Summary: Eigen Hmd Samenvatting Week 4 Tot Week 8
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1 molecular pathology - effects of genetic variation on gene function
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What is a variant and a polymorphism?
Variant = a DNA sequence that does not correspond with the reference genome.
polymorphism = a common (~50% population frequency genetic variant) a benign variant -
What means LoF and GoF?
- Loss-of-function = variant reduce or abrogate gene function
- more likly to happen
- many wyas to lose activity
- acquiring functions requires one specific event
- gain-of-function = variants enhace or create novel gene function
- Loss-of-function = variant reduce or abrogate gene function
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What sort of mutations in dominant disorders? (3)
Gain of functionhaploinsufficieny - dominant negative
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What sort of mutations in recessive disorders?
- Loss of function
- hypomorph
- Loss of function
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1.1 SNVs and indels causing LoF
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What happens if a SNVs (single nucleotide variant) introduce a stopgain?
You cangain stopcodons . Avariant that ischanges to astopcodon gives you los of a part of theprotein . Soloss offuntion .
how much impact it has depends on thelenght of theprotein missing after thepremature stopcodon -
What happens when a SNVs initiate a startloss?
- You loss the AUG
- If you have the SNV that gives you a
startloss than yoy will have a loss of function. In this case you have an other AUG, so you only mis a small part of the protein. In this case you need more moleculair information to kown if it is a loss of function of the protein.
- You loss the AUG
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What does nonsense mediated decay?
- It degrades mRNA with a premature stopcodon, because the exon junction complexes (ECJ) are still present.
- In case of a permature stopcondon the ECJ stays on the mRNA and the mRNA is degrated, by nonsense mediated decay
- if the permature stopcodon occures in the last exon there is no ECJ, so no
nonsense mediated decay.
- pre last exon it is also not always detected
- it needs to be 50NT upstrem of last exon-exon junction
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1.2 structural variation
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What are the 3 sort of copy number gains and the context?
Tandem gene duplicate- it is hypermorph
disruptive insertion- loss of function, the insert part can have a premature stopcodon or frame shift but can also be neomorph
- gene fusion
- gain of function (hypermorph)
- identifying is hard with short reads NGS, because you need to find the overlap
- nanopore is better --> long read
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1.3 repeat expansions
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what occures with repeat expansions?
Slippage canoccure , can cause repeatexpension repeats can fold on to them selfs and givereplication difficulty - repeats near promoter regions
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1.5 missense variants
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Molecular impact of missense variants?
- Often neutral variation, because only one nucelotide is mutated
- can be conservated when functionele
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