.1.630
V8293 18483C>T synonymous_variant ORF1ab_pp1ab V6161V 1.00e+0 B.1.630
V8317 18624C>T synonymous_variant ORF1ab_pp1ab H6208H 7.05e-1 B.1.630
V8338 18789T>C synonymous_variant ORF1ab_pp1ab I6263I 1.00e+0 B.1.630
V8466 19884C>T synonymous_variant ORF1ab_pp1ab F6628F 1.00e+0 B.1.630
V8911 2169C>T synonymous_variant S T723T 1.00e+0 B.1.630
V8929 2367C>T synonymous_variant S Y789Y 1.00e+0 B.1.630
V9110 3621G>A synonymous_variant S E1207E 7.05e-1 B.1.630
V9612 243T>C synonymous_variant N D81D 8.14e-1 B.1.630
V1811 8393A>G missense_variant ORF1ab_pp1a K2798R 7.05e-1 B.1.9
V2761 15914C>T missense_variant ORF1ab_pp1ab S5305L 1.00e+0 B.1.9
V3220 19261G>T missense_variant ORF1ab_pp1ab D6421Y 7.05e-1 B.1.9
V8745 873T>C synonymous_variant S C291C 7.05e-1 B.1.9
V3717 570G>T missense_variant S R190S 8.40e-1 C.1.2
V3742 644A>G missense_variant S D215G 1.00e+0 C.1.2
V3626 407G>T missense_variant S C136F 7.04e-1 C.1
V3717 570G>T missense_variant S R190S 8.65e-1 C.1
V3742 644A>G missense_variant S D215G 1.00e+0 C.1
V4668 61C>A missense_variant E L21I 6.08e-1 C.1
V1970 9602T>C missense_variant ORF1ab_pp1a L3201P 1.00e+0 C.38
V342 794C>T missense_variant ORF1ab_pp1a T265I 7.04e-1 C.38
V3550 74C>T missense_variant S P25L 1.00e+0 C.38
V3717 570G>T missense_variant S R190S 1.00e+0 C.38
V3742 644A>G missense_variant S D215G 1.00e+0 C.38
V3755 727_732delGCTTTA conservative_inframe_deletion S A243_L244del 1.00e+0 C.38
V3761 732A>T missense_variant S L244F 1.00e+0 C.38
V4023 2042C>G missense_variant S P681R 1.00e+0 C.38
V4143 2848G>A missense_variant S D950N 1.00e+0 C.38
V4337 77C>T missense_variant ORF3a S26L 1.00e+0 C.38
V4668 61C>A missense_variant E L21I 1.00e+0 C.38
V4689 202T>C missense_variant E S68P 1.00e+0 C.38
V5020 40_41delTT frameshift_variant ORF7b L14fs 1.00e+0 C.38
V5341 188A>G missense_variant N D63G 1.00e+0 C.38
V5617 1132G>C missense_variant N E378Q -1.00e+0 C.38
V5628 1148C>T missense_variant N P383L 1.00e+0 C.38
V5629 1152G>T missense_variant N Q384H 1.00e+0 C.38
V6604 5319A>G synonymous_variant ORF1ab_pp1a T1773T 1.00e+0 C.38
V6638 5619C>T synonymous_variant ORF1ab_pp1a Y1873Y 1.00e+0 C.38
V7538 12754C>T synonymous_variant ORF1ab_pp1a L4252L 1.00e+0 C.38
V8338 18789T>C synonymous_variant ORF1ab_pp1ab I6263I 1.00e+0 C.38
V8671 297C>T synonymous_variant S N99N 1.00e+0 C.38
V9372 492G>T synonymous_variant M L164L 1.00e+0 C.38
V2927 17254C>T missense_variant ORF1ab_pp1ab L5752F 7.06e-1 CC.1
V6676 5931C>T synonymous_variant ORF1ab_pp1a P1977P 8.64e-1 CG.1
V7491 12411C>T synonymous_variant ORF1ab_pp1a V4137V 9.25e-1 CG.1
V8152 17457G>T synonymous_variant ORF1ab_pp1ab V5819V 9.25e-1 CG.1
V9334 336C>T synonymous_variant M F112F 8.31e-1 CG.1





Manual curation of mutation (648C>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