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The current mutation

ID: V1337
DNA: 5483C>T
Protein: T1828I
Position: 5748








COV2Var annotation categories







Summary information of mutation (5483C>T)

Basic Information about Mutation.

  Gene Information   Gene ID   GU280_gp01_pp1a
  Gene Name   ORF1ab_pp1a
  Gene Type   protein_coding
  Genome position   5748
  Reference genome   GenBank ID: NC_045512.2
  Mutation type   missense_variant
  DNA Level   DNA Mutation: 5483C>T
  Ref Seq: C
  Mut Seq: T
  Protein Level   Protein 1-letter Mutation: T1828I
  Protein 3-letter Mutation: Thr1828Ile

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 (5483C>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.1.1.521 32 22 6.88e-1
2020-10 B.1.1.219 32 4 1.25e-1
2020-10 B.1.1.368 32 2 6.25e-2
2020-11 B.1.1.521 75 46 6.13e-1
2020-11 B.1.1.368 75 14 1.87e-1
2020-11 B.1.1.219 75 8 1.07e-1
2020-12 B.1.1.368 19 10 5.26e-1
2020-12 B.1.429 19 6 3.16e-1
2020-12 B.1.1.214 19 1 5.26e-2
2020-07 B.1.1.33 3 2 6.67e-1
2020-07 B.1 3 1 3.33e-1
2020-08 B.1.1.344 6 2 3.33e-1
2020-08 B.1.565 6 2 3.33e-1
2020-08 B.1 6 1 1.67e-1
2020-09 B.1.1.521 15 12 8.00e-1
2020-09 B.1.565 15 3 2.00e-1
2021-01 B.1.1.368 109 30 2.75e-1
2021-01 B.1.429 109 27 2.48e-1
2021-01 B.1.1.521 109 22 2.02e-1
2021-10 AY.4 71 41 5.77e-1
2021-10 AY.103 71 10 1.41e-1
2021-10 AY.79 71 5 7.04e-2
2021-11 AY.103 84 44 5.24e-1
2021-11 AY.4 84 13 1.55e-1
2021-11 AY.44 84 6 7.14e-2
2021-12 AY.103 151 97 6.42e-1
2021-12 BA.1 151 12 7.95e-2
2021-12 AY.44 151 7 4.64e-2
2021-02 B.1.429 33 15 4.55e-1
2021-02 B.1.1.521 33 8 2.42e-1
2021-02 B.1.1.519 33 4 1.21e-1
2021-03 B.1.429 66 45 6.82e-1
2021-03 B.1.1.7 66 7 1.06e-1
2021-03 B.1.36.16 66 5 7.58e-2
2021-04 B.1.429 55 25 4.55e-1
2021-04 B.1.1.519 55 5 9.09e-2
2021-04 B.1.2 55 5 9.09e-2
2021-05 B.1.351 18 10 5.56e-1
2021-05 B.1.429 18 4 2.22e-1
2021-05 B.1.1.7 18 2 1.11e-1
2021-06 B.1.1.7 9 5 5.56e-1
2021-06 AY.4 9 3 3.33e-1
2021-06 B.1.351 9 1 1.11e-1
2021-07 AY.4 52 41 7.88e-1
2021-07 AY.43 52 2 3.85e-2
2021-07 AY.74 52 2 3.85e-2
2021-08 AY.4 21 14 6.67e-1
2021-08 B.1.1.219 21 2 9.52e-2
2021-08 AY.103 21 1 4.76e-2
2021-09 AY.4 53 30 5.66e-1
2021-09 AY.5 53 4 7.55e-2
2021-09 AY.23 53 3 5.66e-2
2022-01 BA.1.1 59 16 2.71e-1
2022-01 BA.1 59 13 2.20e-1
2022-01 BA.1.15 59 10 1.69e-1
2022-10 BA.5.7 15 5 3.33e-1
2022-10 BF.5 15 3 2.00e-1
2022-10 BA.5.2.19 15 2 1.33e-1
2022-11 BF.7.1 15 3 2.00e-1
2022-11 BA.5.7 15 2 1.33e-1
2022-11 BQ.1.1 15 2 1.33e-1
2022-12 BQ.1.1 11 4 3.64e-1
2022-12 CM.2 11 2 1.82e-1
2022-12 DR.1 11 2 1.82e-1
2022-02 BA.2 97 50 5.15e-1
2022-02 BA.1.1 97 32 3.30e-1
2022-02 BA.1 97 8 8.25e-2
2022-03 BA.2 140 122 8.71e-1
2022-03 BA.1.1 140 10 7.14e-2
2022-03 BA.2.9 140 2 1.43e-2
2022-04 BA.2 76 63 8.29e-1
2022-04 BA.2.12 76 5 6.58e-2
2022-04 BA.2.3.1 76 2 2.63e-2
2022-05 BA.2 29 23 7.93e-1
2022-05 BA.2.3.1 29 2 6.90e-2
2022-05 BA.2.10 29 1 3.45e-2
2022-06 BA.2 24 7 2.92e-1
2022-06 BA.2.42 24 5 2.08e-1
2022-06 BA.2.3.1 24 3 1.25e-1
2022-07 BE.1 15 7 4.67e-1
2022-07 BA.2.52 15 2 1.33e-1
2022-07 BA.2.38 15 1 6.67e-2
2022-08 BA.5.7 12 4 3.33e-1
2022-08 BA.4.1 12 1 8.33e-2
2022-08 BA.5.1.10 12 1 8.33e-2
2022-09 BA.5.7 25 6 2.40e-1
2022-09 BA.5.2.19 25 4 1.60e-1
2022-09 BA.5.1.10 25 3 1.20e-1
2023-01 BQ.1.1 14 2 1.43e-1
2023-01 BQ.1.22 14 2 1.43e-1
2023-01 BQ.1.8 14 2 1.43e-1
2023-02 BQ.1.8 5 2 4.00e-1
2023-02 XBB.1.5 5 2 4.00e-1
2023-02 BQ.1.1 5 1 2.00e-1

The count of genome sequences and the frequency of this mutation in each lineage.
Note: Displaying mutation frequencies (>0.01) among 2,735 lineages. Mutation Count represents the count of sequences carrying this mutation. Users can filter the lineages by entering a search term in the search box. For example, entering "A.1" will display A.1 lineages. The data is obtained from GISAID's metadata, specifically capturing the lineage of genomic sequences. Mutation count: Count of sequences carrying this mutation.

Mutation ID Lineage Mutation frequency Mutation count Earliest lineage emergence Latest lineage emergence
V1337 B.1.1.219 3.66e-2 7 2020-8-1 2021-8-18
V1337 B.1.1.368 1.01e-1 31 2020-6-9 2021-9-14
V1337 B.1.1.521 2.90e-1 56 2020-5-15 2021-10-23
V1337 B.1.36.16 1.19e-2 9 2020-4-26 2021-12-2
V1337 BA.5.7 1.47e-2 17 2022-5-15 2023-1-25






Examining mutation (5483C>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 (5483C>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 -2.21e-15 4.03e+5 -5.47e-21 1.00e+0 Decrease
Deceased 1.11e+2 8.34e+4 1.32e-3 9.99e-1 Increase
Homebound -2.21e-15 4.03e+5 -5.47e-21 1.00e+0 Decrease
Hospitalized -3.08e+1 3.96e+3 -7.78e-3 9.94e-1 Decrease
Mild -2.21e-15 4.03e+5 -5.47e-21 1.00e+0 Decrease
Recovered -5.43e+0 2.40e+3 -2.26e-3 9.98e-1 Decrease

Analyzing the association between mutation and patient status.
Note: we categorized the data into different patient age (0-17, 18-39, 40-64, 65-84, and 85+). In the analysis exploring the association between mutation and patient age, the model included mutation, patient age, gender, sequence region of origin, and sequence collection time point. In the 'increase' direction of the mutation, it means that when this mutation occurs, it increases the corresponding effect proportion. In the 'decrease' direction of the mutation, it means that when this mutation occurs, it decreases the corresponding effect proportion. A p-value lower than 0.001 signifies a notable differentiation between the population with and without the mutation.

Attribute Effect Estimate SE Z-value P-value Direction
Patient age, years 0-17 -1.78e-1 6.61e-1 -2.69e-1 7.88e-1 Decrease
18-39 -7.80e-1 4.35e-1 -1.79e+0 7.33e-2 Decrease
40-64 -4.05e-1 4.57e-1 -8.87e-1 3.75e-1 Decrease
65-84 8.67e-1 4.82e-1 1.80e+0 7.22e-2 Increase
>=85 2.47e+0 6.94e-1 3.56e+0 3.70e-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 3.87e-1 4.08e-1 9.47e-1 3.44e-1 Increase





Investigating natural selection at mutation (5483C>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
nsp3 2720 8554 1945 1010 112.52 6.81 0.00e+0 BA.2.9.3 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
nsp3 2720 8554 1945 1010 9.80e-1 0.00e+0 BA.2.9.3 FUBAR
nsp3 2720 8554 1945 1010 1.00e-2 9.60e-1 B.1.429 FUBAR




Alterations in protein physicochemical properties induced by mutation (5483C>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 490000.97 6.04 543550 89.08 -0.022
Reference ORF1ab_pp1a 489988.91 6.04 543550 88.99 -0.023




Alterations in protein stability induced by mutation (5483C>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
T1828I ORF1ab_pp1a Point 1828 0.08 Increase 7 25 Environment
T1828I ORF1ab_pp1a Point 1828 0.17 Increase 7.4 37 Internal




Impact on protein function induced by mutation (5483C>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
T1828I ORF1ab_pp1a Point 0.183 Altered PPI_residue (Pr = 0.43 | P = 3.8e-04)
Altered Cytoplasmic_loop (Pr = 0.29 | P = 2.3e-04)
Gain of Disulfide_linkage at C1823 (Pr = 0.27 | P = 2.8e-03)
Gain of Zinc_binding at Q1832 (Pr = 0.26 | P = 0.03)
Altered PPI_hotspot (Pr = 0.25 | P = 0.02)
Gain of Strand (Pr = 0.25 | P = 0.09)
Gain of Allosteric_site at Y1827 (Pr = 0.22 | P = 0.02)
Gain of Relative_solvent_accessibility (Pr = 0.22 | P = 0.07)
Altered DNA_binding (Pr = 0.19 | P = 0.02)
Gain of Sodium_binding at Q1832 (Pr = 0.13 | P = 0.10)
Loss of Potassium_binding at Q1832 (Pr = 0.09 | P = 0.06)
Gain of Pyrrolidone_carboxylic_acid at Q1832 (Pr = 0.05 | P = 0.03)




Exploring mutation (5483C>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 (5483C>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
T1828I ORF1ab_pp1a 5748 Thermolysin ASEYIGNYQC (pos: 1827)
 NA




Impact of spike protein mutation (5483C>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 (5483C>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 (5483C>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 (5483C>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
V4574 614G>A missense_variant ORF3a S205N 1.00e+0 BA.1.17
V831 2800G>A missense_variant ORF1ab_pp1a G934S 7.07e-1 BA.5.5
V2022 10067C>T missense_variant ORF1ab_pp1a T3356I 6.76e-1 AY.39
V1151 4283A>G missense_variant ORF1ab_pp1a K1428R 7.07e-1 AY.47
V4379 130G>T stop_gained ORF3a G44* 7.07e-1 AY.47
V8962 2562G>A synonymous_variant S K854K 7.07e-1 AY.47
V7225 10209C>T synonymous_variant ORF1ab_pp1a F3403F 7.65e-1 B.1.1
V6371 3609C>T synonymous_variant ORF1ab_pp1a I1203I 7.74e-1 B.1.429
V9334 336C>T synonymous_variant M F112F 7.96e-1 B.1.429
V673 2028G>T missense_variant ORF1ab_pp1a Q676H 7.07e-1 BA.2.10
V8216 17964T>C synonymous_variant ORF1ab_pp1ab N5988N 1.00e+0 BA.5.6
V4507 392G>T missense_variant ORF3a W131L 7.07e-1 AY.107
V6913 7827C>T synonymous_variant ORF1ab_pp1a L2609L 7.07e-1 AY.107
V8059 16764C>T synonymous_variant ORF1ab_pp1ab S5588S 7.07e-1 AY.107
V8255 18204A>G synonymous_variant ORF1ab_pp1ab G6068G 7.07e-1 AY.107
V9466 252T>C synonymous_variant ORF7a P84P 7.07e-1 AY.107
V2261 11675T>C missense_variant ORF1ab_pp1a V3892A 1.00e+0 AY.120
V7066 8994A>G synonymous_variant ORF1ab_pp1a V2998V 7.07e-1 AY.122.5
V7710 14097T>C synonymous_variant ORF1ab_pp1ab I4699I 1.00e+0 AY.122.5
V1281 5061G>T missense_variant ORF1ab_pp1a E1687D 1.00e+0 AY.124
V3627 412G>C missense_variant S D138H 7.07e-1 AY.124
V6163 2130C>T synonymous_variant ORF1ab_pp1a V710V 9.13e-1 AY.127
V798 2645C>T missense_variant ORF1ab_pp1a T882I 7.71e-1 AY.127
V1985 9808G>A missense_variant ORF1ab_pp1a A3270T 1.00e+0 AY.128
V213 295C>T missense_variant ORF1ab_pp1a R99C 1.00e+0 AY.128
V4246 3601C>A missense_variant S Q1201K 1.00e+0 AY.128
V6798 6840C>A synonymous_variant ORF1ab_pp1a T2280T 1.00e+0 AY.4.15
V5141 180G>T missense_variant ORF8 L60F 1.00e+0 AY.42
V2223 11299C>T missense_variant ORF1ab_pp1a P3767S 6.55e-1 AY.46
V6722 6180C>T synonymous_variant ORF1ab_pp1a D2060D 1.00e+0 AY.53
V8265 18291C>T synonymous_variant ORF1ab_pp1ab D6097D 7.07e-1 AY.53
V1538 6458C>T missense_variant ORF1ab_pp1a T2153I 6.67e-1 AY.79
V4470 301C>T missense_variant ORF3a L101F 8.66e-1 AY.79
V5198 308C>T missense_variant ORF8 S103L 7.06e-1 AY.79
V6493 4567C>T synonymous_variant ORF1ab_pp1a L1523L 7.90e-1 AY.79
V8062 16779T>C synonymous_variant ORF1ab_pp1ab Y5593Y 8.01e-1 AY.79
V8357 18918A>G synonymous_variant ORF1ab_pp1ab V6306V 8.66e-1 AY.79
V4847 4A>G missense_variant ORF7a K2E 8.16e-1 AY.99.2
V2782 16129C>T missense_variant ORF1ab_pp1ab P5377S 7.07e-1 B.1.1.25
V3231 19381G>T missense_variant ORF1ab_pp1ab V6461F 1.00e+0 B.1.1.25
V3837 1099G>T missense_variant S V367F 1.00e+0 B.1.1.25
V7152 9678C>T synonymous_variant ORF1ab_pp1a Y3226Y 1.00e+0 B.1.1.25
V8236 18102A>G synonymous_variant ORF1ab_pp1ab L6034L 1.00e+0 B.1.1.25
V9332 318G>T synonymous_variant M T106T 7.07e-1 B.1.1.25
V628 1877C>T missense_variant ORF1ab_pp1a P626L 1.00e+0 B.1.1.33
V2493 13466C>T missense_variant ORF1ab_pp1ab A4489V 6.01e-1 B.1.1.519
V7279 10674T>C synonymous_variant ORF1ab_pp1a D3558D 6.19e-1 B.1.351
V3508 21204G>T missense_variant ORF1ab_pp1ab M7068I 7.43e-1 B.1.36.16
V9438 120C>T synonymous_variant ORF7a Y40Y 6.77e-1 B.1.36.16
V9485 348C>T synonymous_variant ORF7a L116L 6.06e-1 B.1.36.16
V586 1712A>G missense_variant ORF1ab_pp1a D571G 1.00e+0 B.1.497
V2512 13594G>T missense_variant ORF1ab_pp1ab D4532Y 7.06e-1 B.1.565
V5293 71C>T missense_variant N T24I 8.16e-1 B.1.621.1
V6740 6369T>C synonymous_variant ORF1ab_pp1a A2123A 7.07e-1 B.1.621.1
V7208 10095G>A synonymous_variant ORF1ab_pp1a K3365K 1.00e+0 B.1.621.1
V7830 14976C>T synonymous_variant ORF1ab_pp1ab N4992N 7.07e-1 B.1.621.1
V8194 17796C>T synonymous_variant ORF1ab_pp1ab L5932L 1.00e+0 B.1.621.1
V9199 339C>T synonymous_variant ORF3a Y113Y 1.00e+0 B.1.621.1
V4070 2333C>T missense_variant S T778I 1.00e+0 BA.1.14
V7574 12999C>T synonymous_variant ORF1ab_pp1a H4333H 7.07e-1 BA.1.16
V7921 15688C>T synonymous_variant ORF1ab_pp1ab L5230L 6.17e-1 BA.2.12
V4552 541G>A missense_variant ORF3a E181K 1.00e+0 BA.2.31
V6388 3780T>C synonymous_variant ORF1ab_pp1a N1260N 1.00e+0 BA.2.38
V4222 3484C>T missense_variant S P1162S 6.10e-1 BA.2.42
V614 1821G>T missense_variant ORF1ab_pp1a Q607H 6.10e-1 BA.2.42
V1813 8399C>T missense_variant ORF1ab_pp1a T2800I 1.00e+0 BA.2.52
V9670 534C>T synonymous_variant N G178G 1.00e+0 BA.2.68
V2898 17003A>G missense_variant ORF1ab_pp1ab D5668G 1.00e+0 BA.2.9.3
V3884 1354C>A missense_variant S L452M 8.16e-1 BA.2.9.3
V6614 5388T>C synonymous_variant ORF1ab_pp1a Y1796Y 1.00e+0 BA.2.9.3
V7727 14217C>T synonymous_variant ORF1ab_pp1ab H4739H 1.00e+0 BA.5.1.23
V352 836C>T missense_variant ORF1ab_pp1a S279F 1.00e+0 BA.5.2.6
V5806 *4383A>G downstream_gene_variant S None 1.00e+0 BA.5.2.6
V5946 588C>T synonymous_variant ORF1ab_pp1a Y196Y 1.00e+0 BA.5.3.1
V6035 1206C>T synonymous_variant ORF1ab_pp1a R402R 6.39e-1 BA.5.7
V8530 20526C>T synonymous_variant ORF1ab_pp1ab V6842V 6.91e-1 BA.5.7
V2257 11651C>T missense_variant ORF1ab_pp1a S3884L 7.07e-1 BA.5
V2456 13229G>T missense_variant ORF1ab_pp1ab R4410L 7.07e-1 BA.5
V2823 16529G>T missense_variant ORF1ab_pp1ab R5510L 7.07e-1 BA.5
V50 -85T>C upstream_gene_variant ORF1ab_pp1a None 7.07e-1 BA.5
V3716 569G>T missense_variant S R190M 1.00e+0 BQ.1.1.22
V2528 13694G>T missense_variant ORF1ab_pp1ab R4565L 1.00e+0 BQ.1.1.32
V9566 45T>C synonymous_variant N I15I 1.00e+0 BQ.1.1.32
V533 1556G>A missense_variant ORF1ab_pp1a G519D 1.00e+0 BQ.1.22
V2450 13187C>T missense_variant ORF1ab_pp1a A4396V 8.94e-1 BQ.1.8
V3063 18146A>G missense_variant ORF1ab_pp1ab Y6049C 8.94e-1 BQ.1.8
V671 2021G>T missense_variant ORF1ab_pp1a S674I 8.94e-1 BQ.1.8
V8786 1230C>T synonymous_variant S I410I 6.76e-1 BQ.1.8
V9177 225G>A synonymous_variant ORF3a K75K 1.00e+0 BQ.1
V7963 16029C>T synonymous_variant ORF1ab_pp1ab C5343C 7.75e-1 P.1.14
V2387 12567G>T missense_variant ORF1ab_pp1a Q4189H 1.00e+0 B.1.1.219
V3530 52C>T missense_variant S L18F 8.41e-1 B.1.1.219
V4337 77C>T missense_variant ORF3a S26L 7.50e-1 B.1.1.219
V1748 7975C>T missense_variant ORF1ab_pp1a H2659Y 1.00e+0 B.1.1.344
V1928 9214G>T missense_variant ORF1ab_pp1a G3072C 1.00e+0 B.1.1.344
V5457 604A>T missense_variant N S202C 1.00e+0 B.1.1.344
V5459 605G>C missense_variant N S202T 1.00e+0 B.1.1.344
V5807 *4385C>T downstream_gene_variant S None 7.03e-1 B.1.1.344
V6592 5250G>T synonymous_variant ORF1ab_pp1a V1750V 1.00e+0 B.1.1.344
V713 2243C>T missense_variant ORF1ab_pp1a P748L 1.00e+0 B.1.1.344
V9438 120C>T synonymous_variant ORF7a Y40Y 1.00e+0 B.1.1.344
V7225 10209C>T synonymous_variant ORF1ab_pp1a F3403F 9.31e-1 B.1.1.368
V8380 19122C>T synonymous_variant ORF1ab_pp1ab D6374D 9.31e-1 B.1.1.368
V8944 2461C>T synonymous_variant S L821L 9.31e-1 B.1.1.368
V4546 524C>T missense_variant ORF3a T175I 8.74e-1 B.1.1.521
V7103 9300C>T synonymous_variant ORF1ab_pp1a F3100F 6.03e-1 B.1.1.521
V9328 306G>T synonymous_variant M L102L 1.00e+0 B.1.1.521
V9372 492G>T synonymous_variant M L164L 8.87e-1 B.1.1.521
V1951 9428C>T missense_variant ORF1ab_pp1a A3143V 1.00e+0 B.1.160.30
V4546 524C>T missense_variant ORF3a T175I 1.00e+0 B.1.160.30
V5461 608G>A missense_variant N R203K 7.05e-1 B.1.160.30
V5465 610G>C missense_variant N G204R 7.05e-1 B.1.160.30
V6507 4662C>T synonymous_variant ORF1ab_pp1a D1554D 1.00e+0 B.1.160.30
V6878 7575C>T synonymous_variant ORF1ab_pp1a D2525D 1.00e+0 B.1.160.30
V8292 18480C>T synonymous_variant ORF1ab_pp1ab Y6160Y 1.00e+0 B.1.160.30
V8429 19575T>C synonymous_variant ORF1ab_pp1ab N6525N 1.00e+0 B.1.160.30
V8866 1860C>T synonymous_variant S V620V 1.00e+0 B.1.160.30
V9328 306G>T synonymous_variant M L102L 1.00e+0 B.1.160.30
V9372 492G>T synonymous_variant M L164L 1.00e+0 B.1.160.30
V9682 609G>A synonymous_variant N R203R 7.05e-1 B.1.160.30
V1445 6143C>T missense_variant ORF1ab_pp1a S2048F 7.06e-1 B.1.210
V2918 17146C>T missense_variant ORF1ab_pp1ab R5716C 6.30e-1 B.1.210
V3178 18890C>T missense_variant ORF1ab_pp1ab T6297I 1.00e+0 B.1.210
V5461 608G>A missense_variant N R203K 7.05e-1 B.1.210
V2350 12358C>T missense_variant ORF1ab_pp1a P4120S 1.00e+0 BH.1
V181 245_259delGTCATGTTATGGTTG disruptive_inframe_deletion ORF1ab_pp1a G82_V86del 1.00e+0 XAS
V2241 11485C>T missense_variant ORF1ab_pp1a L3829F 1.00e+0 XAS
V8370 19005C>T synonymous_variant ORF1ab_pp1ab N6335N 1.00e+0 XAS
V8377 19110C>T synonymous_variant ORF1ab_pp1ab F6370F 1.00e+0 XAS
V9463 237C>T synonymous_variant ORF7a A79A 1.00e+0 XAS
V8601 21042C>T synonymous_variant ORF1ab_pp1ab R7014R 7.06e-1 XBB.1.4





Manual curation of mutation (5483C>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