what may changes in DNA sequence cause?
may be benign
can affect any aspect of txn/tln process
what is SNV?
single nucleotide variant
type of genetic variation
what is SNP?
single nucleotide polymorphism
what is a mutation?
must be proven as pathogenic; any change is not necessarily a mutation
what is a VUS?
variant of unknown significance
change without clinical data to support whether it is benign or pathogenic
what is the rate of nucleotide variation in humans?
where do they usually occur?
50-80 de novo variants per generation
usually in intronic sequences, but sometimes not and in that case, could cause change cross-generationally
what information determines pathogenicity of a variant?
1) clinical data/phenotype
2) family info
3) type of variant
4) functional studies
5) databases/prediction models
does a DNA test necessarily make a diagnosis?
no. a variant may look pathogenic on molecular level, but patient may not have any phenotype, so isn't pathogenic for the patient
change in txn factor binding site result?
causes loss of transactivation or inappropriate expression of a gene
result of mutation in conserved intron splice donor/acceptor site?
result of changes deep in intronic sequence?
can be benign
can cause splicing effects - retained intron, skipped exon, alternative splice site usage
what does mutation of ESE (exonic splice enhancer) cause?
what does changes in sequence in coding region of transcript cause?
changes in amino acid identity:
nonsense mutations - premature STOP codon
insertion/deletion - alternations of reading frame
what does insertion/delition that is a multiple of 3 cause?
in-frame changes that result in gain or loss of short runs of amino acids
otherwise intact protein
what is B-globin thalassemia caused by?
decreased amount of transcript
what is gamma-globin persistence of fetal hemoglobin caused by?
increased amount of transcript
what variant effects result from a misspliced transcript?
1) retained intron
2) skipped exon
3) alternative splice junction
4) unstable transcript
what can cause variants due to transcription changes?
keeps RNA Pol Complex from binding to promoter/enhancer region
what does a promoter/enhancer mutation cause?
keeps RNA Pol Complex from binding to promoter/enhancer region
causes variants due to transcription changes
what is a microsatellite? what causes it? what does it cause?
di- and trinucleotide repeats of short tandem sequences
5-6 ntd in length
causes a kink in DNA
disruption of transcription, translation, protein function
major cause of disease in humans
what are the characteristics of a somatic variant?
1) mutation occurred after fertilization
2) not in all cells of the body
3) can be tissue or organ-specific
4) not passed down to offspring
what are the characteristics of a germline variant?
1) mutation occurred before fertilization
2) generally in every cell of body AND in oocytes or spermatocytes
3) passed on to next generation
for a somatic variant, when would more versus less cells be impacted?
if variants occurs closer to fertilizaiton = more cells impacted
later in development = less cells impacted
what is this?
family tree of recessive inheritance
how does recessive inheritance happen?
in enzymes/proteins that perform a function that doesn't require 2 working copies of gene for normal cellular function
how could you test loss of function of recessively inherited protein?
test protein function
look at enzyme activity
via an enzyme assay; if what you're studying is cleaved by an enzyme, light is emitted; those who are affected have low enzyme activity, less light, for example
when does loss of function usually occur? from what?
mutations in recessively inherited genes
from gene deletion, missense mutations affecting imp a.as, nonsense mutations, promoter/enhancer mutations
for disease to manifest in a recessively inherited gene, what must occur?
1 mutation in each chromosomal copy
what is homozygous recessive?
for recessive genes, when have 2 copies of the same recessive gene mutation
need this in order to see effect of a recessive gene
what is consanguineous homozygous mutation?
when parents of an affected individual are related, = consanguineous
same mutation thus presents
what is compound heterozygosit? when does it occur?
if parents are unrelated, get 2 different muations of disease gene in an individual affected by recessive gene muations
what is chance of recurrence of recessively-inherited disorders to parents who are mutation carriers?
1 in 4
what is dominant inheritance?
disorders that occur in succeeding generations
what does dominant inheritance cause?
gain of function - increased acivity, a new activity, or loss of normal regulation
or loss of function
what does recessive inheritance usually cause?
loss of function
what is haploinsufficiency?
loss of function caused when a single functional copy of a gene (single allel) is insufficient for proper cell or tissue function or development
ex. of autosomal dominant disorder loss of function
what is dominant negative effect?
loss of function in autosomal dominant disorder when encoded mutant protein disrupts a multiprotein complex despite the presence of a wild type protein in the cell
aka presence of mutant allele is pathogenic
get overall loss of function
what does x-linked inheritance cause?
who is more effected?
gain of function or loss of function
females less affected by x-linked mutations, males more affected
no male-male transmission
what is constituitive activity of an RTK an example of?
gain of function mutation effect
what is banding gradient in proteins being incorrect an example of?
loss of function by halopinsufficiency
when activity of normal allele is insufficienct
what happens if have mutation in a collagen molecule?
disrupts complex helical conformation of collagen
can impact entire ECM structure, lose ability to form higher order structure
dominant negative issue
what is allelic heterogeneity?
different mutations in 1 gene causes different phenotypes or effects
what is genotype-phenotype correlation?
the association of a specific genetic variant (genotype) w/ a characteristic pattern of physical characteristics (phenotype)
when might genotype-phenotype correlation vary within a single gene?
in a gene that predisposes to milder or more severe diseases
what causes gain of function in FGFR3?
constituitve activity of the RTK, FGFR3
causes baseline to be "on"
where is FGFR3 expressed?
developing bone and growth plate
what do different FGFR3 mutations cause? what is this example of?
middle: achondroplasia (dwarfism)
severe: thanatophoric dysplasia (incompatible w/ life)
example of allelic heterogeneity or allelic series: different variants of a gene that's autosomal dominant inherited causing different phenotypes
what phenotype does a missense mutation cause?
what phenotype does truncation or frameshift mutation cause?
what is genetic or locus heterogeneity?
when mutations in different genes cause a similar phenotype
what is bardet-biedl syndrome an example of?
autosomal recessive disorder that shows genetic or locus heteroeneity for a clinical phenotype
many genes, involved w/ the primary cilia, cause this
what are primary cilia?
sensory cilia that cell puts out during embryogenesis and mitosis to create signaling/receptor antenna
required for cell to receive signal and stimuli (hormones, chemokines, growth factors); important in Wnt & SHH pathways
has microtubule structure but also transports proteins
is implicated in Bardet-Biedl syndrome
presence of a muation doesn't always cause disease
what is genetic inheritane of breast/ovarian cancer an example of?
risk for mutated gene presence is not 100%
what does penetrance depend on?
several other multigenic factors and modifiers
can be "completely penetrant" in a male vs. female
what causes Huntington disease?
the expansion of CAG repeats in the Huntingtin gene ORF
normal: 10-37 repeats; once reach a critical threshold copy number (38-86 repeats), reach disease state
expasion of number of reepats is associated w/ increased disease severity
expansion predominantly in males
clinical features of huntington disease?
progressive movement disorder, dementia, seizures, atrophy of caudate nucleus
what determines Huntington disease penetrance?
incomplete penetrance that's based on age
higher expansion or repeats in a gene at an earlier age, earlier onset disease will be
severity increases over generations
what is complete penetrance
mutation = disease
what is incomplete penetrance
what is age-related penetrance?
symptom onset w/ age
what is anticipation?
when symptoms of genetic disorder become apparent at an earlier age as it's passed on to next generation
also usually see increase of severity of symptoms
occurs in Huntington's disease
mutation in a gene doesn't always have the same phenotypic effect, even in the same family
what is neurofibromatosis 1?
autosomal dominant mutation of NF1 gene
example of variable expressivity - manifestations of skin neurofibromas, cafe au lait spots, lesions, freckles varies
if lose NF1 function, increases RAS signaling; causes neurofibromas, etc
what is pleiotropy?
when a gene defect affects many distinct tissues
what is segmental neurofibromatosis (just on forehead) example of?
somatic mosaicism for NF1 mutation
mutation of NF1 only occurs in localized area rather than all over body
what is somatic mosaicism?
spontaneous mutation acquired after fertilization, during development, that causes segmental disease
depending on when mutation occurred, determines how affected person is/which organ system is affected
what is proteus syndrome?
very early on somatic change causing somatic mosaicism
caused by somatic AKT1 mutation
what might cause this incidence of neurofibromas?
if mutation occurred in gonadogenesis could see mosaic imprint in children even though no disease manifestation in parents
mutation inherited from a parent, present in all cells of the body
when can mutations arise?
any time during organism's life cycle
mutations that aren't inherited, if in non-reproductive tissues
what is smallest scale of mutation?
but event may have signficantly health implications still, i.e. umorigenesis
muation event early in embryogenesis causes?
reproductive consequenes for the individual
might include germ cell mutations
late mutation event causes?
only portion of the body might manifest disease features