Determining pathogenicity of genetic variants Flashcards
What is a pathogenic variant
It is a genetic alteration that increases an individuals susceptibility or predisposition to a certain disease or disorder. When such a variant is inherited, development of symptoms is more likely, but not certain.
What is pathogenicity ?
It is much more complex
All three overlap to cause disease
- genetic change
- environment
- epidemics
Can be:
Polygenic
Monogenic
Mitochondrial
Chromosomal
Alter gene function
- promoter function
- splicing
- intronic
Alter protein function
- alter formation of the protein
- alter structure of protein
- protein aggregation
Why is it important to determine pathogenicity ?
Prognosis
- which gene is affected determines prognosis and monitoring for the disease
Treatment
- determined treatment and possible genetic therapies in the future
Inheritance
- determines inheritance pattern and genetic counselling
Searching for a diagnosis
- If not pathogenic need to keep looking for the underlying causative variant
How we determine pathogenicity
Some key elements:
- patient phenotype
- gene
- type of variant
Patient phenotype
Careful assessment of the patient for the main clinical features
- do they fit a known clinical pattern?
Inheritance
- are other family members affected? Are they alive?
- what is the pattern?
Key clinical signs
- skeletal dysmorphisms
Consider blood tests, imaging and biopsy of affected tissue
- Which gene? Single gene analysis, gene panel analysis, next generation sequencing
Understanding the gene
Are variants in the gene already known to cause this disease?
Is the gene associated with similar diseases?
What is the function of the protein?
Is the gene expressed in the affected tissues?
- Is it a known variant
- Where in the gene is it (intronic, exonic)
- What type of variant is it
- Is it in a highly conserved region
- How often is it seen in the population
- Where in the protein is it
- Does it segregate in the family
Population data
Is the variant present in a frequency > than known prevalence?
(More likely to be pathogenic)
Has it been reported by other groups in affected patients?
If present in a frequency >5%
(Very likely to be benign)
- Control data can contain affected individuals
- Disease variants are not always validated
- Some recessive variants have high rates
- Need ethically- matched controls
Computational data
In silico tools to predict if a change is likely to affect the gene/transcript/ protein.
Look at - missense variants:
- polyPhen2
- SIFT
- Mutation taster
Splicing:
- gene splicer
- human splicing finder
Takes into account
- types of change
- evolutionary conservation of the region
- location of variant in the gene
- effect on structure of protein
- Seen in other databases ? ClinVar, bSNP
- Computational data
Type of change
- certain variants are more likely to be pathogenic if the mechanism is loss of function
(Nonsense, frameshift, deletions)
- some are more likely to be benign
(Synonymous (silent) - does not change protein code) rarely can be pathogenic if it affects splice site
Type of change:
- missense variants
(Has there been a change in the properties of the amino acid?)- acidic -> basic
Polar -> non-polar
Evolutionary conservation
- is it in a highly conserved region through species ?
- highly conserved regions are less able to tolerate changes in genetic code
Location of variant in gene
- is it in a key subunit binding region/ pore forming region?
- effect on structure of protein
(Alter folding of protein?)
Segregation of data
Clear segregation of variant in other affected family members/ not in unaffected members
De novo data
De novo variants are more likely to be pathogenic
- variant occurs in the germline
- parents not carriers
- paternity known
- this is more common in some disease
(Associated with older paternal age)
Allelic data
If recessive - need to check variants are in trans
Paternal testing can confirm this
Functional studies
Extremely valuable in determining pathogenicity
Especially useful in:
- channelopathies
- enzyme function
- mRNA levels - for splicing variants
