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Point MutationsPoint Mutations

Mutations involving a few Mutations involving a few nucleotides, sometimes as few as a nucleotides, sometimes as few as a

single one (SNPs)single one (SNPs)

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SNPsSNPs

(Pronounce: snips) (Pronounce: snips) SSingle ingle nnucleotide ucleotide ppolymorphismsolymorphisms

1 nucleotide variations between alleles1 nucleotide variations between alleles

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A ReminderA Reminder

2 SNPs difference between estrogen receptors 2 SNPs difference between estrogen receptors a and b. a and b. next page next page

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Shape and AA Sequence

Genistein, bound to estrogen receptor-b.

Only two amino acids (shown) differ between the two estrogen receptors. (purple: ER-a) (yellow:yellow: ER-b)

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Point MutationsPoint Mutations

The Genome Map Lists diseases caused by point mutations by Lists diseases caused by point mutations by chromosome – with imageschromosome – with images The – more abstract - The – more abstract - 1998 update The The 2002 update

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LinksLinks

ThinkQuest Genetics Lab - Mutations

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Point MutationPoint Mutation

We will mutate one codon in several ways. We will mutate one codon in several ways. Assume that that codon is, for example, the Assume that that codon is, for example, the 1515thth codon in a chain of 100 codons in an codon in a chain of 100 codons in an mRNA.mRNA.

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Point Mutations: Point Mutations: Mutating a codon – SNP Effects Mutating a codon – SNP Effects

Imagine that this is codon 15 out of 100 codons of a Imagine that this is codon 15 out of 100 codons of a protein gene mRNA. All other codons remain protein gene mRNA. All other codons remain unchanged:unchanged:

ATAATA UAUUAU

tyrtyr

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Point Mutations Point Mutations Mutating a codon – SNP Effects:Mutating a codon – SNP Effects:

ATAATA TTTATA UAUUAU AAUAAU

tyrtyr asn asn

ATTATT

UAAUAA

stopstop

mutation 1

1 AA difference

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Point Mutations Point Mutations Mutating a codon – SNP Effects: Mutating a codon – SNP Effects:

ATAATA TTTATA UAUUAU AAUAAU

tyrtyr asn asn

mutation 1

Mutation types:

1. missense 1 AA difference

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Point Mutations Point Mutations Mutating a codon – SNP Effects:Mutating a codon – SNP Effects:

ATATGG ATA ATA TTTATA

UACUAC UAUUAU AAUAAU

tyrtyr tyr tyr asnasn

mutation 1mutation 2

1 AA difference

Mutation types:

1. Missense

2. Silent Sequence unchanged

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Point Mutations: Point Mutations: Mutating a codon – Effects of SNPsMutating a codon – Effects of SNPs

ATATGG ATA ATA TTTATA

UACUAC UAUUAU AAUAAU

tyrtyr tyr tyr asnasn mutation 3mutation 3

ATATTT

UAAUAA

stopstop

mutation 2 mutation 1

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Point Mutations: Point Mutations: Mutating a codonMutating a codon

ATATGG ATA ATA TTTATA

UACUAC UAUUAU AAUAAU

tyrtyr tyr tyr asnasn 3 3

ATATTT

UAAUAA

stopstop

2 1

Mutation types:

1. missense

2. silent

3. nonsense (stop) – chain is aborted

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Point Mutations Can Happen Point Mutations Can Happen During DNA RepairDuring DNA Repair

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SNP Effects – e.g. SNP Effects – e.g. Frame ShiftFrame Shift

A cytosine A cytosine insertioninsertion in the NOD2 in the NOD2 gene leads to gene leads to Crohn’s diseaseCrohn’s disease (CD). (CD).

CD is a chronic inflammatory gut CD is a chronic inflammatory gut disorder, thought to be caused by disorder, thought to be caused by an abnormal inflammatory an abnormal inflammatory response to enteric microbes.response to enteric microbes.

For more info click For more info click here

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How Mutations May HappenHow Mutations May Happen

Watch this Watch this animation and answer the and answer the following questions:following questions: What type of mutation is the result of What type of mutation is the result of

new strand and new strand and template strand template strand

slippage?slippage?

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Point Mutation Types - Overview

Panel A shows the normal sequence of Panel A shows the normal sequence of DNA from one exon and the protein DNA from one exon and the protein product it encodesproduct it encodes

Panel B shows a silent mutation,Panel B shows a silent mutation, Panel C a conservative missense Panel C a conservative missense

mutation (serine and threonine have mutation (serine and threonine have very similar structures)very similar structures)

Panel D a nonconservative missense Panel D a nonconservative missense mutation (serine and proline have very mutation (serine and proline have very different structures), different structures),

Panel E a nonsense mutation, and Panel E a nonsense mutation, and Panel F a frame-shift mutation. In Panel F a frame-shift mutation. In

Panel F, the insertion of a single G Panel F, the insertion of a single G throws off the reading frame, so that throws off the reading frame, so that all amino acids downstream are all amino acids downstream are changed radically. changed radically.

G

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Silent Mutations – Not Always SilentSilent Mutations – Not Always Silent

Protein folding depends on the speed at Protein folding depends on the speed at which the mRNA moves through the which the mRNA moves through the ribosome, since silent translations can ribosome, since silent translations can alter that speed, they may result in alter that speed, they may result in different protein foldingdifferent protein folding

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Mutations in PIK3CAMutations in PIK3CA

Where is this gene mutated?Where is this gene mutated?

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Structure of phosphoinositide 3-Structure of phosphoinositide 3-kinase gamma kinase gamma

Click on a Click on a domain in the domain in the image in this image in this link for a link for a detailed detailed description of itdescription of it

PIK3CAs have PIK3CAs have several several ddoommaaiinnss with with different different functionsfunctions

A kinase is an enzyme that places a phosphate onto another protein. More specifically, kinases take the gamma (=

3rd) phosphate from ATP and place it on a serine, threonine, or tyrosine amino acid of the target substrate.

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Mutations in PIK3CAMutations in PIK3CA ““Phosphatidylinositol 3-kinases (PI3Ks) are lipid kinases that regulate signaling pathways Phosphatidylinositol 3-kinases (PI3Ks) are lipid kinases that regulate signaling pathways

important for neoplasiaimportant for neoplasia11, including cell proliferation, adhesion, survival, and motility (, including cell proliferation, adhesion, survival, and motility (11––33). ). To determine if PI3Ks are genetically altered in tumorigenesis, we sequenced PI3K genes in To determine if PI3Ks are genetically altered in tumorigenesis, we sequenced PI3K genes in human cancers and corresponding normal tissue.” human cancers and corresponding normal tissue.”

““Arrowheads indicate the location of missense mutations, boxes represent functional domains Arrowheads indicate the location of missense mutations, boxes represent functional domains (the p85 binding domain, Ras binding domain, C2 domain, helical domain, and kinase (the p85 binding domain, Ras binding domain, C2 domain, helical domain, and kinase domain). The percentage of mutations detected within each region is indicated below, and the domain). The percentage of mutations detected within each region is indicated below, and the fraction of tumors with mutations is noted above. fraction of tumors with mutations is noted above.

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Why Might Anyone Want Why Might Anyone Want to Know This?to Know This?

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PIK3CAPIK3CAA Possible Cancer Treatment?A Possible Cancer Treatment?

In most of the tumors listed above, the kinase is over-In most of the tumors listed above, the kinase is over-expressed. Inhibiting the kinase may inhibit expressed. Inhibiting the kinase may inhibit tumorigenesis.tumorigenesis.

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Genes and EnvironmentGenes and Environment

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Gene Expression And The Gene Expression And The EnvironmentEnvironment

Russian rabbits have Russian rabbits have black noses, ears, tails, black noses, ears, tails, and paws.and paws.

Yet, the genes for the Yet, the genes for the black pigment are black pigment are present in ALL their present in ALL their cells.cells.

Develop a hypothesis to Develop a hypothesis to explain the pattern.explain the pattern.

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Genes and EnvironmentGenes and Environment

If this Russian rabbit If this Russian rabbit has its thigh shaved and has its thigh shaved and is then kept in a cold is then kept in a cold environment, what will environment, what will the new fur growth look the new fur growth look like?like?

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Genes & EnvironmentGenes & Environment

Cuttings from the 7 different plants on the left, grown at different altitudes:

Plants with the same genes may Plants with the same genes may exhibit dramatically different growth exhibit dramatically different growth forms, depending on their forms, depending on their environmentenvironment

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Gene, Smoking Combo Boosts Risk Gene, Smoking Combo Boosts Risk of Elderly Vision Lossof Elderly Vision Loss

Specific mutation raises chances of Specific mutation raises chances of age-related macular degenerationage-related macular degeneration

MONDAY, March 20 (HealthDay News) -- A MONDAY, March 20 (HealthDay News) -- A combination of smoking plus a specific gene variant combination of smoking plus a specific gene variant could account for a third of cases of age-related macular could account for a third of cases of age-related macular degeneration (AMD), researchers say. AMD is the most degeneration (AMD), researchers say. AMD is the most common cause of visual impairment and legal blindness common cause of visual impairment and legal blindness in older Americans. Interaction between a specific in older Americans. Interaction between a specific variant of the LOC387715 gene and cigarette smoking variant of the LOC387715 gene and cigarette smoking greatly increases AMD, say researchers at Duke greatly increases AMD, say researchers at Duke University Medical Center and Vanderbilt University University Medical Center and Vanderbilt University Medical Center. The finding emphasizes the importance Medical Center. The finding emphasizes the importance of genetic factors in the onset of AMD, and suggests the of genetic factors in the onset of AMD, and suggests the potential to reduce the incidence of the disease through potential to reduce the incidence of the disease through smoking prevention and cessation programs. "The most smoking prevention and cessation programs. "The most exciting aspect of this research is that it is the exciting aspect of this research is that it is the combination of the gene and smoking that really puts you combination of the gene and smoking that really puts you at risk," study senior author Margaret Pericak-Vance, at risk," study senior author Margaret Pericak-Vance, director of the Duke Center for Human Genetics, said in director of the Duke Center for Human Genetics, said in a prepared statement. a prepared statement.

"We demonstrate, for the first time, that a gene variant "We demonstrate, for the first time, that a gene variant coupled with a modifiable lifestyle factor such as coupled with a modifiable lifestyle factor such as cigarette smoking confers a significantly higher risk of cigarette smoking confers a significantly higher risk of AMD than either factor alone," she said. The findings AMD than either factor alone," she said. The findings appear in the online edition of the appear in the online edition of the American Journal of American Journal of Human GeneticsHuman Genetics, and will be published in the May print , and will be published in the May print issue of the journal. The study included 1,001 people issue of the journal. The study included 1,001 people with all forms of AMD and 394 healthy people in a with all forms of AMD and 394 healthy people in a control group. Researchers analyzed 185 variations in the control group. Researchers analyzed 185 variations in the DNA sequence of genes located in a region believed to DNA sequence of genes located in a region believed to be associated with susceptibility to AMD. The scientists be associated with susceptibility to AMD. The scientists found that 42 percent of the chromosomes of people with found that 42 percent of the chromosomes of people with AMD and 26 percent of the people in the control group AMD and 26 percent of the people in the control group had a specific variant of LOC387715 statistically had a specific variant of LOC387715 statistically associated with the highest risk of developing AMD. In associated with the highest risk of developing AMD. In nonsmokers, this genetic variant increased AMD risk nonsmokers, this genetic variant increased AMD risk twofold. People who had the genetic variant and smoked twofold. People who had the genetic variant and smoked had an eightfold increased risk of AMD, compared to had an eightfold increased risk of AMD, compared to nonsmokers without the variant. The actual function of nonsmokers without the variant. The actual function of the LOC387715 gene in the visual system is unknown, the LOC387715 gene in the visual system is unknown, the researchers said.the researchers said.

-- Robert Preidt -- Robert Preidt

SOURCE: Duke University, news release, March 7, 2006 SOURCE: Duke University, news release, March 7, 2006

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Without the Presence of the Environmental Factor, Without the Presence of the Environmental Factor, These Genes Do Not Lead to DiseaseThese Genes Do Not Lead to Disease

A SAMPLING OF ENVIRONMENTAL GENESA SAMPLING OF ENVIRONMENTAL GENES

PolymorphismPolymorphism FunctionFunction Environmental exposureEnvironmental exposure Associated diseaseAssociated disease

CYP1A1CYP1A1 ActivationActivation SmokingSmoking Lung cancerLung cancer

NAT2NAT2 DetoxificationDetoxification SmokingSmoking Bladder, breast cancerBladder, breast cancer

GSTT1GSTT1 DetoxificationDetoxification Chlorinated solventsChlorinated solvents Cancer, toxicityCancer, toxicity

ParaoxonaseParaoxonase DetoxificationDetoxification Nerve agents, pesticidesNerve agents, pesticides Nervous system damageNervous system damage

HLA-HHLA-H Nutritional factorsNutritional factors Iron in dietIron in diet HemochromatosisHemochromatosis

TGF-alphaTGF-alpha Growth factorGrowth factor Maternal smokingMaternal smoking Cleft lip & palateCleft lip & palate

Locus on chrom. 17 in miceLocus on chrom. 17 in mice Immune/inflammatory responseImmune/inflammatory response OzoneOzone Lung inflammationLung inflammation

HLA-DP bet1 markerHLA-DP bet1 marker Immune responseImmune response BerylliumBeryllium Chronic beryllium disease (lung disorder)Chronic beryllium disease (lung disorder)

ALADALAD BiosynthesisBiosynthesis LeadLead Lead poisoningLead poisoning

Read about: Genetics, race, ethnicity, and health

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More about diseases (heart, cancer, diabetes) and More about diseases (heart, cancer, diabetes) and environment here (very informative!)environment here (very informative!)

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Genes and Skin ColorGenes and Skin Color

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Genes And Skin ColorGenes And Skin ColorFindings From Golden Zebra FishFindings From Golden Zebra Fish““Lighter variations of pigmentation in humans are associated with diminished Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor.melanosome or its precursor.The human ortholog is highly similar in sequence and functional in zebrafish. The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation. “gene in human pigmentation. “

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Two Primary Alleles for Skin Color Two Primary Alleles for Skin Color GeneGene

Data … show … “that Data … show … “that SLC24A5SLC24A5 has two has two primary alleles, which vary by one amino acid. primary alleles, which vary by one amino acid. Nearly all Africans and East Asians have an Nearly all Africans and East Asians have an allele with alanine in a key locus, whereas allele with alanine in a key locus, whereas 98% of Europeans have threonine at that 98% of Europeans have threonine at that locus.” locus.”

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A SNP Determines Skin Color in A SNP Determines Skin Color in Many PeopleMany People

“…“…polymorphisms within the” polymorphisms within the” SLC24A5SLC24A5 “gene. … the G “gene. … the G and A alleles of the single nucleotide polymorphism (SNP) and A alleles of the single nucleotide polymorphism (SNP) rs1426654 encoded alanine or threonine, respectively, at rs1426654 encoded alanine or threonine, respectively, at amino acid 111 in the third exon of amino acid 111 in the third exon of SLC24A5SLC24A5. “. “

““The allele frequency for the The allele frequency for the ThrThr111111 variant variant ranged from 98.7 ranged from 98.7 to 100% among several European-American population to 100% among several European-American population samples, …samples, …

the the ancestral alanine allele (ancestral alanine allele (AlaAla111111)) had a frequency of 93 to had a frequency of 93 to 100% in African, Indigenous American, and East Asian 100% in African, Indigenous American, and East Asian population samples” population samples”

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Gene SLC24A5Gene SLC24A5 … “… “the team measured the pigmentation levels of 203 African the team measured the pigmentation levels of 203 African

Americans and 105 African Caribbeans--groups that represent Americans and 105 African Caribbeans--groups that represent an admixture of African and European ancestry--and an admixture of African and European ancestry--and compared their compared their SLC24A5SLC24A5 genotypes. genotypes.

Subjects Subjects homozygous for the threonine allele tended to be homozygous for the threonine allele tended to be lightest skinnedlightest skinned, ,

those those homozygous for the alanine allele were darkesthomozygous for the alanine allele were darkest, , and and heterozygotes were in betweenheterozygotes were in between, as shown by the degree , as shown by the degree

of reflectance of their skin. The team concludes that of reflectance of their skin. The team concludes that between between 25% and 38% of the skin-color difference between 25% and 38% of the skin-color difference between Europeans and Africans can be attributed to Europeans and Africans can be attributed to SLC24A5SLC24A5 variantsvariants” ”

04/12/2304/12/23 3636Published by AAAS

R. L. Lamason et al., Science 310, 1782 -1786 (2005)

Fig. 6. Effect of SLC24A5 Genotype on Pigmentation in Admixed Populations

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Genes and the Genes and the Size of a DogSize of a Dog

A SNIP in the IGF-1 Gene A SNIP in the IGF-1 Gene Determines Dog SizeDetermines Dog Size

04/12/2304/12/23 3838Published by AAAS

N. B. Sutter et al., Science 316, 112 -115 (2007)

Relationships of skeletal size, SNP markers, IGF1 haplotype, and serum levels of the IGF1 protein in dogs

((BB) … ) … IGF1IGF1 haplotypes and mean skeletal size. haplotypes and mean skeletal size. Haplotypes were inferred for 20 markers Haplotypes were inferred for 20 markers spanning the spanning the IGF1IGF1 gene (chromosome 15: gene (chromosome 15: 44,212,792 to 44,278,140, CanFam1). Out of the 44,212,792 to 44,278,140, CanFam1). Out of the 720 chromosomes with successful inference, 96% 720 chromosomes with successful inference, 96% carry one of just two carry one of just two haplotypes, B and I, haplotypes, B and I, identical to haplotypes inferred for small and identical to haplotypes inferred for small and giant dogs, respectivelygiant dogs, respectively. Data are graphed as a . Data are graphed as a histogram for each genotype: histogram for each genotype:

B/B (closed triangle, black line)B/B (closed triangle, black line) B/I (open square, dashed line)B/I (open square, dashed line) I/I (closed circle, gray line) I/I (closed circle, gray line)

(C) Serum levels of IGF1 protein (ng/ml) as a function of (C) Serum levels of IGF1 protein (ng/ml) as a function of haplotype. haplotype.

This Rabbit Must Have The This Rabbit Must Have The Large VersionLarge Version

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Last Not LeastLast Not Least

Genes and HIV ProgressionGenes and HIV Progression

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Effect of a Single Amino Acid Change in MHC Class I Effect of a Single Amino Acid Change in MHC Class I Molecules on the Rate of Progression to AIDSMolecules on the Rate of Progression to AIDS

Conclusions: Conclusions: This analysis shows that, in patients with HIV-1 infection, a single amino This analysis shows that, in patients with HIV-1 infection, a single amino

acid change in HLA molecules has a substantial effect on the rate of acid change in HLA molecules has a substantial effect on the rate of progression to AIDS. progression to AIDS.

… … different consequences of HLA-B*35-PY and HLA-B*35-Px in terms different consequences of HLA-B*35-PY and HLA-B*35-Px in terms of disease progression …of disease progression …

Human immunodeficiency virus type 1 (HIV-1)-infected individuals with Human immunodeficiency virus type 1 (HIV-1)-infected individuals with HLA-B*35 allelic variants B*3502/3503/3504/5301 (B*35-Px) progress HLA-B*35 allelic variants B*3502/3503/3504/5301 (B*35-Px) progress more rapidly to AIDS than do those with B*3501 (B*35-PY).more rapidly to AIDS than do those with B*3501 (B*35-PY).

'Indians vulnerable to HIV/Aids' 'Indians vulnerable to HIV/Aids' India is home to one in seven HIV-positive people:India is home to one in seven HIV-positive people: Indians infected with the Aids virus are more likely to contract the Indians infected with the Aids virus are more likely to contract the

disease than people in the west, a new study has found.disease than people in the west, a new study has found.

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On the Up-SideOn the Up-Side

Eternal Life?Eternal Life?

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Boosting Gene Extends Mouse Life SpanBoosting Gene Extends Mouse Life Span

Whereas lab mice can live Whereas lab mice can live about 2 years, mice about 2 years, mice engineered to overproduce a engineered to overproduce a protein called Klotho protein called Klotho [Greek goddess who spins [Greek goddess who spins life's thread], have life's thread], have celebrated third birthdays, celebrated third birthdays, … …

The mutant rodents The mutant rodents represent a rare case of a represent a rare case of a single gene substantially single gene substantially influencing life span in influencing life span in mammals. mammals.

These mice, which These mice, which overexpress the gene for overexpress the gene for Klotho, have celebrated Klotho, have celebrated their third birthdays.their third birthdays.

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The EndThe End