Osteogenesis Imperfecta Flashcards by Robbo .

What is Osteogenesis imperfecta and how is it characterised?

Collective term for a heterogeneous group of connective tissue syndromes

Characterized primarily by liability to fractures throughout life

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Clinical features of Osteogenesis imperfecta?

Bone fractures (brittle bones) with little trauma
Loose joints
Weak teeth (dentinogenesis imperfecta)
Blue sclera, or a bluish colour in the white of the eye.
Bowed legs and arms
Short stature
Hearing loss
Estimated incidence approximately 1 per 20,000 births

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What is blue sclera caused by?

blue sclera, caused by thinness of collagen fibers of thesclerathat allow visualization of the underlying uvea.

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What genetic testing is used?

Genomic sequencing - Next generation

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How is the patient tested properly?

By sequencing over 30 different genes

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Why would WHole genome sequencing not be used?

A whole genome sequence would be over the top. We have less than 50 genes to analyse.

Whole genome sequence only becomes a cost effective tool once we being to need 100s of genes sequenced at once.

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What happens in OI

Defects in collagen

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Why is collagen important?

Collagen fibres form major component of bones and extra cellular matrix

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WHat collagen genes are involved in 90% of cases?

COL1A1 & COL1A2 collagen genes

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What other gene are invovled?

Autosomal recessive genes e.g. BMP1
X-linked genes e.g. PLS3
Other types in genes involved in collagen processing
Have related but different symptoms

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How man COL1 associated OI types? How are they inherited?

These are the four COL1 associated OI types.
These are all inherited in an autosomal dominant manner.

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COL1A1 and COL1A2 OI Type 1

Type 1, classic OI, is the most common and most mild. With classic OI features of bone fractures and blue sclerae.

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COL1A1 and COL1A2 OI Type 2

Type 2, lethal OI, is lethal in pregnancy. The fetus will have severe skeletal abnormalities and fractures. The rib cage collapses and internal organs damaged.

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COL1A1 and COL1A2 OI Type 3

Type 3, progressively deforming OI, is severe but not lethal. Its features will be apparent at birth with multiple fractures, very short stature and wheelchair bound.

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COL1A1 and COL1A2 OI Type 4

Type 4, common variable OI, is similar but has dentinogenesis imperfecta.

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WHat other OI type worth remebering?

OI type 5 and is caused by a single variant, a c.-14C>T in the IFITM5.
This variant is within the 3’ non coding DNA before the first exon and interefreres with correct transcription of the gene.
It is inherited in an autosomal dominant manner.

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Why is an NGS analysis necessary?

Because there are many genes can be involved in causing one type of disorder,

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COL1A1
c.[600G>A];[=]
p.[(Gly200Val)];[(=)]

COL1A1 gene
Change of nucleotide G at position 600 for an A in one allele
Glycine at position 200 changed for a Serine
Missense amino acid change
The second allele is wild type

What information do we need to do an variant analysis?

So we need to know the frequency of the variant in the normal population – is it seen in the normal population?

Whether the gene that the variant is found in is consistent with the features the patient has, or are the features seemingly unrelated to this gene?

Is the variant located in an important part of the gene (mutation hotspot) or a part of the gene with no known function attached?

Has the variant previously been reported in an affected patient? It could be a well established variant.

Is the amino acid change predicted to effect the protein structure and / or function?

Meaning how different are the amino acids in terms of size and properties?

Case study - Variant analysis
Frequency
Not reported in normal control population genome database (Gnomad)

ACGS Variant Classification Guidelines:
PM2 - Absent from controls (or at extremely low frequency if recessive).

Whats the most common mechnanism of OI disorder?

Changing a Gly of the Gly-X-Y repeat

Whats the role of glycine in collagen?

Glycine in collagen is vital for structural integrity of the helix.
Every third amino acid is in the centre of the helix, this is glycine.
Glycine is the smallest amino acid.
The only amino acid that can be located here and maintain the helix.

What happens if you swap glycine for anyother amino acid?

Swap Glycine for any other amino acid and the structure of the triple helix is disrupted.

Describe the collagen triple helix

Collagen helix - intertwining of the 3 collagen COL1A chains (2x COL1A1, 1x COL1A2)
Forms helix with every third residue (Gly) located in the centre of the triple helix
Here there is only space for glycine, the smallest amino acid
Therefore the amino acid sequence of the α-chain is characterised by the Gly-X-Y repeat

Whats the normal assembly of collagen type 1?

Two COL1A1s and one COL1A2 are produced from the genes and then intertwined in a helix.

Describe effect of qualitative structural mutation - Gly triple helix mutations

Disrupts the Gly-X-Y sequence Disturbs collagen structure Result in impaired collagen function, OI types II-IV

What are qualitative defects?

Qualitative differences are those that are characterized by differences in processes, mechanisms, and structures Qualitative defects describe the situation where mutations result in the synthesis of a structurally abnormal alpha collagen that then forms, or try’s to form, a helix with structurally normal alpha collagens. This causes a disturbed helical folding resulting in impaired helical function.

WHat mutations can cause a qualitative defect.

Mutations such as glycine changes, C-terminal mutations, inframe variants and some splice changes can cause a qualitative defect. (Qualitative is defect of structure or function)

Examples of changes that cause qualitative defects?

Mutations such as glycine changes, C-terminal mutations, inframe variants and some splice changes can cause a qualitative defect.

What mutations are type 2 causing?

Those mutations closer to the C-terminus tend to be more severe, type 2 OI causing.

What do qualitative defects tend to cause?

Type 2 to type 4

According to the ACGS 2020 variant classification, what can be used and why?

classification PM1 strong can be used. This is because the Gly of the Gly-X-Y repeat is considered to a mutation hot spot.

WHat are quantitative defects?

Quantitative defects are where the mutation causes a reduction in the amount of collagen.

Describe quantitative defects

Mutations that lead to premature truncation – nonsense, frameshifts Result of these mutations is a quantitative defect in collagen type I, Only about half of the normal amount of the protein is produced (reduced quantity) But the collagen type I protein that is produced has a normal structure Collagen fibre maintains some functionality Tends to cause mild OI type I

Variant assessment The Glycine of the Gly-X-Y triplet repeat is changed for a valine Predicted to disrupt the collagen helix Common mechanism of disease for OI

ACGS Variant Classification Guidelines: PM1_strong - Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme)

COL1A1 c.[600G>A];[=] p.[(Gly200Val)];[(=)]

Not seen in normal population database PM2 Glycine vs valine PP3 Located in collagen triple helix repeat PM1_Strong Variant database: reported to occur in another patient with OI type 1. PP5 COL1A1 gene consistent with patients clinical symptoms PP4

COL1A1 c.[600G>A];[=] p.[(Gly200Val)];[(=)] Pathogen or bengin?

Class 5 - Pathogenic

Treatment

Treatment with bisphosphonates Increases bone strength/density, reduces fractures Osteoclast cells break down/dissolve old bone, absorb the bisphosphonate drug. Osteoclast activity is slowed down. This reduces bone breakdown, increases density. No cure.

What condition is COL1A1 related Osteogenesis

COL1A1 related Osteogenesis is an autosomal dominant condition

What does autosomal mean?

“Autosomal" means that the gene is located on one of the autosome chromosomes

What does dominant mean?

Dominant" means that a pathogenic variant in a single copy of the disease-associated gene is enough to cause the disease

Autosomal dominant inheritance

A parent with one gene mutated will pass this or the normal copy to offspring, therefore there is a 50% chance of their offspring inheriting the mutation and being affected with the disorder.

What further testinc ould be done?

Relative testing

Familial testing

Family members with variant can start treatment early Inform life choices - Know to avoid contact sports! Prenatal diagnosis available. Family members without variant Reassured that they do not have OI No need to test their offspring