Genome variation & terminology

25 important questions on Genome variation & terminology

How many libraries is the reference human genome made up of?

Seven, each being a different person.

What are the three different changes that can occur in a genome?

Substitution, deletion and insertion.

What does a silent mutation lead to?

The same amino acid.
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What does a missense mutation lead to?

An altered amino acid that may affect protein function or stability.

What does a nonsense mutation lead to?

A stop codon which may cause loss of function or expression due to degradation of mRNA.

What does a splice site mutation lead to?

Abnormal splicing and exon skipping or intron retention/conservation.

What does a promotor mutation lead to?

Altered gene expression.

What does an in frame insertion or deletion of a codon lead to?

Deletion or insertion of one or more amino acids, which may affect protein function.

What does a frameshift of one or more amino acids lead to?

Premature termination with loss of function or expression.

What does a partial gene duplication lead to?

Premature termination with loss of function or expression.

What can a whole gene duplication lead to?

Increased gene dosage.

What does a dynamic mutation lead to?

Altered gene expression or altered protein stability or function.

When a silent mutation occurs what does c.6T>C; p.(=) encode?

c. change of the 6th T to a C, which results in the same amino-acid so p. (=) means no changes in the protein.

When a missense mutation occurs, what does c.4T>C; p.(Tyr2His) encode?

c. change of the 4th T to a C, which results in a p. change from the 2th amino acid Tyr to His, so a different protein.

When a nonsense mutation occurs, what does c.10C>T; p.(Arg4*) encode?

c. change of the 10th C to a T, which results in a premature stopcodon p. after the 4th amino acid arg, so half a protein.

When a frameshift occurs, what does c.13delA; p.(Met5fs*) encode?

c. deletion of the 13th amino-acid, changes the p. 5th amino-acid met and results in frameshift and a premature stopcodon.

When a insertion or duplication occurs, what does c.13dupA; p.(Met5Asnfs*) encode?

c. duplication of the 13th A, changes the 5th amino-acid met and the frameshift results in a change of met to asn.

When an in frame deletion occurs, what does c.10_12delCGA; p.(Arg4del) encode?

c. deletion of the 10 – 12th amino-acids (in this case CGA), this results in the deletion of the 4th amino-acid arg.

When a splice site changes, what does c.33-1G>A; p.(?) encode?

c. one position left of the 33th basepair a G changed to an A (33–1 is position minus the amount of base pairs there) p. (?) means we don't know what is going to happen next.

When a splice site changes, what does c.67+2T>C; p.(?) encode?

c. two positions right of the 67th basepair the 2th T changed to an A (67 + 2 is position plus the amount of base pairs there) (?) means unknown what happens next.

What is the result of a single nucleotide variant?

Alteration of a single amino acid, creation of a stop codon or nothing.

What is the result of a single nucleotide polymorphism?

A change in gene expression or protein function.

What is the result of copy number variations?

Changes in gene dosage, which could lead to over-expression, under-expression or loss of gene function.

What is the result of structural variations?

Disruption of genes.

What are structural variations?

Genomic regions that involve breakage and rejoining of DNA segments.

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