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 - IC2 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.
