Many mutations have already been linked with disease, others are known to be benign. If the variant is novel, then look in the parents or other family members if possible.

If the mutation was carried by the parents and they are not affected, it is not likely to be pathogenic. If it is novel then more likely to be disease-causing.

If there is no family information, then there are a number of online tools available. No tool is perfect! You need to use a number of different tools and take a consensus view.

Page with explanation and links to some tools:

http://www.gen2phen.org/wiki/protein-level-predictions-1-pathogenic-or-not-predictors

Pathogenic-or-not Pipeline:

http://bioinf.uta.fi/PON-P/

Individual online tools to predict pathogenicity

http://mmb2.pcb.ub.es:8080/PMut/

http://snps.biofold.org/phd-snp/pages/PhD-SNP_Help.html

https://mutalyzer.nl/

http://sift.bii.a-star.edu.sg/

http://genetics.bwh.harvard.edu/pph2/

http://agvgd.iarc.fr/agvgd_input.php

https://www.rostlab.org/services/SNAP/

http://snps-and-go.biocomp.unibo.it/snps-and-go/

http://www.pantherdb.org/tools/csnpScoreForm.jsp

http://snpanalyzer.uthsc.edu/

http://www.moseslab.csb.utoronto.ca/amin/indelz.html

http://www.proweb.org/parsesnp/

http://folding.biofold.org/i-mutant/

Tools to predict effect of intronic variant on splicing:

http://www.phenosystems.com/www/index.php/links-to-various-tools-and-information/splice-prediction-tools

http://www.umd.be/HSF/

http://www.cbs.dtu.dk/services/NetGene2/

http://spliceport.cbcb.umd.edu/SplicingAnalyser.html

Mutation that can change the structure may contribute to pathogenesis. Nonsense mutation, missense mutation(resulting in an amino acid that differ in charge from the previous one ), can lead to some diseases, whereas if the change in codon does not change the amino acid or the change is not significant enough to alter the structure (resulting from replacement with same type of charge &/ almost same size) then the chances are minimum to induce any harmful effect.

By definition, mutations are pathogenic. However, as stated by Debasish it depends on the type of substitution and where it is located. You can have non-synonymous and synonymous substitutions. In this case the non-synonymous (ala>thr) should be unwanted. Moreover, it is important to remember that subsitution at a particular site could be common. Therefore, you should always check if the amino acid is conserved. If so, this particular amino acid should be important for the function-structure relation. However, even if you have checked the above mentioned ponits and come up with no real "important" results, remember there are still a view things you should consider too. As you might have read or learned, exons are spliced by a spliceosome, thereby getting rid of the introns. Each spliceosome requires a recognising site at the end on the exon. In addition, these spliceosomes also need splicing enhancers and suppressors. These are located within the exons. Such sites, or even better, these sites once mutated could have drastic effects on the totall protein.

Good luck,

René

Thank you Debaish & Rene. So basically if there is a mutation in a conserved region which may lead to synthesis of a different amino acid is pathogenic? I'm sorry Im nor an expert in genetics or molec biology.

Yes, but keep in mind that some substitutions are not that harmful. Look at this link. The figure below Venn diagram grouping amino acids according to their properties. This was adapted from Livingstone & Barton, CABIOS, 9, 745-756, 1993 (PubMed), and is just one of many classifications that are possible, but is probably that which most people would agree covers the most protein contexts.

http://www.google.nl/search?ei=MNZ9UrqRNbHM0AXr6IDIAw&q=venn+diagram+amino+acids&oq=venn+diagram+am&gs_l=mobile-gws-serp.1.0.0i19j0i10i19j0i19l3.13568.19278.0.21594.15.11.4.0.0.1.320.2382.1j4j5j1.11.0....0...1c.1.31.mobile-gws-serp..9.6.1172.fM51F007Wig#biv=i%7C0%3Bd%7C4FXrS1abDjJStM%3A.

Thank you Rene that helps. I have a simple molecular biology question for you. I have the sequence of the gene I'm interested in as well as introns and exons. However I'd like to have a nice graphical representation of which part of the sequence is going to be in exons and which is removed as introns. Also if it could give an idea about the bases in exon/intron junctions and which amino acid will be translated once the codon is formed after the splicing. A web based application would be nice. Because I just need to give other a more comprehensive explanation on what happens how such amino acids are translated (especially at junctions). Thanks

If you want to know whether the mutation is pathogenic or not you need to consider a number of points.

say for..

1) mutation is non-synonymous or synonymous

2) site of mutation is conserved or not

3) mutation is able to change the structure or not

4) affecting active site or not

5) promoting alternative splicing or not

6) introducing unexpected stop codon or not

7) even mutation in promoter region can hamper the protein production leading to a disease state

[so absence of protein, low level of protein, miss-folded protein, truncated protein, can lead to pathogenesis ]

and others....

(please add some points if I am missing any)

Dear Harindra,

You can use this link. It gives a lot of options to get more info for your protein.

http://www.uniprot.org/

If you are just interested in the conjuntion area you can use these

http://www.genepalette.org/GenePalette/Home.html

http://www.altanalyze.org/

http://splicenest.molgen.mpg.de/

http://bio.ieo.eu/fancygene/

Good luck

Dear Rene,

Thank you. Those applications are just wonderful.

Dear it is very simple just check if the mutation in conserved amino acid then have effect on expression which is easily check by any protein database

I disagree vigorously with the statement "By definition, mutations are pathogenic." By definition, pathogenic means "disease causing", and certainly most mutations are not disease causing. Most mutations are in fact neutral, having no effect on the viability of the organism. And many mutations are beneficial - this is what drives evolution. Sean Carroll, in Endless Forms Most Beautiful, documents numerous examples of single point mutations in the animal kingdom which confer a survival advantage.

As to Harindra's question, if the receptor is a human gene you do have a number of options. I don't know how you're planning on demonstrating that a mutation is "novel". If the mutation is a single point mutant or a small indel you can check dbsnp. If the mutation is in a coding region you can check the exome variant server.

http://evs.gs.washington.edu/EVS/

If the mutation changes the amino acid sequence, you can use the tools Abhishek lists above. If the mutation does not change the amino acid sequence, demonstrating pathogenecity bioinformatically is much more difficult, as the methods have not been validated to the same degree.

If the mutation truly is novel, ultimately you will have to do some wet biology to prove that it is pathogenic.

If you're asking about human mutations, I'd say that one of the first things you should do is look at the mutations' frequency in the genome. If the mutation is found in >1% of the normal population, then you can't simply examine the protein sequence for predicted changes and assign pathogeneity to the mutation. You can compare the mutation to EVS as Eric suggested if it is within the coding sequence or even use some of the software programs suggested above. But be careful to say that your mutation is disease-causing without first seeing if it is present in similar/higher frequencies in normal populations first.

Hi - check out snp-nexus.org => they offer a web portal which, given coordinates or rsID's (dbSNP) will give you SIFT and polyphen annotations. They are your easiest way (as a experimentalist) to get the answer.

Best,

non-coding variants are intronic, they may therefore affect gene splicing. there are a number of bioinfo tools that can predict whether it may have an effect. Unfortunately these 'intronic' predictive tools have a long way to go and you may want to do some lab work to confirm any 'promising' predictions.

I do not have a list of these predictive tools at hand (and its been a while) but you could google the following key words: alternative, splicing, prediction, donor, acceptor, etc.

True. Are any of yours located there?

Many mutations have already been linked with disease, others are known to be benign. If the variant is novel, then look in the parents or other family members if possible.

If the mutation was carried by the parents and they are not affected, it is not likely to be pathogenic. If it is novel then more likely to be disease-causing.

If there is no family information, then there are a number of online tools available. No tool is perfect! You need to use a number of different tools and take a consensus view.

Page with explanation and links to some tools:

http://www.gen2phen.org/wiki/protein-level-predictions-1-pathogenic-or-not-predictors

Pathogenic-or-not Pipeline:

http://bioinf.uta.fi/PON-P/

Individual online tools to predict pathogenicity

http://mmb2.pcb.ub.es:8080/PMut/

http://snps.biofold.org/phd-snp/pages/PhD-SNP_Help.html

https://mutalyzer.nl/

http://sift.bii.a-star.edu.sg/

http://genetics.bwh.harvard.edu/pph2/

http://agvgd.iarc.fr/agvgd_input.php

https://www.rostlab.org/services/SNAP/

http://snps-and-go.biocomp.unibo.it/snps-and-go/

http://www.pantherdb.org/tools/csnpScoreForm.jsp

http://snpanalyzer.uthsc.edu/

http://www.moseslab.csb.utoronto.ca/amin/indelz.html

http://www.proweb.org/parsesnp/

http://folding.biofold.org/i-mutant/

Tools to predict effect of intronic variant on splicing:

http://www.phenosystems.com/www/index.php/links-to-various-tools-and-information/splice-prediction-tools

http://www.umd.be/HSF/

http://www.cbs.dtu.dk/services/NetGene2/

http://spliceport.cbcb.umd.edu/SplicingAnalyser.html

Debasish Mukherjee can you explain some of the points that you have put up there, I am not getting it, can you help me out in it,

Are these human B cells? The tools described above are fine for research purposes, but most are not validated for use in clinical decision making.

You may find a clade of B cells with a new mutation that isn't in the individual's germline. Then there are two different questions here. It could be pathogenic to the B cell, leading to apoptosis, but do no harm to the person. Or it could lead to vigorous growth of the B cell line, and kill the person (or mouse).

Good point Chris - I didn't notice the bit in the question about B-cell surface receptors! My answer is more applicable to known disease genes like BRCA1, etc.

I worked in a clinical diagnostic lab for a few years - for novel non-synonymous mutations in known disease genes we would use some of these tools then, classify the risk into categories... e.g. benign, possibly damaging or highly likely to be damaging.

For variants/mutations in humans, you can check if curated variant databases exist for these genes, and check if the variant (and its effect) has been reported before:

http://www.lovd.nl/lsdbs

I'd recommend using the Ensembl VEP tool:

http://www.ensembl.org/info/docs/tools/index.html

Hello everybody;

I´m trying to find out whether a stop mutation is damaging or not. I´ve tried polyphen2, SIFT, Provean, MutPred and Alamut but in all cases they asked me for a substitution of amino acid. since I want to introduce a STOP I´m not sure how to indicate that.

Does someone know any tool for my purpose?

Dear Beatriz, 

A stopcodon can be a X or Ter. Sift and polyphen don't predict functional consequences of nonsense  mutations. Mutationtaster and provean do. What I read was you should introduce a stopcodon by adding an * to the substitution  equation (Q24*). 

Good luck,

René  

Synonymous mutation can be related to misfolding and dysfunction of the protein.

I recently proposed that translational rate is modulated by pairs of consecutive codons or bicodons [1]. By a statistical analysis of coding sequences, we compute a rate translational measure of all bicodons. We found that bicodons associated with sequences encoding low abundant proteins are involved in translational rate attenuation. Furthermore, we observe that the misfolding in many protein, such MDR1 gene [2], is better explained by a big change in the translational rate due to the synonymous bicodon variant, rather than by a relatively small change in the codon usage.

1.- Coding translational rates: the hidden genetic code

http://biorxiv.org/content/early/2016/07/08/062935

2.- Kimchi-Sarfaty, et al. A silent polymorphism in the MDR1 gene changes substrate specificity.

Science 315, 525–528 (2007).