Session 3 Flashcards
What are the possible Aetiology of abnormal phenotypes in Balanced Karyotypes ?
Disruption of a gene by breakpoints
Cryptic imbalance
Position effect
Disturbance of imprinting
UPD
Involvement of X chromsome
What are the two mechanisms of disease in Osteogenesis Imperfecta (OI)?
How do they differ in phenotype?
Haploinsufficiency (OI type 1 )
- Less severe disease with NMD of null variants causing reduction in amount of protein
Dominant negative (OI type II, III and IV)
- more severe disease. Disrupt formation of collagen helix (mainly glycine losses) so effect both alleles
What is SMA?
What is the frequency?
Spinal Muscular atrophy (AR)
Estimated incidence of 1 in 6,000 to 1 in 10,000
Carrier frequency of 1/40 to 1/60 ( ~ 1/50 in the UK)
Most frequent genetic cause of infant mortality
What is the overall phenotype of SMA?
Wweakness and paralysis of voluntary muscles due to degeneration of Anterior horn motor neurons in the spinal cord.
* Progressive proximal, symmetrical limb and trunk muscle weakness (typically lower limbs before upper)
*Intercostal muscle weakness that results in breathing difficulties.
* Fine tremor in the fingers
* Muscle twitches in tongue (fasciculation) result in poor suck and swallow with increasing swallowing and feeding difficulty over time
* Facial weakness
How does prenatal SMA present?
Prenatal SNA - arthrogryposis multiplex congenita, absence of movement except for extraocular and facial movement, death usually occurs from respiratory failure before age one month
How does Type 1 SMA present?
- Most common form, accounts for 60% of all SMA patients
- Typically diagnosed before six months
- Present with profound hypotonia and symmetrical flaccid paralysis (“floppy baby”)
- Progressive weakness at infancy – death at an early age.
- Lack of motor development: Inability to lift head, poor head control, never able to sit without support.
- Swallowing and feeding can be difficult due to tongue fasciculation
- Mild contractures at the knee joint and absence of tendon reflexes
- Aspiration pneumonia is an important cause of morbidity and mortality (usually before the age of 2)
How does Type 2 SMA present?
- Intermediate subtype – accounts for 27% SMA patients.
- Age of onset of muscle weakness is between 6 - 12 months
- Low muscle tone
- These children may be able to sit unaided, but will never be able to walk without support
- Finger trembling common
- Absent tendon reflexes in 70% of cases
- Life expectancy is significantly reduced but ~70% of patients reach adulthood
How does Type 3 SMA present?
- ~12% of SMA patients.
- Includes clinically heterogeneous patients
- Can usually stand and walk alone, but may show difficulty walking at some point
- Proximal muscular weakness develops in infancy: legs more severely affected than arms
- Onset usually after age ten months; patients can be subdivided into 2 groups depending on age of onset:
o IIIa is diagnosed before 3 years
o IIIb after 3 years
How does Type 4 SMA present?
Type IV SMA (Adult onset)
* The onset of muscle weakness is usually in the second or third decade of life.
* Normal life expectancy.
* ~1% SMA patients
* The findings are similar to those described for SMA III
Outline the SMN region
Two genes in SMN region on 5q12.2q13.3- SMN1 and SMN2
SMN1 is telomeric and SMN2 is centromeric
Most people have 1 SMN1 on each chromosome, but 4% people have 2 copies on 1 chromosome. SMN2 copy number ranges from 0-5 (in tandem cis configuration).
SMN1 and SMN2 differ by 5 base pairs - critical one being c.840c>T in exon 7. This change effects exon 7 splicing and means that exon is missing in 90% of SMN2 transcripts which are then non-functional.
What is the function of the SMN protein?
ubiquitously expressed, and abundant in motor neurons of the spinal cord
SMN forms a complex with Gemin proteins and acts as a chaperone to assist in the assembly of U small nuclear ribonuclear protein (snRNPs). SMN is an essential component of the spliceosome and is localized to novel nuclear structures called ‘gems’. Loss SMN predicted to cause either in impaired mRNA production and the neurons become deficient in proteins or SMN required for mRNA transport along axon.
SMN is essential and loss of SMN1 (and no SMN2) is not compatible with life
What is most SMN1 common genotype for patient with SMA?
~95-98% are homozygous for a deletion of at least exon 7 of SMN1 (whole gene deletions or smaller) Can also be gene conversions to SMN2
What are the more rare SMN1 genotypes for patient with SMA?
~2-5% are compound heterozygous for a deletion of at least exon 7 of SMN1 and a pathogenic inactivating mutation in SMN1 detectable by sequence analysis
<1% are homozygous for a pathogenic inactivating mutation in SMN1
What percentage of SMN1 deletions are de novo?
~2% (usually paternal in origin)
What is SMN2 copy number an indicator for?
Severity - increased SMN2 copies relate to less severe disease
What drug was previously used most for SMA?
Nusinersen - modulated SMN2 splicing to produce more functional mRNA. But required multiple injections and not a cure
What treatment is now available for SMA type 1 from NICE?
Zolgensma - gene therapy - deliver SMN1 in viral vector before 13 months
What imprinted region is responsible for for BWS and RSS?
11p15 imprinting cluster
What is normal imprinting pattern and expression of 11p15?
Two imprinting centres at work:
IC1 - regulates IGF2 - a fetal growth factor, and H19 - non-translated mRNA that may function as a tumor suppressor. On paternal allele IC1 is methylated - H19 not expressed and IGF2 is expressed. On maternal allele IC1 is not methylated - H19 expressed and works on enhancer of IGF2 to stop its expression.
IC2 - regulates KCNQ1, KCNQ1OT1(non-coding RNA with antisense transcription to KCNQ1) and CDKN1C (cyclin dependent kinase inhibitor which arrests the cell cycle in G1). On paternal allele no methylation and KCNQ1OT1 inhibits KCNQ1 and CDKN1C expression. On maternal allele - methylation imcludes KCNQ1OT1 promoter and stops its expression. KCNQ1 and CDKN1C are expressed.
What are the clinical features of BWS?
Paediatric overgrowth disorder with estimated incidence of 1 in 13,700
Positive family history of BWS, Macrosomia, Macroglossia, Omphalocele, Visceromegaly, Embryonal tumor, Cleft palate (rare)
What percentage of BWS are sporadic?
And what are the types?
~85%
IC2 hypomethylation 50-60% (mosaic): due to loss (complete or partial) of maternal methylation at IC2
Paternal UPD (~20%) mainly mosaic - IC1 hypermethylation and hypomethylation of IC2
CDKN1C point mutation (5-10%) - associated with cleft palate
IC1 hypermethylation 2-7% (mosaic): IC1 gain of methylation on maternal allele
Translocations/Inversions (<1%).
What is first line testing for BWS in most cases?
MS-MLPA
What other types of testing are used for BWS and why?
CDKN1C sequencing - family history and cleft palate
Karyotype - for structural abnormalities
Name two other overgrowth syndromes
Costello - HRAS
Sotos - NSD1
What are the clinical features of RSS?
Intrauterine and Postnatal growth retardation, Normal head circumference, Triangular facies, short arm span and body asymmetry
What are mechanisms for 11p15.5-related RRS?
IC1 hypomethylation 30-50%: most common cause, loss of methylation on paternal chr 11p15 (mosaic)
maternal duplication of 11p15 region 1-2%
Mosaic matUPD11 - very rare
Paternally inherited IGF2 loss‑of‑function variants - very rare and familial
What other type of UPD is a cause of RRS?
matUPD 7 account for 7-10%
Name two differentials for RSS syndrome
Bloom syndrome - IUGR
Mat UPD14 - Temple syndrome - pre and post natal growth retardation
What is first line testing for RSS?
MS-MLPA
What are the main Chromosome Breakage Syndromes?
Fanconi anaemia (FA), ataxia telangiectasia (AT), Nijmegen breakage syndrome (NBS), Bloom syndrome (BS),
What is the clinical phenotype of Fanconi Anaemia?
1 in 350,000
Pre & postnatal growth retardation, microcephaly, developmental delay, skeletal malformations (radial defects and hypoplastic or absent thumbs), hypogonadism, hyper/hypopigmentation, pancytopenia, progressive bone marrow failure and increased susceptibility to leukaemia and other malignancies. Recurring infection usually appears in children. An early onset of malignancy occurs in 10-15% of affected patients. The average age of death in FA patients is 16 years. Most individuals die from marrow aplasia (haemorrhage, sepsis), and others from malignancies; MDS and AML in FA have a very poor prognosis (median survival of about 6 mths)
What are the common genetic causes of Fanconi Anaemia?
AR in FANCA, FANCC, FAND2, FANCE, FANCF and FANCG
X linked FANCB
What the mechanism of disease in Fanconi anaemia?
Complex involved in recognition and repair of damaged DNA and thus individuals with FA are susceptible to haematological malignancy. Mutated cells have deficient ability to excise UV-induced pyrimidine dimers from the cellular DNA, they are sensitive to small concentrations of DNA crosslinking agents or lesions arising from oxidative damage. Leads to double-strand breaks in the S phase of the cell cycle and accumulation of cells in G2 biallelic mutation leads to a particularly severe form of FA with a very high cancer risk.
What is testing stratergy?
Diagnosis and exclusion should be made by analysis in cultures exposed to clastogenic agents to look for breakage and complex rearrangements
What is the clinical phenotype of Bloom syndrome?
1/160,000 in the UK population
Growth deficiency, triangular shaped face, long narrow head, narrow cranium, cheekbone hypoplasia, nasal prominence, small mandible and prominent ears, sun-sensitive skin rash, telangiectatic, immunodeficiency and marked predisposition to malignancy. Butterfly-shaped patch of reddened skin across the nose and cheeks
Males infertile and females struggle to conceive
What is the genetic cause of Bloom syndrome?
Bi-allelic variants in the BLM gene
What the mechanism of disease in Bloom syndrome?
BLM encodes DNA helicase at 15q26.1. Functions as a caretaker tumor suppressor gene; it is essential for the maintenance of genome stability because it suppresses inappropriate recombination. Catalyze dissolution of double Holliday junctions at stalled replication forks. BLM has a role in telomere maintenance. Lack of BLM results in hyper-recombination and telomere association, to genomic instability and cancer predisposition.
What are typical cytogenetic findings in Bloom syndrome?
Quadriradial configurations and increased SCE
What is the clinical phenotype of Ataxia Telangiectasia?
~ 1 case per 40,000-100,000 live births worldwide
Cerebellar ataxia, truncal ataxia (jerky movements) progressing to peripheral ataxia, ocularmotor apraxia, telangiectasias, immunodeficiency, hypogonadism, and predisposition to neoplasias. Patients become wheelchair-bound by age 10-15 years. Severely affected patients usually do not survive childhood. Pulmonary disease is still the leading cause of death.
What is the genetic cause of Ataxia telangiectasia ?
Bi-allelic ATM variants on 11q22.3
What the mechanism of disease in Ataxia telangiectasia?
ATM gene codes for a large serine-threonine kinase, involved in signalling the existence of dsDNA breaks. It delays G1 to S and G2 to M stages of mitosis in the presence of DNA damage. Telomeres degrade faster is AT patients. Ataxia develops due to brain cells dying due to defective DNA damage repair of neurons caused by processes such as oxidative stress.
What type of cancer is more common in carriers of ATM?
Breast cancer ( 4 fold risk)
What is the clinical phenotype of Nijmegen Breakage Syndrome ?
1:100,000
short stature, microcephaly, distinctive facial features, developmental delay, recurrent respiratory tract infections/sinopulmonary infections, increased risk of cancers, intellectual disability
What is the genetic cause of Nijmegen Breakage Syndrome ?
BI-allelic NBN variants (8q21.3)
What the mechanism of disease in Nijmegen Breakage Syndrome ?
Nibrin involved in repairing damaged DNA and regulates cell division and proliferation
What phenotypes are associated with the FMR1 gene?
Fragile X syndrome
FXTAS
FMR1-related POI
What is the function of FMRP?
fragile X mental retardation 1 protein
thought to act as a shuttle within cells by transporting messenger RNA (mRNA) from the nucleus to areas of the cell where proteins are assembled.
What are the clinical features of Fragile X syndrome?
Males - moderate to severe intellectual and social impairment, characteristic appearance, joint laxity and macro-orchidism
females - phenotypes ranging from apparently normal (about 50%) to mild to moderate mental and social impairment, with or without fragile site expression.
What is the mechanism of disease for the different FMR1 phenotypes?
Fragile X syndrome - expansion >200 of CGG in 5’ UTR leads to methylation and silencing. Rare mutations
FXTAS and FMR1-related POI - pre-mutation expansions mRNA expressed at higher level than normal but does not correspond to increased FMRP - possible toxix mRNA effect
What is FXPOI?
FMR1-related primary ovarian insufficiency (POI)
cessation of menses before age 40 years and occurs in approximately 20% of females with an FMR1 premutation
What is FXTAS?
fragile X-associated tremor/ataxia syndrome
late-onset progressive cerebellar ataxia and intention tremor. Onset is typically between ages 60 and 65 years. Both age of onset and disease severity are related to repeat length, sex, and other features. More common in males
Name another expansion on ChrX similar to FRAXA
FRAXE - large expansions of a GCC tract in the 5’ UTR of FMR2. Less severe than FRAXA and no phenotype for premutation carriers
What are the CGG repeat sizes for FRAXA?
Normal - 6-50
Intermediate - 46- 58 (50-58 show instability)
Permutations - 55-200
Full mutation - >200
What is thought to help keep intermediate FRAXA alleles more stable?
2 or more interspersed AGG motifs within the tract (lost in premutation)
What is likelihood of expansion to full FRAXA mutation from premutation?
Only by female carriers
low if 59-70 repeats. >90% if >90 repeats
What type of variation is observed in FRAXA full mutations?
Somatic mosaicism in terms of size or methylation status
Name 2 a genetic therapies in use/trials for DMD
Antisense Oligonucleotides - e.g. Golodirsen which incudes exon skipping
Ataluren - read through of PTCs
What four drugs are currently available on NHS for CF?
Kalydeco, Orkambi, Symkevi and Kaftrio
What is the only autosomal recessive condition which only effected women?
Familial biparental hydatidiform mole (FBHM) - recurrent pregnancy loss with full mole due to genome-wide failure to correctly specify or maintain a maternal epigenotype
What are requirements for Kaftrio?
F508del;F508del
Or F508del;any CFTR variant
Name an imprinting condition involving chromosome 6
Transient Neonatal Diabetes Mellitus Type 1 - IUGR and hyperglycaemia due to insulin deficiency with abnormal development or absence of the pancreas or pancreatic islets
Outline the genetics of Transient Neonatal Diabetes Mellitus Type 1
TNDM locus on chromosome 6q24, causes overexpression of two maternally imprinted genes, PLAGL1 (ZAC) (Pleomorphic Adenoma Gene-Like 1) and HYMAI (Hydatidiform Mole Associated and Imprinted)
1) Paternal UPD6 ~40%
2) Duplications of 6q24 on the paternal allele (~32%)
3) Hypomethylation of maternal DMR resulting in inappropriate expression of PLAGL1 and HYMAI (~28%)
What are the two syndromes associated with UPD14
Maternal UPD14 (aka TS14, Temple Syndrome) - IGUR, hypotonia, feeding difficulties, growth failure, early puberty
Paternal UPD14 (aka Kagami-Ogata syndrome) - more severe = Placentomegaly and polyhydramnios and Small bell-shaped thorax with coat hanger appearance of the ribs
What is normal imprinting pattern and expression of the 14q32.2 loci
Both IG-DMR and MEG3-DMR are methylated on paternal and unmethylated on maternal
MEG3, RTL1as and MEG8 are maternally expressed and DLK1 and RTL1are paternally expressed
Name an imprinting region on chromosome 20
Guanine nucleotide binding protein, alpha-stimulating (GNAS) complex locus on 20q13
Outline the GNAS complex loci
GNAS exons 1-13 encode Gsα which is bi-allelically expressed.
Alternate 1st exons are used to create novel coding and non-coding transcripts - and these have imprinting.
“XL” is coding for GNASXL from the paternal allele - has two isoforms XLas and ALEX that are principally expressed in neuroendocrine
cells.
A/B - noncoding transcript is paternally expressed
What is underlying genetic cause of the different phenotypes in the GNAS loci?
PHP-Ia - maternal Heterozygous GNAS variant in exon 1-12
PHP-Ib - maternal imprinting defect or paternal UPD
PHP-Ic - Heterozygous GNAS variant in exon 13 on maternal chromosome
PPHP - Paternal Heterozygous GNAS
What are the phenotypes associated with the GNAS loci?
Albright hereditary osteodystrophy (AHO) - short stature, obesity, round facies, subcutaneous ossifications, brachydactyly, and other skeletal anomalies
Pseudohypoparathyroidism type
Ia - AHO + hormone resistance
Ib - No AHO but renal PTH resistance + IUG increase
Ic - AHO
Pseudopseudohypoparathyroidism - AHO + IUGR
Name a reciprocal microdeletion/duplication pair that arises from NAHR
17p11.2 (PMP22)-
Dup = Charcot-Marie-Tooth (CMT1A)
Del = Hereditary neuropathy with liability to pressure palsies (HNPP)
What is Miller-Dieker syndrome?
Deletion of 17p13.3. Lissencephaly, microcephaly and severe mental retardation.
Name two terminal microdeletion syndromes
Wolf-Hirschhorn syndrome (WHS): del 4pter - (‘Greek warrior helmet appearance’): broad bridge of the nose, microcephaly, high forehead, hypertelorism, epicanthus, highly arched eyebrows, short philtrum, downturned mouth, micrognathia, growth delay, developmental delay/intellectual disability of variable degree, and seizures.
Cri-du-chat syndrome: del 5pter - distinctive cat-like cry (due to anomalies of the larynx and epliglottis), severe developmental delay/intellectual disability, microcephaly, low birth weight, hypontonia in infancy and distinctive facial features including hypertelorism, low-set ears, small jaw and rounded face
What are the hallmarks of the mtDNA?
16.6kb circular dsDNA molecule encoding 37 genes: 13 polypeptides of the OXPHOS system, 2 ribosomal RNAs and 22 tRNAs
mtDNA is almost exclusively transmitted through the maternal line.
No introns so no splicing
Termination codons are created post-transcriptionally by polyadenylation
Higher mutation frequency (~10x) than nDNA due to inefficient mtDNA repair, a localized oxidative environment
Each cell can contain 100 to 10,000 copies of the mt genome
mtDNA can homoplasmic or heteroplasmic
At what levels of heteroplasmy to mt variants become clinically significant ?
50-60% for deleted mtDNA molecules
> 90% point mutations in tRNA.
What is the most common mtDNA variant?
What feature of mitochondrial disease does it exemplify?
m.3243A>G
The complexity and lack of specific phenotypes - this one variant can cause MELAS, MIDD, SNHL, myopathy, cardiomyopathy, bowel dysmobility, short stature, diabetes, external opthalmoplegia or Leigh syndrome and 9% are asymptomatic
How can nuclear variants cause mitochondrial disease?
Mito depletion by effect on mtDNA maintenance or expression :
- Direct mutations in POLG, POLG2 (mt specific DNA polymerase
- Indirect effects include disruption of nucleoside transport into mitochondria (SLC25A4)
Mito dysfunction:
- Variant in components and assembly factors of the respiratory chain
Name 3 mitochondrial depletion syndromes and their phenotypes
Pearson = Pancytopoenia, anaemia, lactic acidosis, pancreatic failure, infancy onset
Kearns-Sayre = Progressive myopathy, deafness, opthalmoplegia, cardiomyopathy, adult onset
CPEO (Chronic Progressive External Opthalmoplegia) = Opthalmoplegia, ptosis, impaired eye movement
Name 3 mitochondrial point mutation syndromes and their phenotypes
MELAS = Myopathy, encephalopathy, lactic acidosis, stroke-like episodes
NARP = Sensory neuropathy, ataxia, retinitis pigmentosa
Leigh/Leigh like = Encephalopathy, lactic acidosis
What types of testing are needed for mitochondrial variants?
MtDNA rearrangements by longPCR
common mtDNA point mutations (e.g. pyro)
mtDNA copy number - realtime PCR
mtDNA sequencing
What sample types are used for mtDNA testing?
Muscle is best
Urine
Blood (but with caveats if -ve)
In what two patient populations are small supernumerary marker chromosome (sSMC) more common than in general population?
Seven times more prevalent in individuals with intellectual disability
Three times more prevalent in individuals with infertility
What are the main types of small supernumerary marker chromosome (sSMC)?
Acrocentric mainly invdup
Non-acrocentric - e.g. i(12p)
Ring
Neocentromere
Complex SMC
What clinical syndromes are associated with markers?
Pallister-Killian syndrome - i(12p)
Isochromosome 18p syndrome
Emanuel syndrome - +der(22)t(11;22)
Cat-eye syndrome - inv dup(22)
Idic(15) syndrome - inv dup (15)
What are most common X chromosome markers?
Ring(X) - worse if XIST not involved
What are most common Y chromosome markers?
idic / inv dup Y - SRY involved must be considered for sex determination
Where are poly-alanine tracts most commonly found?
transcription factors
What happens to proteins with repeats above the 19 alanine threshold?
polypeptide aggregates and forms intracellular inclusions (will sequester the normal protein too)
Why are polyA tracts more stable than other expansions?
What is the likely mechanism of expansion?
They are interrupted (not always same triplet coding the alanine- GCX)
Unequal crossing-over between two mispaired normal alleles
What is FSHD?
What is genetic difference of both types?
Facioscapulohumeral muscular dystrophy caused by aberrant expression of the DUX4. o Asymmetrical, progressive proximal muscle weakness presenting in the face, progressing to muscles in scapula, upper arm, hip girdle, lower leg.
FSHD1 - D4Z4 repeat number
FSHD2 - variants in SMCHD1
Outline the genetic aetiology of FSHD1
Tandem array of 3.3kb D4Z4 repeats in the subtelomere of chromosome 4q35.
Each repeat has a copy of DUX4 - hypermethyaltion of the majority of the repeat causes only the most telomeric copy to be expressed.
Distal of the repeat is polyadenylation site which is either active (4qA) or inactive (4qb)
Contraction of the repeat size is associated with hypomethylation and relaxation of chromatin, which activates expression of the toxic DUX4 gene. Development of FSHD1 requires contraction on same allele as the polyadenylation active 4qA polymorphism
Normal repeat = 11-100
Pathogenic = 1- 10
What testing is used for FSHD1?
Southern blotting
Outline the genetic aetiology of FSHD2
Mutations in the SMCHD1 gene which is an epigenetic modifier of D4Z4
Requires 4qA haplotype
What is incidence of PWS?
What is the phenotype?
1 in 10,000 - 1 in 30,000
Early infancy-severe hypotonia, delayed cognitive development and behavioural complications.
Hyperphagia leading to obesity
Narrow forehead, almond shaped eyes, triangular mouth
Genital hypoplasia, incomplete pubertal development, infertility
Short stature and small hands and feet for height age
What is incidence of Angelman syndrome?
What is the phenotype?
1 in 12,000 to 1 in 20,000
Severe developmental delay and speech impairment
Movement or balance problems
Epilepsy/seizures - onset usually when 1-3 years old
Sleep disorder
Microcephaly
Hyperactivity and short attention span
Happy demeanour, frequent laughing and smiling, hand-flapping, fascination with water
What genes in 15q11-13 locus are expressed from paternal allele?
Which is thought to be most important for PWS?
SNURF/SNRPN, MKRN3, MAGEL2 and NDN
Within the introns of SNURF/SNRPN are clusters of snoRNAs. SNORD116 is a multi copy gene clusters encoding SNORD116 snoRNAs and also a spliced long non-coding RNA (lncRNA) host gene (116HG) that is stably retained in the nucleus. Loss of the SNORD116 region encoding the 116HG lncRNA is sufficient to cause PWS
What gene in 15q11-13 locus is(mainly) expressed from maternal allele?
UBE3A is driver of AS- biallelically expressed in most tissues, but preferentially expressed from maternal allele in brain
What are genetic defects in PWS?
What proportion of cases are they involved in?
What is the recurrence risk?
1) De novo deletion of paternal 15q11q13 in 70-75% of cases with recurrence of <1% (for normal paternal karyotype)
2) Mat UPD in 25-30% of cases with recurrence of <1% (for normal parental karyotype)
3) Imprinting centre defect in <1% of cases with recurrence of <1%
3a) Imprinting centre deletion in ~10-15% of patient with Imprinting centre defect and have recurrence risk of 50% if in non-mosaic state in father
What are genetic defects in AS?
What proportion of cases are they involved in?
What is the recurrence risk?
1) De novo deletion of maternal 15q11q13 in 75% of cases with recurrence of <1% (for normal maternal karyotype)
2) Paternal UPD in 1-2% of cases with recurrence of <1% (for normal parental karyotype)
3) Imprinting centre defect in 3% of cases with recurrence of <1%
3a) Imprinting centre deletion in ~10-15% of patient with Imprinting centre defect and have recurrence risk of 50% if in non-mosaic state in mother
4) UBE3A variant in 5-10% cases with recurrence risk of 50% if in non-mosaic state in mother
5) No cause found in 10-15% cases with recurrence risk of up to 50% in theory
What are thought to underlie deletions in 15q11-13?
What are the breakpoints? And which are most commonly involved?
Unequal cross over between low copy repeats of HERC2
BP1-BP5. BP1 and 2 both centromeric of 15q11-13 and BP3-5 are telomeric.
Deletion between BP2 and BP3 is most common
BP1 and BP2 next most common
What are the most common genetic causes o short stature?
SHOX haploinsufficiency
RASopathy variants
Breakage
Growth hormone deficiency
CNVs - 22q11.2, 7q11.23
What are the most common genetic causes o hearing loss?
Mutations in GJB2 (Connexion 26)/GJB6 variants (Connexion 30).
What are the most common genetic cause of SCID?
20-40% of cases of SCID caused by deleterious variants in IL2RG which is the X-linked
Complete absence of T and natural killer lymphocytes and non functional B lymphocytes. It is almost universally fatal in the first two year of life.
What are the most common genetic cause of Skeletal dysplasia?
Variants in FGFR3
What is the link between paternal age and FGFR3?
The c.1138A>C p.(Gly380Arg) variant in FGFR3 has a dominant negative affect that causes achondroplasia and the frequency of this variant gets higher with paternal age and the high incidence of the variant may be caused by a highly mutable CpG island
What are the common genetic causes of Polycystic kidney disease?
AD variants in PKD1 and PKD2
What is the most common inherited ataxia?
What is the phenotype?
Friedreich’s Ataxia
Multi-systemic degenerative disease characterised by progressive ataxia with mean age of onset between 10 and 15, usually before age 25, and hypertrophic cardiomyopathy.
What is the genetic cause of Friedreich’s Ataxia?
AR variants in FXN gene on 9q13
~98% of FRDA patients are homozygous for an expansion of a GAA repeat in intron 1 (glutamic acid)
Remaining 2% patients have an expansion on one allele and a second sequence variant on other allele
What are the repeat sizes in FXN gene?
Normal alleles (5-33 GAA repeats)
Premutation (mutable) alleles (34-65 GAA repeats)
Borderline alleles (44-66 GAA repeats)
Full penetrance (disease-causing) alleles (66-~1700 GAA repeats)
Outline GAA repeat expansion instability in Friedreich’s ataxia
Expanded alleles arise from large normal alleles
Both expansions and contractions of expanded alleles can occur - maternal transmission is associated with expansions and contractions; paternal transmission is associated primarily, but not exclusively, with contractions
Expansions of >10X original size in one generation have been observed on both maternal and paternal transmission
How do GAA expansions cause loss of function of FXN?
GAA expansion causes formation of DNA-RNA hybrid forms R-loops which block RNA polymerase. Also causes repressive chromatin marks (i.e. methylation)
What is the function of Frataxin?
nuclear encoded mitochondrial protein involved in iron homeostasis. LoF leads to iron accumulation in the mitochondria which has negative impact on mitochondria-rich tissues including heart cardiomyocytes and neuronal cells
What defines a PolyQ disorder?
What are their shared characteristics?
Expansion of translated CAG repeats
- Onset is mostly in adulthood
- The disease course is progressive, unremitting and usually fatal
- The clinical symptoms appear above a threshold number of CAG repeats
- There is a strong negative correlation between the number of CAG repeats and age at onset
- The repeat sequence is unstable and its increase in size during transmission results in genetic anticipation
- The gene is expressed ubiquitously
- The pathological protein accumulates in ubiquitinated neuronal intranuclear inclusions
What is the incidence and overall phenotype of Huntington Disease?
3-10 in 100,000 in Western European populations
o Psychiatric disturbances (mood swings, personality changes, depression, paranoia)
o Motor (chorea, and later on, dystonia, bradykinesia and decreased voluntary movements)
o Cognitive (progressive cognitive decline)
What is the underlying genetic cause of HD? And its forms?
(CAG)n repeat in exon 1 of HTT gene
normal allele <27 repeats
intermediate (‘mutable normal’) 27-35 repeats
affected >36 repeats (36-39 reduced penetrance, elderly asymptomatic individuals exist)
>39 affect complete penetrance range
Juvenile >60 repeats
What is notable about expansion inheritance in HD?
almost exclusively on paternal transmission; this can be attributed to the increased number of meiotic divisions in spermatogenesis.
What is the evidence for GoF of PolyQ expansions in HD?
HD homozygotes are clinically identical to heterozygotes
Patients with chromosomal deletions including the HD gene fail to manifest HD
What are the theories for the pathology of HD?
Aggregation theory
The toxic fragment hypothesis
Transcription dysregulation hypothesis
Cytoskeletal defects and axonal transport - blocks transport down neurons
What is the most prevalent form of muscular dystrophy?
What is the overall phenotype?
Myotonic Dystrophy DM1
Myotonia (muscle hyperexcitability), progressive muscles weakness and wasting (ptosis and drooping mouth), cataract development, testicular atrophy and cardiac conduction defects,
What is underlying genetics of Myotonic Dystrophy DM1?
CTG repeat in the 3’ UTR of DMPK gene encoding DMPK protein on 19q13.3
Normal alleles 5-36 repeats
premutation 37-50
full penetrance alleles 51-150 (minimal or classical DM1)
150-1000 classical
1000-2000 juvenile
>2000 congenital DM1 (maternal only inheritance)
What three models are postulated for Pathogenesis of DM1 (CTG repeats)?
- Haploinsufficiency - decreased DMPL mRNA and protein is observed but het knockout mice do not develop DM1 (and homozygous knockout not DM1 either)
- Chromatin structure - expansion causing silencing of nearby DMWD which has reduced levels in DM1 patients
- RNA gain of function - CUG repeats fold into RNA hairpins that t accumulate within the ribonuclear foci and trap essential cellular RNA-binding proteins. Main theory is MBNL1 - regulates spliced isoforms during normal skeletal muscle and heart development and in DM1 patients reduced levels are seen and accumulation of embryonic-specific transcripts and their protein products in adult muscle leads to atrophy. MBNL1 knockout mice show whole range of DM phenotypes
What is underlying genetics of Myotonic Dystrophy DM2?
Expansion of complex repeat motif (TG)n(TCTG)n(CCTG)n in intron 1 of the CNBP on 3q21
The overall length of the (TG)n(TCTG)n(CCTG)n complex repeat in normal alleles ranges from 104 to 176 base pairs.
Normal CCTG repeat tract ranges from 11 to 26 tetranucleotide repeats
Full penetrance, mutation alleles are greater than 75 repeats, up to 11,000 repeats.
Name a repeat expansion that does not demonstrate usual type of anticipation
DM2 - repeat length increases correlated with age at onset but not severity
