Seassion 4 Flashcards
What 6 metabolic disorders are included in NBS?
- phenylketonuria (PKU)
- medium-chain acyl-CoA dehydrogenase deficiency (MCADD)
- maple syrup urine disease (MSUD)
- isovaleric acidaemia (IVA)
- glutaric aciduria type 1 (GA1)
- homocystinuria (pyridoxine unresponsive) (HCU)
What are the four pathogenic mechanisms for Inborn errors of metabolism?
A - Toxic substrate accumulation
B - Product deficiency
C - Activation of alternate pathway
D - diversion of metabolic flux to secondary pathways and alternative metabolite production
What are benefits of genetics testing for Inborn errors of metabolism?
Biochem has diagnose most of them however not always disease specific
Genetics allows:
· reproductive options
· determine carrier status
· an exact diagnosis
· prevents the need for invasive procedures
· can decrease the length of time it takes to obtain a diagnosis
· the use of specific therapies: e.g. nonsense mutation suppression
· can provide prognostic information for the patient
What is the phenotype of Peroxisome Biogenesis Disorders?
What are the three types?
Hypotonic, feed poorly, and have distinctive facies, seizures, and liver cysts with hepatic dysfunction
Zellweger syndrome (ZS) - most severe
neonatal adrenoleukodystrophy (NALD)
Infantile Refsum disease (IRD) - least severe
What metabolite is affected in Peroxisome Biogenesis Disorders?
plasma very-long-chain fatty acid (VLCFA)
Variants in which genes are associated with Peroxisome Biogenesis Disorders?
The PEX genes (13 in total). Most commonly PEX1
Name an X linked Inborn error of metabolism?
Ornithine Transcarbamylase Deficiency: Urea cycle deficiency disorder
What is Smith-Lemli-Opitz Syndrome?
How can effect sexual development?
Cholesterol biosynthetic disorder
AR condition - DHCR7 gene
Cholesterol needed for testosterone synthesis
What is Wilson Disease?
What is phenotype?
Copper transport disorder - AR variants in ATP7B
Liver disease includes recurrent jaundice, autoimmune-type hepatitis, chronic liver disease.
movement disorders
rigid dystonia
Kayser-Fleischer rings in cornea
Where do ovaries/testes arise from?
The gonodal ridge
What gene in an XY embryo drives testes differentiation?
SRY
What happens in genital differentiation?
Female - regression of Wolffian ducts and development of Mullerian ducts to make fallopian tubes, uterus and upper vagina. happens independently
Male - Testosterone drives Wolffian ducts to create seminal vesicles and vasa defentia. DHT droves external genitalia. AMH binding causes regression of Mullerian ducts
What is the most common cause of a 46,XX phenotypic male?
80-90% of cases are due to an XY translocation with SRY being on top of an X chromosome
What is Swyer syndrome?
Complete XY gonadal dysgenesis caused by variants in SRY
*‘streak’ gonads
*Female external genitalia
*Failure of pubertal development
*Infertile
*High risk (~30%) of developing gonadoblastoma
What is Complete androgen insensitivity syndrome?
XY by female phenotype
caused by variants in AR gene
*Female external genitalis, Normal development of breasts and female characteristics at puberty, Primary amenorrhea. Infertility, Intra-abdominal testes, Low risk (2-5%) of gonadoblastoma
What is Congenital adrenal hyperplasia (CAH)?
Group of disorders caused by by enzyme deficiencies affecting steroidogenesis most commonly caused by 21-hydroxylase deficiency. Reduced cortisol biosynthesis results in accumulation of its precursors which are also in the androgen synthesis pathway – and increased androgen synthesis;
In 46,XX foetuses it causes masculinisation of external genitalia
What treatment is needed for CAH?
Treat the mother with dexamethosone (a corticosteroid) during the pregnancy - otherwsie babies are born “salt-waster” and die in neonatal period
Hormone treatment after birth
What gene dels and dups are involved in DSDs?
o Deletion of SOX9, NF5A1 or WT1 can lead to 46XY gonadal dysgenesis
o Duplication of DAX1 or WNT4 can lead to 46XY gonadal dysgenesis
o Duplication of SOX9 or SOX3 in 46XX can lead to testicular DSD
What are the four terms for sperm quality?
Azoospermia - Absent sperm in ejaculate
Oligozoospermia - Reduced sperm count < 15x106/ml
Asthenozoospermia - Reduced sperm motility (<40% motile)
Teratozoospermia - Morphologically abnormal sperm
Which sex chromosome abnormalities are most associated with infertility?
47,XXY Klinefelter syndrome (KS)
45,X/46,XY mosaicism
46,XX male Disorder of Sex Development (DSD) - Y material on X chromosome
Y isochromsome
X;autosome translocations
Y;autosome translocations
What is most frequent cause of male infertility?
Klinefelters
What underlies Y microdeletions?
How common are they in infertility?
Non-allelic homologous recombination
2-10% of azoospermic and oligospermic men
What are the four most common Y microdeletions?
AZFa - deletion of USP9Y and DDX3Y. Rarest but also most severe. Sertoli cell-only syndrome (SCOS), bilaterally small testes and azoospermia
AZFb - 6.2Mb in size and accounts for 1-5% of deletions
AZFbc - 1-3% of deletions
AZFc - Most frequent deletion type (approx. 80%). Variable clinical phenotype and generally compatible with residual spermatogenesis.
What genes are thought to be key in AZFc deletions?
DAZ genes
What is CHH?
Which syndromes are associated?
Congenital hypogonadotropic hypogonadism - deficiency in gonadotrophic releasing hormone leads to central hypogonadism
Kallmann syndrome
Bardet-Biedl syndrome
CHARGE syndrome (CHD7)
Prader-Willi syndrome
Waardenburg syndrome (SOX10)
Outline the globin genes
2 α globin genes on Chr16 (HBA1 and HBA2= 4 α globin genes per diploid cell) which are controlled by a single locus control region (α2 expressed at 3:1 ratio of α1).
ζ gene on chromosome 16 and closest to LCR (embryo)
1 β globin gene (HBB) on Chr11
ε gene (embryo) and then γ gene (fetal) on Chr11
What Haemoglobin types are expressed in embryo, fetal and adult red blood cells ?
Embryo:
Hb Gower 1 (ζ2ε2)
Hb Gower 2 (α2ε2)
Hb Portland (ζ2γ2)
Fetal:
Fetal Hb (α2γ2)
Adult:
α2β2
What the possible Alpha-Thalassemia syndromes?
- Alpha Plus-Thalassaemia Carrier - deletion of one alpha-globin = asymptomatic
- Single Thalassaemia variant in HBA2 - mild phenotype
- Homozygous or heterozygous for two deletions - asymptomatic but microcytic anaemia on testing
- Three alpha-globin deletions: HbH Disease - shortage of alpha globin leads B globin tetramers ( HbH).
- Deletion of all 4 alpha globin genes - still birth or early neonatal death
What are some genetic modifiers which effect severity of beta-thalasaemia?
- co-inheritance of Alpha-Thalassemia lessens imbalance = better
- variation which allows persistence of fetal gamma globin = better
- co-inheritance with duplicated Alpha-Globin genes = worse
What is most severe form of Beta-thalassaemia?
Beta-Thalassaemia Major (AR - worst variants)
severe anaemia and hepatosplenomegaly. Tranfusion dependent. Iron overload possible
What is the other mina form of Beta-thalassaemia?
Beta-Thalassemia Intermedia
mild-moderate anaemia and require transfusions for quality of life not survival
Why are Sickle cell carriers more common in some areas of world?
Carrier status provides protection from severe malaria in infancy - West Africa - 1 in 4 of the population
What is Sickle cell anaemia?
AR condition due to homozygosity for HBB c.20A>T (p.Glu7Val) variant (or comp het for HBB c.20A>T and other HBB variant)
Characterised by RBCs with an abnormal rigid sickle shape. Can lead to lead to vascular occlusion causing sickle crisis:
o bone pain, joint necrosis
o Acute chest disease
o Damage to major organs including lungs and kidneys
o Increased vulnerability to severe infections
o Anaemia
o Stroke
What is antenatal screening programme for Sickle cell and thalassaemia?
Women offered screening at 10+0 weeks.
Carriers then have screening offered to partner.
At-risk couples are offered reproductive choice (if risk of serious form of disease)
What are lysosomes?
Cellular membrane-bound organelles, present in all nucleated cells - ATP driven proton [H+] pump creates acidic environment.
Hydrolytic enzymes then breakdown ingested materials and aged/damaged organelles into substances that the cell can re-utilise
What are the four sub types of Lysosomal storage disease? What defines them?
Mucopolysaccharidoses - accumulation of glycosaminoglycans
Oligosaccharidoses - accumulation of Oligosaccharides
Sphingolipidoses - accumulation of membrane glycosphingolipids
Others - accumulation outside these categories
What is usual diagnostic pathway for the Lysosomal storage diseases?
Urine tests - as stored material leaks into tissues and excreted in urine
Confirmation in other tissues
Genetic testing
Outline Gaucher disease
AR mutations in GBA gene (Chr 1) leads to accumulation of Glucocerebrodides in liver and spleen
Type 1: 90% of cases. Chronic and non-neurological form, hepatosplenomegaly, anaemia and thrombocytopenia, lung disease
Type 2: Acute neurological form. Onset usually <2yrs, with rapid progression; death by age 2-4.
Type 3: Subacute neurological form. Onset usually <2yrs, survival into 30/40’s
Outline Niemann Pick Disease types A & B
AR variants in SMPD1 (Chr 11) gene leads to sphingomyelin in brain
Niemann–Pick disease type A: classic infantile, death in early childhood
Niemann–Pick disease type B: visceral, milder phenotype
Outline Niemann Pick Disease type C
AR variants in NPC1 (90%) or NPC2 genes which effects intracellualr lipid trafficking
Clinical classification:
-Neonatal and infantile presentations
-Classic presentation: Middle-to-late childhood
-Adolescent/adult
Outline Fabry disease
Variants in X-linked GLA gene cause accumulation of glycolipids in brain, heart and kidney
Classic (<1% enzyme activity)
Cardiac variant (>1% enzyme activity)
Renal variant (>1% enzyme activity)
What treatment is available for Fabry disease?
enzyme replacement therapies; Fabrazyme and Replagal
What are the Mucopoly-saccharidoses?
Defects in 11 enzymes which breakdown long chain Glycosaminoglycans.
Patients can present with a spectrum of clinical phenotypes and have symptoms which include somatic, skeletal and neural dysfunction
What are the Oligo-saccharidoses?
Defects in enzymes responsible for degradation of oligosaccharide chains in glycoproteins and glycolipids resulting in the accumulation of oligosaccharides
Outline Pompe disease
AR variants in GAA (chr 17) results in accumulation of glycogen
Classic (severe) infantile form characterised by severe cardiomyopathy (even in utero) and muscular hypotonia in the absence of hypoglycaemia, acidosis, and liver involvement. Death usually occurs before 1 year old.
High protein diet effective for milder forms
What are the treatments for the Lysosomal Storage diseases?
- Treat for the deficient enzyme e.g. ERT/gene therapy
- Substrate reduction therapy
- Chemical chaperon therapy
Outline Phenylketonuria (PKU), testing and treatment
AR variants in the PAH gene phenylalaine hydroxylase enzyme which metabolises phenylalanine (Phe) to tyrosine (Tyr) - accumultation of toxic phenylalanine.
Babies seem normal at birth but around 6 months of age develop serious, irreversible, mental disability.
Testing on NBS - mass spec on bloodspot for concentrations of Phe and Tyr as well as the ratio of the two.
Affected babies on special diet allows normal life
Outline MCADD (medium-chain acyl-CoA dehydrogenase deficiency), testing and treatment
AR variants in ACADM on 1p31.1 leads to accumulation of medium-chain fatty acids (c.985A>G most common)
Inability to use fats for of gluconeogenesis and liver function is not sufficient for glyconeolysis in periods of starvation, leading to decreased energy availability for the body, in particular the developing brain.
Testing on NBS - mass spec on bloodspot for C8 levels relative to the longer-chain fatty acid C10
special attention to be given to their diet, including making sure they eat regularly and avoid body entering starvation mode
Outline Maple Syrup Urine Disease , testing and treatment
AR variants in genes encoding BCKAD complex (BCKDHA, BCKDHB, DBT, DLD) leads to accumulation of leucine, isoleucine, allo-isoleucine and valine
Presents as
progressive neurological deterioration, neurological and developmental delay, encephalopathy, feeding problems and maple syrup odour to the urine.
Testing on NBS - mass spec on bloodspot for amino acid peak
a low protein diet to prevent accumulation of the harmful amino acids
Outline Homocystinuria, testing and treatment
AR variants in CBS leads to accumulation of homocysteine
Presents with learning difficulties, skeletal abnormalities, myopia and thrombotic episodes.
Testing on NBS - mass spec on bloodspot for methionine and total homocysteine
strict low methionine diet and Vitamin B6
What are the clinical features of Von Willebrand disease?
Abnormal menstrual bleeding
Bleeding gums
Nosebleeds
Bruising
Skin rash
What gene and protein causes Von Willebrand disease?
VWF encodes VWF protein which is essential for primary haemostasis.
Adhesive protein important in adhering platelets to sites of vascular injury. Functions as carrier and stabilizer for coagulation factor VIII in circulation, protecting it from proteolytic degradation
Outline the three types of Von Willebrand disease
Type 1 = Partial quantitative deficiency of VWF protein. Most common but least characterised. Previously AD but now suspected complex trait.
Type 2 = Qualitative deficiency of VWF protein. 4 sub types - 3 dominant and 1 recessive
Type 3 = Most severe quantitative deficiency of VWF protein. Autosomal Recessive.
What are the two most common congenital coagulation factor deficiencies?
What proteins are effected?
What are the phenotypes?
Haemophilia A and Haemophilia B
Factor (VIII) 8 or Factor (VIIII) 9 respectively
severe bleeding disorder
Loss of/reduced clotting leads to bleeding in joints, muscles and inner organs. Recurrent bleeding into joints causes chronic synovitis. Leading cause of death is caused by haemorrhage into the CNS.
Outline the genetics of Haemophilia A
X-linked variants in F8 gene on Xq28
Most common inversion between intron 22 and telomeric CpG repeat (50%) cases, followed by intron 1 inversion (2-3%) and then all other types of variants
Outline the genetics of Haemophilia B
X-linked variants in F9 gene on Xq27.1-27.2
No common structural variants but several founder mutation. Variants of all types reported.
What is the rarest bleeding disorder?
Congenital afibrinogenemia (Factor 1 deficiency) - Fibrin essential for clotting
Absence of fibrinogen protein – compound heterozygous or homozygous mutations in one of three genes – Fibrinogen alpha-chain (FGA), Fibrinogen beta-chain (FGB) and Fibrinogen gamma-chain (FGG) found on 4q28-q31
2/3 patients are identified from birth due to uncontrolled bleeding from the umbilical cord after birth. Excess bleeding is common and bleed in brain most common cause of death.
What is the commonest bleeding disorder?
Factor VII deficiency (Alexander’s Disease)
AR variants in F7 gene on 13q34
Variable phenotypes
Outline 3 example Thrombophilias
Factor V Leiden
p.(Arg506Gln) change in Factor V gene (1q24.2) reduces ability of to activated Protein C to cleave Factor V and inactive it. This leads to increased thrombin production due to Factor V = more clotting
Factor II Prothrombin Thrombophilia
p.(Gly20210Ala) in the F2 gene (found on 11p11) that results in overexpression of the F2 gene. This results in over production of prothrombin – promoting the formation of blood clots.
Hereditary antithrombin deficiency
Autosomal dominant disorder caused by mutations in SERPINC1 gene on 1q25.1. Decreased Antithrombin = more active thrombin and more clots
What are the important steps in sex determination for males?
SRY and SF1 bind TESCO and cause expression of SOX9
SOX9 then binds TESCO to form positive feedback loop
SOX9 expression is sufficient and necessary for testis determination
What are the important steps in sex determination for females?
Less well established than males
In absence of SRY - Wnt4, RPSO1 and Foxl2 are expressed in females specific manner
This leads to activation of beta-catenin signalling pathway and production of oocytes and ovarian follicles
What is the most common sex chomosome aneuploidy?
Klinefelters (1 in 500 to 1 in 1000 male live births)
What are the clinical features of Klinefelters?
Mostly hypogonadism, reduced fertility/ infertility; decreased testosterone/endocrine function; speech deficit, DD, gynecomastia, small testes, long legs/arms; tall stature; though severity varies
How does Klinefelters arise?
Nondisjunction of one X during meiosis I in the father or meiosis II in the mother
What is effect of increasing numbers of X chromosomes in males and females?
More severe Klinefelter phenotypes - worse dev delay, more dysmorphic
Above XXX - phenotype more severe
What karyotypes are seen in patients with Turner syndrome?
chromosomal abnormality caused by partial or complete X chromosome monosomy
50% are monosomy X
Other 50% made up by 46,X,del(Xp), 46,X, i(X)(q10), 46,X,r(X) or other X chromosome structural abnormalities.
Where do most Turner syndromes cases arise?
Paternal non-disjunction
How common is Turner syndrome?
1 in 2,500 female live births
BUT much more common than that and common cause of miscarriage and stillbirth (occurs in 99% of Turner conceptus)
What are the features of Turner syndrome?
short stature, high palate, short and webbed neck, early loss of ovarian function, lymphoedema, hypothyroidism, failure to develop secondary sexual characteristics
What are the features of Triple XXX?
Generally very mild and “normal” . Most common phenotype include tall stature, epicanthal folds, hypotonia and clinodactyly
Why are i(Xp) not seen?
Loss of Xist on q arm
What are phenotypes associated with r(X)?
Ring with Xist = preferentially inactivated and likely present as Turner
Ring without Xist = Stays active and may cause severe phenotype due to large regions of X disomy
What is associated with Xq28 duplications?
MECP2 duplication syndrome
Moderate to severe intellectual disability (in males mainly)
Name two common Y chromosome normal variants
Yqh length
Pericentric inversion Y
What is most common Y;autosome translocation?
t(Y;15)(p11-13;q12)
What occurs due to Y;autosome translocations?
Male infertility as cause spermatogenic arrest. The autosomal components of the quadrivalent are dragged into the sex vesicle and can have a sabotaging effect disrupting meiosis.
But is variable
What is most common X;Y translocation?
t(X;Y)(p22.3;q11) leads to 46,X/Y, der(X) t(X;Y)(p22.3;q11) karyotype
What underlies t(X;Y)(p22.3;q11) formation?
NAHR at spermatogenesis of the female carrier’s father, usually between genes PRKX and PRKY.
paracentric inversion on Yp, placing PRKY in the same orientation as PRKX, is a risk factor
What phenotype is observed in 46,X/Y, der(X) t(X;Y)(p22.3;q11)?
Depends how much of Xp lost - key genes are: ARSE, SHOX, STS , KAL , MRX and OA1.
Females - fertile female and of normal intelligence. Can have phenotype depending on which genes deleted. X-inactivation tends towards the der(X), but it can be variable and unpredictable
Males - Infertility. Phenotype as per genes lost
What translocation accounts for most 46,XX and 45,X males?
Cryptic Xp;Yp translocation
Transfer of SRY onto Xp due to abnormal XY recombination during paternal meiosis
What phenotype is associated with r(Y)?
sexual infantilism, ambiguous genitalia, hypospadias, or azoospermia, small testes/penis, short stature. (depends if SRY lost)
What phenotype is associated with Idic Y?
Idic(Yp) - 1/3 male with abnormal testes, azoospermia, short stature, TS like features, ambiguous genitalia. 2/3 female with streak gonads, enlarged clitoris, short stature, TS like features
Idic(Yq) - 1/3 male with abnormal testes, azoospermia, short stature, TS like features, ambiguous genitalia. 1/3 intersex with ambiguous genitalia. 1/3 female with streak gonads, enlarged clitoris, short stature, TS like features
