| S. No. | Method | Year | Type | Description | Reference |
|---|
| 1 | SIFT (Sorting Intolerant From Tolerant) | 2003 | AAC | Predicting amino acid changes that affect protein function | 12824425 |
| 2 | PhD-SNP | 2006 | with support vector machines and evolutionary information | Predicting the insurgence of human genetic diseases associated to single point protein mutations | 16895930 |
| 3 | SeqProfCod | 2008 | protein sequence, multiple protein sequence alignments, and the estimation of selective pressure at the codon level | Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans. | 17935148 |
| 4 | SNPs&GO | 2009 | protein sequence, evolutionary information, and function as encoded in the Gene Ontology terms | Functional annotations improve the predictive score of human disease-related mutations in proteins | 19514061 |
| 5 | Mutationassessor | 2011 | evolutionary conservation patterns | Predicting the functional impact of protein mutations: application to cancer genomics | 21727090 |
| 6 | | 2011 | Review+Datasets | Performance of mutation pathogenicity prediction methods on missense variants. | 21412949 |
| 7 | Combined Annotation scoRing toOL (CAROL) | 2012 | MetaServer | A Combined Functional Annotation Score for Non-Synonymous Variants | 22261837 |
| 8 | FunSAV | 2012 | two-stage random forest model | predicting the functional effect of single amino acid variants | 22937107 |
| 9 | Functional Analysis Through Hidden Markov Models (FATHMM) | 2013 | Domain + hidden Markov models | Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. | 23033316 |
| 10 | WS-SNPs&GO | 2013 | GO terms | Predicting disease associated variations using GO terms | 23819482 |
| 11 | Meta-SNP | 2013 | MetaServer | Collective judgment predicts disease-associated single nucleotide variants. | 23819846 |
| 12 | CoVEC (Consensus Variant Effect Classification) | 2013 | MetaServer | Predicting the functional consequences of non-synonymous DNA sequence variants | 23831115 |
| 13 | Cancer-specific High-throughput Annotation of Somatic Mutations (CHASM) | 2013 | protein sequence, evolutionary information, and function as encoded in the Gene Ontology terms | Predicting the functional consequences of somatic missense mutations found in tumors. | 24233781 |
| 14 | PolyPhen-2 (Polymorphism Phenotyping v2) | 2013 | structural and comparative evolutionary considerations | Predicting functional effect of human missense mutations | 23315928 |
| 15 | PredictSNP | 2014 | MetaServer | consensus classifier for prediction of disease-related mutations | 24453961 |
| 16 | SuSPect (Disease-Susceptibility-based SAV Phenotype Prediction) | 2014 | Using Network Features | Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype | 24810707 |
| 17 | PON-P2 | 2015 | evolutionary information+protein properties( 622 features) | PON-P2: prediction method for fast and reliable identification of harmful variants. | 25647319 |
| 18 | SNAP2 | 2015 | evolutionary information+protein properties | Better prediction of functional effects for sequence variants. | 26110438 |
| 19 | | 2015 | Review+Datasets | The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity. | 25684150 |
