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١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 1
Dr. Faisal Al-AllafAssistant Professor of Genetics and Molecular Medicine
Umm Al-Qura University Faculty of Medicine, Makkah, Saudi Arabia
fallaf@uqu.edu.saTel/Fax: 5270000 Ext: 4198
Types of Mutations
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 2
Mutations Types of mutations
Base substitutions Synonymous Nonsense Missense
Conservative Non conservative Readthrough
Insertions Duplication Deletions Splicing
Basic nomenclature Functional effects of mutations on the proteins
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 3
Mutations Mutation is a permanent change in nucleotide
sequence. It can be at chromosomal or DNA levels. Gross lesions (chromosomal accounts for
less than 8%) Micro-lesions (molecular accounts for more
than 92%)
At the chromosomal level: Numerical abnormalities include
Aneuploidy (Monosomy, Trisomy and Tetrasomy) and Polyploidy (Triploidy and Tetraploidy)
Structural abnormalities includes translocations, deletions, insertions, inversions and rings formation
Cell fusion and mosaicism
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 4
Mutations At the molecular level: range from single
base substitutions, through insertions and deletions of single or multiple bases.
It can occur in somatic or germline cells. Mutations which occur in germline
cells (gametes) are inherited and therefore pass to future generations unless it affects fertility or survival.
Mutations which occur in somatic cells may cause adult-onset disease such as cancer but cannot be transmitted to offspring.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 5
Mutations Mutations drive evolution but can
also be pathogenic.
A conservative estimate suggests that each individual carries up to six lethal or semi-lethal recessive mutant alleles that in homozygous state would have very serious effects.
Mutations can occur either in non-coding or coding sequences, it is only when they occur in the latter that they are recognized as an inherited disorder or disease.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 6
Types of mutations Base substitutions
Synonymous or Silent mutations Nonsense mutation Missense mutation
Conservative Non conservative Readthrough
Insertions may cause frameshift
Duplication duplications of part of a gene or DNA sequence
Deletions may cause frameshift
Splicing mutations may cause truncation
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 7
Base substitutions Substitution is the replacement of a
single nucleotide by another with no net gain or loss of chromosomal material.
Base substitutions are most prevalent and missense mutations accounts for nearly half of all mutations.
If the substitution involves replacement by the same type of nucleotide, i.e. a pyrimidine for a pyrimidine (C for T or vice versa) or a purine for a purine (A for G or vice versa), this is termed a transition.
Substitution of a pyrimidine by a purine or vice versa is termed a transversion.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 8
Base substitutions Point mutations may arise as a result
of mistakes in DNA replication, mistakes in repair following DNA damage, or most commonly as the result of the spontaneous deamination of methylated cytosine to thymine.
Point mutations may be silent or deleterious depending upon the site.
Rarely, a mutation may be advantageous and favored by natural selection.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 9
Synonymous or silent mutations Based on the structural effects of the
mutations on the polypeptide sequence of the encoded protein, mutations can also be subdivided into two main groups, being either synonymous or non- synonymous mutations.
Synonymous or Silent mutations: when a mutation does not alter the polypeptide product of the gene
Because of the degeneracy of the genetic code, a single base pair substitution, particularly if it occurs in the third position of a codon, will often result in another triplet which codes for the same amino acid with no alteration in the properties of the resulting protein.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 10
Non synonymous mutation Non synonymous mutation occurs
when the mutation leads to an alteration in the encoded polypeptide.
Alteration of the amino acid sequence of the protein product of a gene is likely to result in abnormal function. Occur less frequent than
synonymous mutation
Non-synonymous mutations can occur in one of two main ways. Nonsense mutation Missense mutation
Conservative Non conservative Readthrough
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 11
Missense mutations A single bp substitution can
result in coding for a different amino acid and the synthesis of an altered protein, a so-called missense mutation.
The wrong sense (but it still makes a kind of sense)
Examples: Cystic fibrosis: CFTR G551D Sickle cell anaemia: defective
haemoglobin due to mutation in β-globin gene
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 12
Nonsense mutations A substitution which leads to the
generation of one of the stop codons will result in premature termination of translation of a peptide chain or what is termed a nonsense mutation.
Makes no sense Change of a codon for an AA to a
STOP codon Eg: Cystic fibrosis: CFTR G542X
Premature termination of translation produces truncated (shortened) protein
Almost always pathogenic due to loss of large amount of the normal protein
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 13
Deletions and insertions Deletions and insertions/duplications
involves the loss or gain of one or more nucleotides.
The addition or deletion of a single nucleotide will cause the amino acids to be grouped incorrectly.
The effects of deletion and insertion on protein depend on:
The amount of material lost Whether the reading frame is affected
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 14
Deletions and insertions of multiples of 3 nucleotides
Small insertions and deletions in coding sequences of multiples of 3 nucleotides will retain the frame (NOT cause frameshift but extra amino acid(s) will be encoded)
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 15
Deletions and insertions of multiples of 3 nucleotides
ك ع غ ف ت ر س ك و م م ل ج ك ا ع م ر ب م ل ق م ر ف مل ي س ه ط ح ر خ ص ي د ل ب ع س ز ر ك ف ر ط س
سيل مكر حطه صخر مود كجل معا مبر مقل مفرعلي
مبر مكر مقل سيل ...مفر حطه صخر مود كجلعلي
صخر مكر مود كجل معا مبر مقل صلبمفرسيل عليحطه
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 16
Deletions and insertions of NOT multiples of 3 nucleotides
Small deletions and insertions in coding sequences of one, two or more nucleotides which are not a multiple of three will destroys the reading frame causing frameshift and may be premature terminations or readthrough.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 17
Deletions and insertions of NOT multiples of 3 nucleotides
ك ع غ ف ت ر س ك و م م ل ج ك ا ع م ر ب م ل ق م ر ف مل ي س ه ط ح ر خ ص ي د ل ب ع س ز ر ك ف ر ط س
سيل مكر حطه صخر مود كجل معا مبر مقل مفرعلي
مق مكر يلع ممفر طهس خرح ودص جلم عاك برمليس
ص مكر مود كجل معا مبر مقل رحط بمفر خي لعل هسي
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 18
Mutations in non-coding DNA Mutations in non-coding DNA are
less likely to have a phenotypic effect. Exceptions include mutations in promoter sequences, or other regulatory regions. Mutations in in the splicing of introns, e.g. the highly conserved GT and AG dinucleotides at the end of introns.
Mutations in regulatory elements can affect the level of gene expression while mutations in splice junctions can result in coding sequences being lost or intronic sequences being added to the mRNA molecule.
Recently, it has become apparent that mutations in miRNA or siRNA binding sites within UTRs are also likely to result in disease.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 19
Splicing mutations Splicing mutations affect the splice
donor (GU), splice acceptor (AG) or splice regulatory sites and results in aberrant splicing.
Often results in truncating – loss of sequence + possibility remaining sequence is out-of-frame.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 20
Transcription and RNA processing
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 21
Splicing mutations Splicing mutations can results in
The loss of coding sequence (exon skipping), or
Retention of intronic sequence Or may lead to frameshift
mutations
Cryptic splice sites, which resemble the sequence of an authentic splice site, may be activated when the conserved splice sites are mutated.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 22
Mutations in promoter and regulatory elements
It may lead to up-regulation or to down-regulation of transcription which may be detrimental
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 23
Stable and unstable mutations Mutations which transmitted unaltered are termed fixed or stable
mutations and mutations which undergo further alteration as they are transmitted in families are termed dynamic or unstable mutations.
Fixed/stable mutations are point mutation (single base pair substitutions, insertions, deletions or duplications of part of a gene or DNA sequence).
Unstable or dynamic mutations consist of triplet repeat expansion which, in affected persons, occur in increased copy number when compared to the general population.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 24
Unstable or dynamic mutations Runs of triplet repeats are found in all members of the population, but
in individuals affected with these diseases the triplet repeats generally occur in a higher copy number in the disease gene (the triplet repeat has expanded).
All these repeats involve cytocine/guanine (C/G)-rich trinucleotides (CGG, CCG, CAG, CTG), and they may involve a few copies to several thousand repeats.
Triplet repeat expansions are a type of unstable insertion that have been associated with a variety of neurological disorders, many of which show anticipation. Most of these disorders are inherited dominantly but Friedreich’s ataxia is an example of a recessive triplet repeat disorder.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 25
Unstable or dynamic mutations Triplet repeats below a certain length (which varies between the
different disorders) are transmitted faithfully after meiosis and mitosis. However, if they expand above a certain size they become likely to expand or (rarely) contract during cell division. This phenomenon is the molecular basis of anticipation.
Anticipation is a phenomenon in which a genetic disease appears earlier and possibly with increased severity in succeeding generation
Depending on the disorder, the repeats may arise in coding or non-coding sequence and they may affect the protein in a variety of ways.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 26
Examples of unstable trinucleotide repeat expansions
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 27
Functional effects of mutations on the protein
The mutations effect can appear either through Loss-of-function or Gain-of-function
Loss-of-function mutations can result in either reduced activity or complete loss of the gene product. In the heterozygous state would be associated with half normal levels of the protein product. They may be dominantly or recessively inherited.
Gain-of-function mutations, are inherited dominantly and result in either increased levels of gene expression (simple gain of function) or the development of new protein function (dominant negative mutations).
Rarely, a mutation may be advantageous and favored by natural selection.
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 28
Basic nomenclature (Nucleotide)
1078delT (more correctly, c.1078delT, to indicate that the numbering is using coding nucleotide sequence, where 1 is A of ATG) the T at position 1078 is deleted
457TAT>G (or c.457_459delTATinsG) nucleotides 457 to 459 (TAT) have been deleted and a G has been inserted instead
1525-1G>A (or c.1525-1G>A) the nucleotide just preceding 1525 of the coding sequence is changed to A (+ or – numbers indicate that the sequence is intronic: 1525 is an exon start)
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 29
Basic nomenclature (Protein)
G551D (more correctly p.G551D to indicate protein sequence) normal glycine (G) at position 551 is altered to aspartate (D) in the mutant
G542X (p.G542X) codon for glycine 542 in the protein has been altered to a stop codon
F508del (p.508del) the normal phenylalanine (F) at position 508 is missing due to deletion of this codon
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 30
Summary of mutation types
Mutations and their effects on protein products
Class Group Type Effect on protein product
Stable/ fixedSynonymous Substitution Silent – same amino acid
Non-synonymousSubstitution 1.Missense Non-conservative Conservative
Altered amino acidAltered activity, function or stabilityNo effect
2. NonsenseStop codon – premature termination with loss of function/activity/stability
Deletions/insertion1.Multiple of 3 (codon)
2.Not multiple of 3
In frame deletion/insertion of one or more amino acid(s) in protein – may altered activity/ function/stability
Altered reading frame (frameshift), premature termination of protein – altered amino acid sequence, loss of function/activity/stability
Dynamic/unstable
Triplet repeatExpansion Altered gene expression, reduced transcription or translation, altered transcript – altered activity/ function/stability
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 31
References and Private Reading1. Emery’s Elements of Medical Genetics, 13th edition 2007, by Peter TURNPENNY and
Sian ELLARD. Churchill Livingstone ELSEVIER. ISBN: 978-0-7020-2917-2
2. Medical Genetics at a Glance, 2nd edition 2008, by Dorian PRITCHARD and Bruce KORF. Blackwell Publishing. ISBN: 978-1-4051-4846-7
3. Elsevier's Integrated Genetics, 2007, by Linda Adkison and Michael Brown. MOSBY ELSEVIER. ISBN: 978-0-323-04329-8
4. Genetics for Dummies, 2005, by Tara Robinson, Wiley Publishing, Inc. ISBN: 978-0-7645-9554-7
5. New Clinical Genetics, 2007, by Andrew Read and Dian Donnai. Scion. ISBN: 978-1-904842-31-6
6. Cell Biology and Genetics, Crash Course, 2nd edition 2006, by Manson, Jones, Morris, Michael STEEL and Dan HORTON-SZAR. MOSBY ELSEVIER. ISBN: 0-7234-3248-1
7. Human Molecular Genetics, 3rd edition, 2003, by STRACHAN T. and A. READ. Garland science/Taylor and Francis group. ISBN: 978-0-8153-4182-6
8. Human Genetics: Concepts and Applications, 7th edition 2007, by Ricki LEWIS. McGraw Hill international. ISBN: 978-0-07-110779-2
9. Genomes, 3rd edition 2006, by T.A. BROWN. Garland science, ISBN: 978-0-8153-4138-3
10. Colour Atlas of Genetics, 2007, by Eberhard Passarge. Thieme. ISBN: 978-1-58890-3365
١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, fallaf@uqu.edu.sa 32
Acknowledgments For the providers of all the educational materials
(video clips, pictures, diagrams and charts) including publishers, pharmaceutical companies or unknown internet users who made their material available for use, in this and other presentations, I offer heartfelt thanks and deep appreciation.
I feel particularly grateful to faculty, staff, and our brilliant students who provided a unique intellectual and wonderful environment for work.
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