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The current mutation

ID: V163
DNA: 184C>T
Protein: P62S
Position: 449








COV2Var annotation categories







Summary information of mutation (184C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   449
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 184C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: P62S
  Protein 3-letter Mutation: Pro62Ser

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 (184C>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.1.177 30 22 7.33e-1
2020-10 B.1.160 30 8 2.67e-1
2020-11 B.1.177 15 8 5.33e-1
2020-11 B.1.2 15 3 2.00e-1
2020-11 B.1.362.2 15 2 1.33e-1
2020-12 B.1.111 11 4 3.64e-1
2020-12 B.1.429 11 2 1.82e-1
2020-12 A.23.1 11 1 9.09e-2
2020-03 B.1 1 1 1.00e+0
2020-04 B.1 3 2 6.67e-1
2020-04 B.1.1 3 1 3.33e-1
2020-05 B.1 2 2 1.00e+0
2020-06 B.1.1 5 2 4.00e-1
2020-06 B.1.1.128 5 2 4.00e-1
2020-06 B.1 5 1 2.00e-1
2020-07 B.1.1.512 4 2 5.00e-1
2020-07 B.1.111 4 1 2.50e-1
2020-07 B.1.369 4 1 2.50e-1
2020-08 B.1.160 1 1 1.00e+0
2020-09 B.1.177 17 12 7.06e-1
2020-09 B.1.160 17 4 2.35e-1
2020-09 B.1.111 17 1 5.88e-2
2021-01 B.1.497 23 4 1.74e-1
2021-01 B.1.1.222 23 2 8.70e-2
2021-01 B.1.1.274 23 2 8.70e-2
2021-10 AY.44 1087 393 3.62e-1
2021-10 B.1.617.2 1087 255 2.35e-1
2021-10 AY.4 1087 181 1.67e-1
2021-11 AY.44 1533 465 3.03e-1
2021-11 AY.4 1533 266 1.74e-1
2021-11 B.1.617.2 1533 218 1.42e-1
2021-12 AY.133 1627 324 1.99e-1
2021-12 AY.4 1627 280 1.72e-1
2021-12 AY.44 1627 274 1.68e-1
2021-02 B.1.617.2 40 23 5.75e-1
2021-02 B.1.1.7 40 5 1.25e-1
2021-02 AY.133 40 4 1.00e-1
2021-03 B.1.617.2 72 36 5.00e-1
2021-03 B.1.1.7 72 17 2.36e-1
2021-03 AY.133 72 8 1.11e-1
2021-04 B.1.1.7 53 36 6.79e-1
2021-04 B.1.617.2 53 10 1.89e-1
2021-04 AY.133 53 2 3.77e-2
2021-05 B.1.1.7 41 22 5.37e-1
2021-05 B.1.617.2 41 7 1.71e-1
2021-05 B.1.630 41 3 7.32e-2
2021-06 AY.4 140 69 4.93e-1
2021-06 AY.122 140 20 1.43e-1
2021-06 AY.44 140 19 1.36e-1
2021-07 AY.44 731 385 5.27e-1
2021-07 AY.4 731 186 2.54e-1
2021-07 AY.122 731 38 5.20e-2
2021-08 AY.44 1283 667 5.20e-1
2021-08 B.1.617.2 1283 207 1.61e-1
2021-08 AY.4 1283 126 9.82e-2
2021-09 AY.44 1178 578 4.91e-1
2021-09 B.1.617.2 1178 222 1.88e-1
2021-09 AY.4 1178 175 1.49e-1
2022-01 AY.4 237 63 2.66e-1
2022-01 AY.133 237 50 2.11e-1
2022-01 BA.1.1 237 30 1.27e-1
2022-10 BQ.1.1 30 13 4.33e-1
2022-10 BA.5 30 5 1.67e-1
2022-10 BA.5.2.9 30 2 6.67e-2
2022-11 BQ.1.1 121 60 4.96e-1
2022-11 BQ.1.1.1 121 9 7.44e-2
2022-11 BQ.1.1.18 121 8 6.61e-2
2022-12 BQ.1.1 179 84 4.69e-1
2022-12 BQ.1.1.18 179 42 2.35e-1
2022-12 BQ.1.1.1 179 10 5.59e-2
2022-02 BA.1.1 110 48 4.36e-1
2022-02 BA.1 110 14 1.27e-1
2022-02 BA.2.1 110 11 1.00e-1
2022-03 BA.2.1 247 181 7.33e-1
2022-03 BA.2 247 25 1.01e-1
2022-03 BA.1.1 247 23 9.31e-2
2022-04 BA.2.1 83 58 6.99e-1
2022-04 BA.2 83 18 2.17e-1
2022-04 BA.2.10 83 2 2.41e-2
2022-05 BA.2.1 45 25 5.56e-1
2022-05 BA.2 45 10 2.22e-1
2022-05 BC.1 45 3 6.67e-2
2022-06 BA.5.3.2 53 25 4.72e-1
2022-06 BA.5.5 53 9 1.70e-1
2022-06 BA.2.1 53 7 1.32e-1
2022-07 BA.5.3.2 53 14 2.64e-1
2022-07 BA.5.6 53 9 1.70e-1
2022-07 BA.4.4 53 7 1.32e-1
2022-08 BA.5.6 31 11 3.55e-1
2022-08 BF.5 31 4 1.29e-1
2022-08 BA.5.9 31 3 9.68e-2
2022-09 BA.5.6 30 4 1.33e-1
2022-09 BF.1 30 3 1.00e-1
2022-09 BA.5 30 2 6.67e-2
2023-01 BQ.1.1 71 35 4.93e-1
2023-01 BQ.1.1.18 71 7 9.86e-2
2023-01 BF.7 71 3 4.23e-2
2023-02 BQ.1.1 11 4 3.64e-1
2023-02 XBB.1.5 11 2 1.82e-1
2023-02 BA.2.10.1 11 1 9.09e-2

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
V163 AY.133 9.97e-1 318 2021-2-18 2022-1-19
V163 AY.33 1.57e-2 327 2020-10-26 2022-4-25
V163 AY.44 1.15e-2 2791 2020-7-14 2022-12-21
V163 B.1.630 2.70e-2 5 2021-3-17 2022-8-22
V163 BA.2.1 1.94e-2 283 2021-12-8 2023-2-17
V163 BA.5.3.2 1.61e-2 39 2021-12-20 2022-11-1
V163 BE.1.4.2 1.01e-2 5 2022-8-5 2023-2-10
V163 CR.2 1.16e-2 2 2022-7-21 2023-2-5






Examining mutation (184C>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 (184C>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 -1.52e+1 4.93e+2 -3.08e-2 9.75e-1 Decrease
Deceased 2.56e+0 9.60e-1 2.67e+0 7.64e-3 Increase
Homebound -1.36e+1 2.11e+3 -6.46e-3 9.95e-1 Decrease
Hospitalized -1.06e+0 5.04e-1 -2.10e+0 3.56e-2 Decrease
Mild -1.09e-1 1.06e+0 -1.03e-1 9.18e-1 Decrease
Recovered 1.67e+0 4.58e-1 3.64e+0 2.72e-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 -1.39e-1 7.89e-2 -1.76e+0 7.77e-2 Decrease
18-39 -5.17e-2 4.89e-2 -1.06e+0 2.91e-1 Decrease
40-64 8.57e-2 5.00e-2 1.71e+0 8.64e-2 Increase
65-84 1.01e-1 7.45e-2 1.36e+0 1.74e-1 Increase
>=85 -1.85e-1 1.69e-1 -1.09e+0 2.74e-1 Decrease

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

Attribute Effect Estimate SE Z-value P-value Direction
Patient gender Male 1.84e-2 4.79e-2 3.85e-1 7.00e-1 Increase





Investigating natural selection at mutation (184C>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
leader 266 805 180 62 3.00e-2 BA.5.1.27 MEME
leader 266 805 180 62 4.00e-2 BA.2.1 MEME
leader 266 805 180 62 3.00e-2 BA.4.6 MEME

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
leader 266 805 180 62 5.17 0.00 5.00e-2 BA.1.14 FEL
leader 266 805 180 62 0.00 7.04 3.00e-2 BA.2.1 FEL
leader 266 805 180 62 0.00 3.07 4.00e-2 BA.4.6 FEL
leader 266 805 180 62 0.00 3.92 4.00e-2 AY.4.2 FEL

The FUBAR method within the HyPhy software was employed to analyze both positive and negative selection. FUBAR: pervasive selection on large datasets.
Note: List of sites found to be under pervasive selection by FUBAR (prob > 0.95). A prob[alpha < beta] value exceeding 0.95 indicates positive selection, while a prob[alpha > beta] value exceeding 0.95 indicates negative selection. "Protein Start" corresponds to the protein's starting genomic position. "Protein End" corresponds to the protein's ending genomic position. The term 'site' represents a selection site within the protein.

Protein name Protein start Protein end Protein length Site Prob[alpha>beta] Prob[alpha<beta] Lineage Method
leader 266 805 180 62 1.00e-2 9.80e-1 BA.2.1 FUBAR




Alterations in protein physicochemical properties induced by mutation (184C>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 489978.88 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 (184C>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
P62S ORF1ab_pp1a Point 62 -1.84 Decrease 7 25 Environment
P62S ORF1ab_pp1a Point 62 -1.77 Decrease 7.4 37 Internal




Impact on protein function induced by mutation (184C>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
P62S ORF1ab_pp1a Point 0.148 Altered Cytoplasmic_loop (Pr = 0.17 | P = 9.6e-03)
Altered DNA_binding (Pr = 0.12 | P = 0.07)




Exploring mutation (184C>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 (184C>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
P62S ORF1ab_pp1a 449 Pepsin (pH1.3) VLSQLEQPYV (pos: 63)
 NA
P62S ORF1ab_pp1a 449 Thermolysin EKGVLSQLEQ (pos: 60)
 NA
P62S ORF1ab_pp1a 449 Chymotrypsin-low specificity KGVLSQLEQP (pos: 61)
 NA
P62S ORF1ab_pp1a 449 Pepsin (pH>2) VLSQLEQPYV (pos: 63)
 NA




Impact of spike protein mutation (184C>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 (184C>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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        Show interface residues:





Impact of mutation (184C>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 (184C>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
V9152 108G>A synonymous_variant ORF3a P36P 7.13e-1 B.1.177
V2228 11330A>G missense_variant ORF1ab_pp1a Q3777R 8.12e-1 AY.4
V5205 334C>T missense_variant ORF8 H112Y 6.00e-1 BA.1.1.18
V9269 78C>T synonymous_variant E F26F 7.07e-1 BA.1.1.2
V6703 6099G>A synonymous_variant ORF1ab_pp1a A2033A 8.32e-1 AY.125
V4203 3371G>T missense_variant S G1124V 6.92e-1 AY.4.2
V5746 *4335C>T downstream_gene_variant S None 8.09e-1 AY.4.2
V6166 2136C>T synonymous_variant ORF1ab_pp1a H712H 7.28e-1 AY.4.2
V8449 19719C>T synonymous_variant ORF1ab_pp1ab V6573V 6.86e-1 AY.4.2
V730 2305C>T missense_variant ORF1ab_pp1a P769S 9.07e-1 AY.44
V2603 14236G>T missense_variant ORF1ab_pp1ab V4746L 6.15e-1 AY.9.2
V4032 2062G>A missense_variant S A688T 7.34e-1 AY.9.2
V4297 3790G>T missense_variant S V1264L 6.83e-1 B.1.617.2
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 8.99e-1 B.1.617.2
V9127 3771T>C synonymous_variant S D1257D 9.50e-1 B.1.617.2
V1180 4514T>C missense_variant ORF1ab_pp1a I1505T 7.07e-1 XBB.1.5
V5170 216G>T missense_variant ORF8 Q72H 1.00e+0 A.23.1
V1458 6181G>T missense_variant ORF1ab_pp1a V2061F 7.07e-1 AY.101
V526 1535C>A missense_variant ORF1ab_pp1a T512K 7.07e-1 AY.101
V9765 987G>A synonymous_variant N T329T 7.07e-1 AY.101
V6070 1476A>G synonymous_variant ORF1ab_pp1a K492K 1.00e+0 AY.109
V1704 7751C>T missense_variant ORF1ab_pp1a A2584V 1.00e+0 AY.10
V2968 17526G>T missense_variant ORF1ab_pp1ab Q5842H 1.00e+0 AY.10
V4297 3790G>T missense_variant S V1264L 1.00e+0 AY.10
V4883 100C>T missense_variant ORF7a P34S 1.00e+0 AY.10
V546 1606T>G missense_variant ORF1ab_pp1a F536V 1.00e+0 AY.10
V6035 1206C>T synonymous_variant ORF1ab_pp1a R402R 1.00e+0 AY.10
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 1.00e+0 AY.10
V797 2638A>G missense_variant ORF1ab_pp1a I880V 1.00e+0 AY.10
V9127 3771T>C synonymous_variant S D1257D 1.00e+0 AY.10
V4509 393G>T missense_variant ORF3a W131C 6.32e-1 AY.119.2
V5854 108G>A synonymous_variant ORF1ab_pp1a E36E 1.00e+0 AY.119.2
V6506 4656C>T synonymous_variant ORF1ab_pp1a T1552T 7.07e-1 AY.119.2
V6530 4803A>G synonymous_variant ORF1ab_pp1a G1601G 8.16e-1 AY.121.1
V9439 123G>A synonymous_variant ORF7a E41E 1.00e+0 AY.121.1
V1755 8022G>T missense_variant ORF1ab_pp1a M2674I 1.00e+0 AY.124
V2229 11331G>T missense_variant ORF1ab_pp1a Q3777H 1.00e+0 AY.124
V2496 13498G>T missense_variant ORF1ab_pp1ab G4500C 1.00e+0 AY.124
V5891 276C>T synonymous_variant ORF1ab_pp1a L92L 7.07e-1 AY.124
V8369 18999C>T synonymous_variant ORF1ab_pp1ab N6333N 1.00e+0 AY.124
V4315 45G>T missense_variant ORF3a L15F 6.71e-1 AY.127
V4297 3790G>T missense_variant S V1264L 6.54e-1 AY.24
V5140 179T>A stop_gained ORF8 L60* 7.66e-1 AY.24
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 9.70e-1 AY.24
V9127 3771T>C synonymous_variant S D1257D 8.74e-1 AY.24
V552 1624C>T missense_variant ORF1ab_pp1a R542C 9.01e-1 AY.2
V5894 291C>T synonymous_variant ORF1ab_pp1a Y97Y 9.31e-1 AY.2
V6891 7680C>T synonymous_variant ORF1ab_pp1a Y2560Y 8.80e-1 AY.3.1
V6921 7875C>T synonymous_variant ORF1ab_pp1a S2625S 8.09e-1 AY.3.1
V504 1405C>T missense_variant ORF1ab_pp1a L469F 7.68e-1 AY.33
V5935 543A>G synonymous_variant ORF1ab_pp1a A181A 9.44e-1 AY.33
V9805 1206T>C synonymous_variant N D402D 7.61e-1 AY.33
V9127 3771T>C synonymous_variant S D1257D 1.00e+0 AY.34.1
V1455 6178G>A missense_variant ORF1ab_pp1a D2060N 6.32e-1 AY.34
V2545 13849A>G missense_variant ORF1ab_pp1ab T4617A 7.75e-1 AY.34
V3861 1251G>T missense_variant S K417N 7.75e-1 AY.34
V7779 14529C>T synonymous_variant ORF1ab_pp1ab S4843S 6.32e-1 AY.34
V3063 18146A>G missense_variant ORF1ab_pp1ab Y6049C 1.00e+0 AY.42
V7254 10452T>C synonymous_variant ORF1ab_pp1a N3484N 1.00e+0 AY.42
V2228 11330A>G missense_variant ORF1ab_pp1a Q3777R 1.00e+0 AY.4.4
V4967 280C>T stop_gained ORF7a Q94* 7.55e-1 AY.4.4
V6070 1476A>G synonymous_variant ORF1ab_pp1a K492K 7.47e-1 AY.4.4
V1308 5305A>G missense_variant ORF1ab_pp1a M1769V 9.53e-1 AY.45
V4078 2386G>C missense_variant S D796H 8.45e-1 AY.45
V17 -174C>T upstream_gene_variant ORF1ab_pp1a None 7.07e-1 AY.46
V1331 5452C>T missense_variant ORF1ab_pp1a H1818Y 1.00e+0 AY.4.7
V7472 12174C>T synonymous_variant ORF1ab_pp1a P4058P 1.00e+0 AY.4.7
V1704 7751C>T missense_variant ORF1ab_pp1a A2584V 1.00e+0 AY.59
V2828 16582G>T missense_variant ORF1ab_pp1ab D5528Y 1.00e+0 AY.59
V3484 21040C>A missense_variant ORF1ab_pp1ab R7014S 6.10e-1 AY.59
V3486 21041G>A missense_variant ORF1ab_pp1ab R7014H 6.20e-1 AY.59
V4297 3790G>T missense_variant S V1264L 8.65e-1 AY.59
V4497 375G>T missense_variant ORF3a M125I 8.94e-1 AY.59
V5807 *4385C>T downstream_gene_variant S None 7.19e-1 AY.59
V7062 8958C>T synonymous_variant ORF1ab_pp1a H2986H 8.70e-1 AY.59
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 9.57e-1 AY.59
V9127 3771T>C synonymous_variant S D1257D 1.00e+0 AY.59
V235 350C>T missense_variant ORF1ab_pp1a A117V 6.31e-1 AY.61
V4297 3790G>T missense_variant S V1264L 7.99e-1 AY.61
V9127 3771T>C synonymous_variant S D1257D 8.94e-1 AY.61
V3101 18388C>T missense_variant ORF1ab_pp1ab R6130C 1.00e+0 AY.62
V5140 179T>A stop_gained ORF8 L60* 1.00e+0 AY.62
V6794 6816C>T synonymous_variant ORF1ab_pp1a N2272N 1.00e+0 AY.62
V8016 16413G>A synonymous_variant ORF1ab_pp1ab L5471L 1.00e+0 AY.62
V8279 18393C>T synonymous_variant ORF1ab_pp1ab T6131T 1.00e+0 AY.62
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L 1.00e+0 AY.62
V843 2834C>A missense_variant ORF1ab_pp1a T945N 1.00e+0 AY.62
V871 2950A>G missense_variant ORF1ab_pp1a S984G 1.00e+0 AY.62
V1262 4918C>T missense_variant ORF1ab_pp1a P1640S 1.00e+0 AY.67
V4297 3790G>T missense_variant S V1264L 1.00e+0 AY.67
V680 2069C>T missense_variant ORF1ab_pp1a A690V 1.00e+0 AY.67
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 1.00e+0 AY.67
V757 2410C>T missense_variant ORF1ab_pp1a P804S 1.00e+0 AY.67
V9127 3771T>C synonymous_variant S D1257D 1.00e+0 AY.67
V9801 1176G>T synonymous_variant N V392V 1.00e+0 AY.67
V3283 19735G>T missense_variant ORF1ab_pp1ab V6579F 1.00e+0 AY.69
V9127 3771T>C synonymous_variant S D1257D 8.16e-1 AY.70
V6237 2577C>T synonymous_variant ORF1ab_pp1a A859A 1.00e+0 AY.7.1
V947 3218G>A missense_variant ORF1ab_pp1a G1073E 1.00e+0 AY.7.1
V3483 21038C>T missense_variant ORF1ab_pp1ab P7013L 7.07e-1 AY.71
V3486 21041G>A missense_variant ORF1ab_pp1ab R7014H 7.07e-1 AY.71
V4034 2063C>T missense_variant S A688V 7.07e-1 AY.71
V4497 375G>T missense_variant ORF3a M125I 7.07e-1 AY.71
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 7.07e-1 AY.71
V8943 2460T>C synonymous_variant S D820D 7.07e-1 AY.71
V9127 3771T>C synonymous_variant S D1257D 7.07e-1 AY.71
V306 607G>A missense_variant ORF1ab_pp1a D203N 1.00e+0 AY.73
V4297 3790G>T missense_variant S V1264L 1.00e+0 AY.73
V4879 83C>T missense_variant ORF7a T28I 1.00e+0 AY.73
V4918 184C>T stop_gained ORF7a Q62* 7.55e-1 AY.73
V6064 1419C>T synonymous_variant ORF1ab_pp1a I473I 1.00e+0 AY.73
V7251 10437C>T synonymous_variant ORF1ab_pp1a D3479D 9.35e-1 AY.73
V7414 11760C>T synonymous_variant ORF1ab_pp1a S3920S 1.00e+0 AY.73
V8361 18948A>G synonymous_variant ORF1ab_pp1ab R6316R 9.35e-1 AY.73
V8658 231G>A synonymous_variant S K77K 1.00e+0 AY.73
V9127 3771T>C synonymous_variant S D1257D 1.00e+0 AY.73
V9227 630C>T synonymous_variant ORF3a D210D 1.00e+0 AY.73
V9127 3771T>C synonymous_variant S D1257D 6.65e-1 AY.75
V1109 3883G>T missense_variant ORF1ab_pp1a V1295F 1.00e+0 AY.85
V4663 26C>T missense_variant E T9I 1.00e+0 AY.86
V5050 121T>G missense_variant ORF7b C41G 1.00e+0 AY.86
V5052 122G>T missense_variant ORF7b C41F 1.00e+0 AY.86
V5057 128C>T missense_variant ORF7b A43V 1.00e+0 AY.86
V5889 270A>G synonymous_variant ORF1ab_pp1a A90A 1.00e+0 AY.86
V6070 1476A>G synonymous_variant ORF1ab_pp1a K492K 1.00e+0 AY.86
V1627 7037T>C missense_variant ORF1ab_pp1a I2346T 1.00e+0 AY.9
V347 812C>T missense_variant ORF1ab_pp1a P271L 1.00e+0 AY.9
V4355 104T>C missense_variant ORF3a I35T 7.07e-1 AY.9
V4374 125C>T missense_variant ORF3a P42L 8.16e-1 AY.9
V4604 686C>T missense_variant ORF3a T229I 8.16e-1 AY.9
V48 -92G>T upstream_gene_variant ORF1ab_pp1a None 8.16e-1 AY.9
V6968 8271G>A synonymous_variant ORF1ab_pp1a K2757K 1.00e+0 AY.9
V7943 15847C>T synonymous_variant ORF1ab_pp1ab L5283L 1.00e+0 AY.9
V8039 16651C>T synonymous_variant ORF1ab_pp1ab L5551L 1.00e+0 AY.9
V5451 595C>T missense_variant N P199S 7.96e-1 B.1.111
V6489 4530C>T synonymous_variant ORF1ab_pp1a S1510S 6.53e-1 B.1.111
V7754 14379T>C synonymous_variant ORF1ab_pp1ab L4793L 1.00e+0 B.1.111
V5909 381T>C synonymous_variant ORF1ab_pp1a G127G 1.00e+0 B.1.1.39
V7814 14844C>T synonymous_variant ORF1ab_pp1ab T4948T 1.00e+0 B.1.1.39
V1423 6077A>C missense_variant ORF1ab_pp1a D2026A 1.00e+0 B.1.177.17
V2120 10844C>T missense_variant ORF1ab_pp1a A3615V 7.07e-1 B.1.177.17
V2920 17176C>T missense_variant ORF1ab_pp1ab P5726S 1.00e+0 B.1.177.17
V3658 448A>G missense_variant S K150E 1.00e+0 B.1.177.17
V3907 1447G>T missense_variant S V483F 1.00e+0 B.1.177.17
V3909 1450G>A missense_variant S E484K 1.00e+0 B.1.177.17
V3961 1749G>C missense_variant S E583D 1.00e+0 B.1.177.17
V5346 209A>G missense_variant N Q70R 1.00e+0 B.1.177.17
V5653 1240G>T missense_variant N A414S 1.00e+0 B.1.177.17
V702 2188C>T missense_variant ORF1ab_pp1a L730F 1.00e+0 B.1.177.17
V9152 108G>A synonymous_variant ORF3a P36P 1.00e+0 B.1.177.17
V471 1293A>G missense_variant ORF1ab_pp1a I431M 1.00e+0 B.1.177.75
V3450 20846C>T missense_variant ORF1ab_pp1ab T6949I 1.00e+0 B.1.258.17
V9782 1077A>T synonymous_variant N A359A 7.07e-1 B.1.351
V2132 10881G>T missense_variant ORF1ab_pp1a M3627I 1.00e+0 B.1.36.1
V7272 10603C>T synonymous_variant ORF1ab_pp1a L3535L 1.00e+0 B.1.497
V8284 18423C>T synonymous_variant ORF1ab_pp1ab C6141C 1.00e+0 B.1.497
V204 269C>T missense_variant ORF1ab_pp1a A90V 1.00e+0 BA.2.10.1
V1431 6097G>A missense_variant ORF1ab_pp1a A2033T 1.00e+0 BA.2.18
V8412 19398C>T synonymous_variant ORF1ab_pp1ab H6466H 9.28e-1 BA.2.1
V8259 18219C>T synonymous_variant ORF1ab_pp1ab H6073H 7.07e-1 BA.2.3.13
V9471 264C>T synonymous_variant ORF7a I88I 1.00e+0 BA.2.3.13
V211 292G>A missense_variant ORF1ab_pp1a G98S 1.00e+0 BA.2.3.18
V254 412G>A missense_variant ORF1ab_pp1a A138T 1.00e+0 BA.2.3.18
V9707 747A>G synonymous_variant N K249K 7.50e-1 BA.2.65
V1061 3652A>G missense_variant ORF1ab_pp1a S1218G 1.00e+0 BA.2.9.4
V8116 17175C>T synonymous_variant ORF1ab_pp1ab D5725D 7.07e-1 BA.4.1.8
V4497 375G>T missense_variant ORF3a M125I 9.35e-1 BA.4.4
V7168 9765C>T synonymous_variant ORF1ab_pp1a T3255T 1.00e+0 BA.4.4
V330 694C>T missense_variant ORF1ab_pp1a R232C 7.07e-1 BA.5.1.10
V8169 17577A>G synonymous_variant ORF1ab_pp1ab S5859S 1.00e+0 BA.5.1.10
V2613 14321C>T missense_variant ORF1ab_pp1ab A4774V 1.00e+0 BA.5.1.12
V3523 24G>T missense_variant S L8F 1.00e+0 BA.5.1.12
V403 1037C>T missense_variant ORF1ab_pp1a T346I 1.00e+0 BA.5.1.12
V7417 11784C>T synonymous_variant ORF1ab_pp1a N3928N 7.07e-1 BA.5.1.12
V5982 828C>T synonymous_variant ORF1ab_pp1a P276P 1.00e+0 BA.5.1.3
V7455 12045G>A synonymous_variant ORF1ab_pp1a Q4015Q 1.00e+0 BA.5.1.3
V2299 11906C>T missense_variant ORF1ab_pp1a A3969V 7.07e-1 BA.5.2.6
V1334 5465C>T missense_variant ORF1ab_pp1a T1822I 6.45e-1 BA.5.2.9
V4131 2806G>T missense_variant S D936Y 9.87e-1 BA.5.3.2
V5148 190G>T stop_gained ORF8 E64* 9.60e-1 BA.5.3.2
V4804 25G>T missense_variant ORF6 V9F 1.00e+0 BC.1
V4842 -5C>T upstream_gene_variant ORF7a None 7.74e-1 BC.1
V5913 408C>T synonymous_variant ORF1ab_pp1a Y136Y 8.66e-1 BC.1
V9580 105G>A synonymous_variant N A35A 1.00e+0 BC.1
V410 1057G>A missense_variant ORF1ab_pp1a G353S 7.07e-1 BE.1.2
V8046 16686T>C synonymous_variant ORF1ab_pp1ab P5562P 7.07e-1 BE.1.2
V933 3163A>G missense_variant ORF1ab_pp1a T1055A 7.07e-1 BE.1.2
V5114 112C>T missense_variant ORF8 P38S 1.00e+0 BE.1.3
V85 -44C>T upstream_gene_variant ORF1ab_pp1a None 1.00e+0 BE.1.3
V3835 1076G>A missense_variant S S359N 7.07e-1 BF.10
V8852 1758C>T synonymous_variant S D586D 7.07e-1 BF.10
V4888 110C>T missense_variant ORF7a S37F 8.16e-1 BF.11
V7025 8715C>T synonymous_variant ORF1ab_pp1a Y2905Y 7.30e-1 BF.1
V2783 16130C>T missense_variant ORF1ab_pp1ab P5377L 6.54e-1 BQ.1.10
V4324 59T>C missense_variant ORF3a I20T 1.00e+0 BQ.1.10
V7368 11482C>T synonymous_variant ORF1ab_pp1a L3828L 9.26e-1 BQ.1.10
V1388 5848C>T missense_variant ORF1ab_pp1a P1950S 1.00e+0 BQ.1.1.11
V4524 463G>T missense_variant ORF3a D155Y 7.07e-1 BQ.1.1.11
V5597 1087T>C missense_variant N F363L 1.00e+0 BQ.1.1.17
V6080 1560C>T synonymous_variant ORF1ab_pp1a A520A 7.07e-1 BQ.1.1.22
V7946 15906T>C synonymous_variant ORF1ab_pp1ab D5302D 7.07e-1 BQ.1.1.22
V7347 11322T>C synonymous_variant ORF1ab_pp1a N3774N 7.07e-1 BQ.1.1.5
V8594 20997A>G synonymous_variant ORF1ab_pp1ab S6999S 7.07e-1 BQ.1.1.5
V1073 3690G>T missense_variant ORF1ab_pp1a K1230N 6.32e-1 BQ.1.1.6
V5712 85C>T stop_gained ORF10 Q29* 1.00e+0 BQ.1.18
V2546 13850C>T missense_variant ORF1ab_pp1ab T4617I 7.07e-1 BQ.1.23
V7974 16113G>T synonymous_variant ORF1ab_pp1ab P5371P 7.07e-1 BQ.1.23
V8339 18807T>C synonymous_variant ORF1ab_pp1ab A6269A 7.07e-1 BQ.1.23
V3318 19969C>T missense_variant ORF1ab_pp1ab P6657S 7.07e-1 BU.1
V6580 5157T>C synonymous_variant ORF1ab_pp1a N1719N 7.07e-1 C.36.3
V8357 18918A>G synonymous_variant ORF1ab_pp1ab V6306V 1.00e+0 CH.1.1
V1579 6746C>T missense_variant ORF1ab_pp1a A2249V 7.07e-1 CK.2.1.1
V1206 4639G>T missense_variant ORF1ab_pp1a D1547Y 8.16e-1 CL.1
V7648 13659C>T synonymous_variant ORF1ab_pp1ab D4553D 1.00e+0 DN.1
V4794 -6C>T upstream_gene_variant ORF6 None 7.07e-1 P.1.2
V6193 2271C>T synonymous_variant ORF1ab_pp1a V757V 1.00e+0 P.1.2
V8994 2820C>T synonymous_variant S S940S 7.07e-1 P.1.2
V3876 1334T>C missense_variant S V445A 7.07e-1 XAZ
V4093 2492C>T missense_variant S A831V -1.00e+0 AY.133
V4448 266C>T missense_variant ORF3a T89I -1.00e+0 AY.133
V5602 1097C>T missense_variant N T366I -1.00e+0 AY.133
V5621 1136C>T missense_variant N T379I -1.00e+0 AY.133
V6069 1473G>T synonymous_variant ORF1ab_pp1a V491V -1.00e+0 AY.133
V7915 15666T>C synonymous_variant ORF1ab_pp1ab P5222P -1.00e+0 AY.133
V8359 18922C>T synonymous_variant ORF1ab_pp1ab L6308L -7.06e-1 AY.133
V8436 19620C>T synonymous_variant ORF1ab_pp1ab Y6540Y -1.00e+0 AY.133
V8536 20580C>T synonymous_variant ORF1ab_pp1ab P6860P -1.00e+0 AY.133
V979 3322C>T missense_variant ORF1ab_pp1a H1108Y -1.00e+0 AY.133
V1627 7037T>C missense_variant ORF1ab_pp1a I2346T 1.00e+0 AY.56
V3138 18664C>T missense_variant ORF1ab_pp1ab P6222S 1.00e+0 AY.56
V347 812C>T missense_variant ORF1ab_pp1a P271L 1.00e+0 AY.56
V393 998C>T missense_variant ORF1ab_pp1a T333M 1.00e+0 AY.56
V4355 104T>C missense_variant ORF3a I35T 1.00e+0 AY.56
V4374 125C>T missense_variant ORF3a P42L 1.00e+0 AY.56
V4604 686C>T missense_variant ORF3a T229I 1.00e+0 AY.56
V48 -92G>T upstream_gene_variant ORF1ab_pp1a None 7.06e-1 AY.56
V6451 4245G>T synonymous_variant ORF1ab_pp1a V1415V 1.00e+0 AY.56
V6968 8271G>A synonymous_variant ORF1ab_pp1a K2757K 1.00e+0 AY.56
V7943 15847C>T synonymous_variant ORF1ab_pp1ab L5283L 1.00e+0 AY.56
V8039 16651C>T synonymous_variant ORF1ab_pp1ab L5551L 1.00e+0 AY.56
V5772 *4354C>T downstream_gene_variant S None 1.00e+0 AZ.1
V6516 4728C>T synonymous_variant ORF1ab_pp1a N1576N 1.00e+0 B.1.1.128
V7185 9891C>T synonymous_variant ORF1ab_pp1a D3297D 1.00e+0 B.1.1.128
V9345 372C>T synonymous_variant M L124L 1.00e+0 B.1.1.128
V513 1442C>T missense_variant ORF1ab_pp1a S481F 1.00e+0 B.1.1.274
V5513 702G>T missense_variant N M234I 1.00e+0 B.1.1.512
V7126 9538C>T synonymous_variant ORF1ab_pp1a L3180L 1.00e+0 B.1.1.512
V8451 19752C>T synonymous_variant ORF1ab_pp1ab D6584D 7.06e-1 B.1.177.72
V1975 9663G>T missense_variant ORF1ab_pp1a M3221I 1.00e+0 B.1.523
V3927 1501A>T missense_variant S N501Y 1.00e+0 B.1.523
V4328 64G>C missense_variant ORF3a D22H 1.00e+0 B.1.523
V4990 329T>C missense_variant ORF7a I110T 1.00e+0 B.1.523
V5021 41delT frameshift_variant ORF7b L14fs 1.00e+0 B.1.523
V6999 8541T>C synonymous_variant ORF1ab_pp1a N2847N 1.00e+0 B.1.523
V8714 639G>T synonymous_variant S V213V 7.06e-1 B.1.523
V8933 2388T>C synonymous_variant S D796D 1.00e+0 B.1.523
V1266 4946C>T missense_variant ORF1ab_pp1a A1649V 6.27e-1 B.1.630
V489 1336C>T missense_variant ORF1ab_pp1a L446F 7.37e-1 B.1.630
V8536 20580C>T synonymous_variant ORF1ab_pp1ab P6860P 6.27e-1 B.1.630
V141 111G>T missense_variant ORF1ab_pp1a E37D 1.00e+0 BA.2.75.10
V7798 14668C>T synonymous_variant ORF1ab_pp1ab L4890L 7.06e-1 BA.2.75.10
V7206 10071C>T synonymous_variant ORF1ab_pp1a A3357A 6.31e-1 BE.1.4.2
V3812 925G>C missense_variant S E309Q 1.00e+0 BN.1.8
V7128 9540G>T synonymous_variant ORF1ab_pp1a L3180L 1.00e+0 BN.1.8
V4618 758C>T missense_variant ORF3a S253F 1.00e+0 CR.2
V4256 3656G>T missense_variant S G1219V 1.00e+0 P.1.9





Manual curation of mutation (184C>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