Lecture 2 types of mutation-dr. al-allaf-md-y3-2009

١٤٤٤/٠٩/٢٣ Dr. Faisal Al-Allaf, [email protected] 1

Dr. Faisal Al-AllafAssistant Professor of Genetics and Molecular Medicine

Umm Al-Qura University Faculty of Medicine, Makkah, Saudi Arabia

[email protected]/Fax: 5270000 Ext: 4198

Types of Mutations


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


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


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.


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.


Types of mutations Base substitutions

Synonymous or Silent mutations Nonsense mutation Missense mutation


Insertions may cause frameshift

Duplication duplications of part of a gene or DNA sequence

Deletions may cause frameshift

Splicing mutations may cause truncation


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.


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.


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.


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



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


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


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


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)


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


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.


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


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.


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.


Transcription and RNA processing


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.


Mutations in promoter and regulatory elements

It may lead to up-regulation or to down-regulation of transcription which may be detrimental


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.


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.


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.


Examples of unstable trinucleotide repeat expansions


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.


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)


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


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


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


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.

Lecture 2 types of mutation-dr. al-allaf-md-y3-2009

Education

mutations mutations

nonsense mutations

mutations mutationis

single base substitutions

deletions of single

single nucleotide

single base pair substitution

protein product