2 Genetic nomenclature Flashcards

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1
Q

What is a mutation?

A

○ An intrinsic change in DNA

○ Can be described at

  • Chromosomal or
  • DNA level
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2
Q

Types of mutation level?

A
  • Genome mutaiton: whole chromosome excess or absence
  • Chromosome mutation: chromosome rearrangement (i.e. translocations)
  • Gene mutation: mutationi of a single gene
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3
Q

What type of mutation level is a translocation?

A

It’s a chromosome mutation

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4
Q

What is an allele?

A

Its 1 of the two copies of a locus

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5
Q

What type of alleles (or alternative copies of a locus can you have?

A
  • Wild type
    • The normal version, the prevailing version
  • Polymorphism
    • “many forms”
    • More than one allele is present at a locus within a population
    • May lead to disease
    • Frequency of >1%
  • Mutation
    • It’s a permanent change in the nucleotide sequence
    • Causes disease
  • Rare variant - VOUS
    • Allele that does not cause disease VOUS
    • Frequency less than 1%
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6
Q

If you find a variant in the human genome, how do you call it if its >1% or <1% of frequency?

A
  • >1% polymorphism
  • <1% Rare variant
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7
Q

What are the types of polymorphism?

A
  • SNP
  • VNTR - variable number tandem repeats
  • STR short tandem repeats
  • RFLP restriction fragment length polymorphism
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8
Q

Difference mutation and polymorphism? Main

A
  • Mutation = disease
  • Polymorphism= benign mutation
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9
Q

What are “Snips” SNP’s

A
  • Single nucleotide polymorphisms
  • It’s a genetic variation among people
  • It’s a single NUCLETIDE change a C for T for example
  • Occur normally in normal people
  • Occur once every 300 nucleotides
  • There are 10 million SNPS in the human genome
  • Most commonly they are located between genes
  • They can act as biological markers or position hints
  • If they are within a gene or closer to a gene they can have something to do about causing a disease
  • Most SNPs do not cause disease
  • They are useful to
    • Predict responses to drugs
    • Susceptibility to environmental factors
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10
Q

What are the 2 reasons for mutations to occur?

A
  • Spontaneous (DNA replication errors)
  • Induced
    • By radiation
    • Chemicals - mutagenesis
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11
Q

What are examples of diseases causes by advanced maternal and paternal mutations?

A
  • Maternal - down syndrome (cytogenetic)
  • Paternal - Achondroplasia (single locus)
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12
Q

What are the prefixes in mutations nomenclature?

A
  • “c” for a coding DNA sequence (c.76A>T)
  • “g” for genomic sequence (g.476A>T)
  • “m” for a mitochondrial sequence (m.8993T>C)
  • “n” for non-coding RNA reference sequence (gene producing an RNA transcript but not a protein)
  • “r” for and RNA sequence (r.76a>u)
  • “p” for a protein sequence (p.Lys76Asn)
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13
Q

c for

A

coding DNA sequence (c.76A>T)

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14
Q

“g” for…

A

for genomic sequence (g.476A>T)

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15
Q

“m” for

A

mitochondrial sequence (m.8993T>C)

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16
Q
A
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17
Q

“n” for

A
18
Q

for non-coding RNA reference sequence (gene producing an RNA transcript but not a protein)

A
19
Q

“r” for

A

RNA sequence (r.76a>u)

20
Q

“p” for

A

a protein sequence (p.Lys76Asn)

21
Q

when enumerating, which is the #1 nucleotide?

A

the A of the ATG (initiator)

22
Q

when using gene nomenclature you have two options (C&G) what are they?

A

These are Reference Sequences (RS)

genomic reference sequence or coding reference sequence

  • g for genome — impractical because it counts from the begining of genome so it has high numbers
  • c for coding - more practical. The position 1 is the A of the ATG

There is also protein reference sequence

23
Q
A
24
Q

what are point mutations?

A

when there is a change in ONE SINGLE nucleotide

  • the numbering always starts at the A of the ATG (methionine)
25
Q

interpret this mutation

c.9A>G or p. (Lys=)

A

these are two forms to call a mutation

coding reference:

c.9A>G in the coding reference sequence - at the position 9 there is a substitution of A for G

protein reference:

Lys no change

It was a SILENT mutation (there was a change in thenucleotide that did not change the AA

the () means its a prediction

26
Q

interpret the following mutation

c.8A>G or p.Lys3Arg

A

This is a missense Mutation/variant (missense - pierde sentido - there is an AA substitution

coding sequence

at position 8 A was changed to G

protein level

the 3rd AA was Lys but has changed to Arg

27
Q

how do I know if this is a disease causing mutaiton /variant

A

check in the dbSNP for:

  • allelic frequency
  • has it been seen in random controls?
  • seen only in patients with disease?
  • is the protein functional with the change?
  • is it conserved across species?
28
Q

what is a :

  1. silent mutation
  2. missense mutaiotn
  3. non-sense mutation
  4. no-stop-mutation
  5. splicing mutation
A
  1. SILENT -change in nucleotide that does not change the AA and thus does not change the protein
  2. MISSENSE - change in nucleotide that changes the AA and MAY CHANGE the PROTEIN
  3. NON-SENSE - change in nucleotide that creates an STOP CODON
  4. stop codon is changed to AA and thus the reading keeps going
  5. splicing mutation = intron/exon splicing sites
29
Q

interpret this mutation

c. 7A>T or
p. Lys3Ter or
p. Lys3*

A

this is a NONSENSE mutation

at position 7 there is a change in A for T

this change causes Lys to be changed to an TERMINATION codon

Which are the stop codons?

UAA, UAG, UGA

30
Q

Which are the stop codons?

A

UAA, UAG, UGA

  • UAA
  • UAG
  • UGA
31
Q

what are NONSENSE mutations?

what do they do?

A

change in nucleotide that creates a TERMINATION CODON

IT creates a TRUNCATED protein (but not always

32
Q

what does the NMC (nonsense mediated decay)

A

mecanism to clean up truncated proteins

degrades mRNA truncated

because its toxic for the cell

33
Q

if you have a nonsense mutation can you write a paper on this?

A

no

you still need to investigate supporting info like

  • allele frequency
  • how frequent in the idsease
  • is it only present in disease patients

conserved among species etec

34
Q

interpret this mutation

c. 25T>C or
p. Ter9GlnextTer5 or
p. 9*Glnext*5

A

this meanes that the normal termination codon it was changed to glutamine and extended for 5 more nucleotides (because wo the stop codon the reading kept going)

Result = many AA added to protein

35
Q
A
36
Q

interpret this mutation

c.200+1G>A

A

this is an splicing mutation

when you see this +1 or -1 or + something or -somthing its an SPLICING mutation

  • this means that at position 200+1 (at the intron) a G was mutated to A. This will likely qaffect splicing.
  • this means that it may cause that an exon is skipped for example.
37
Q

can silent mutation cause disease?

A

yes!

example PROGERIA

38
Q

what is a frameshift mutation?

A

when the number of bases involved is not a multiple of 3

39
Q

interpret the following mutation

c. 4delG or
p. Val2LeufsTer6

or

p.Val2Leufs*6

A

this is a frameshift mutaiton because many AAs were changed

  • menas at position 4 there was a G deletion
  • also at codon 2 there was supposed to be a Val that was changed for Leu and created a Ter codon in codon 6
40
Q

interpret

c.16_17insAC

or

p.Leu6HisfsTer3

A

basically and insertion

an AC was inderte in 16&17

41
Q

most common deletion?

A

cystic fibrosis

c.1521_1523delCTT