Inheritance Patterns

Question 1

Hypermorphic?

Answer 1

GOF - mutant gene has increased activity due to higher expression or constitutive activation

Question 2

Amorphic?

Answer 2

Also known as null

Complete LOF

Question 3

Hypomorphic?

Answer 3

Partial LOF

Usually AR but can be AD if haploinsufficient

Question 4

Antimorphic?

Answer 4

Also known as dominant negative

Dominant mutations that act in opposition to normal gene function

Question 5

Neomorphic?

Answer 5

Dominant GOF different to normal function

Question 6

How does WT gene dose effect dom neg and neomorphic variants?

Answer 6

Dom neg - increase WT gene function (due to duplication) = decreased severity

Neomorphic - WT gene dose has no effect on phenotype severity

Question 7

Describe the dominant negative effect

Answer 7

Heterozygous variant whose mutant gene product interferes with normal function of WT gene product

Question 8

What kind of proteins are vulnerable to dominant negative mutations?

2x examples

Answer 8

Proteins that form homo or heteropolymeric complexes as they depend on oligomerisation of normal proteins for activity

Dimeric ligand receptors
Multimeric enzyme complexes

Question 9

Why can NMD ameliorate the effect of dominant negative mutations?

Answer 9

More NMD of variant mRNA = less variant protein = less potency = decreased severity

Question 10

2 examples of dominant negative diseases

Answer 10

FBN1 in Marfan syndrome

COL1A1/2 in osteogenesis imperfecta

Question 11

What are fibrillar collagens?

Answer 11

Major structural protein of connective tissue. Assemble triple helices of homo or heterotrimeric polypeptide chains assembled in cross-linked formation

Question 12

What is the importance of the Gly-X-Y repeats in collagen proteins?

Answer 12

Spatially allow helix formation through every 3rd Glycine residue

Question 13

Name 2 genes that encode type 1 procollagen chains

Answer 13

COL1A1 and COL1A2

Question 14

Describe the DomNeg effect on COL1A1/2

Answer 14

Variants within glycine residues = production of abnormal protein = disruption of triple helix

Question 15

What is Marfan syndrome?

Answer 15

Connective tissue disorder called by FBN1 variants that have a structural role in large arteries. Causes aortic dissection or aneurysms

Question 16

Describe the DomNeg effect on FBN1

Answer 16

Disturbed interactions between WT fibrillin-1 and other structural proteins = disorganised ECM = decreased aortic wall strength

Question 17

4 differences between mtDNA and gDNA

Answer 17

Fraction of the size of the nuclear genome (~16.5kb)

Small circular molecule

Maternally-inherited

No introns (aberrant splicing not a feature)

Question 18

How many genes are encoded by mtDNA? What do they encode?

Answer 18

37

13 OXPHOS proteins
2 rRNAs
22 tRNAs

Question 19

What does mtDNA have higher mutation frequency?

Answer 19

Localised oxidative environment causing DNA damage, increased replication rates and inefficient repair

Question 20

What is the copy number of mtDNA?

Answer 20

Depends on energy demand of tissue

100-10k copies per cell

Question 21

Inheritance patterns of mitochondrial disease?

Answer 21

Pathogenic variants in the mtDNA itself (maternally inherited only)

Pathogenic variants in nuclear genes involved in mitochondrial DNA maintenance which can be autosomal dominant or recessive

Question 22

Define Heteroplasmy and homoplasmy

Answer 22

Heteroplasmy - two or more different variants of mtDNA exist within a cell

Homoplasmy - all copies of the mtDNA are identical within a cell

Question 23

Define Mitochondrial bottleneck

Answer 23

A random shift of mtDNA mutational load between generations (and even siblings) due to unequal transfer of mtDNA molecules during oogenesis

Question 24

Describe 3 considerations for interpretation of pathogenicity unique to mtDNA variants

Answer 24

There are currently no mitochondrial DNA specific guidelines for interpreting variants

Inheritance pattern (maternal or nuclear)

Population databases used (Mitomap instead of gnomAD for example)

Question 25

State 4 tissues with high metabolic demand and frequently affected in mt disorders

Answer 25

Nervous system Skeletal & cardiac muscles B cells of pancreas Inner hair cells of cochlear & renal tubules

Question 26

Gene that encodes mitochondrial DNA polymerase

Answer 26

POLG (polymerase gamma)

Question 27

Testing pathway for adult presenting with optic neuropathy

Answer 27

Optic neuropathy is a generic term and can be caused by pathogenic variants in mtDNA (e.g. Leber’s hereditary optic neuropathy) typically in adults or nuclear DNA, typically in children 1. Common LHON mutations 2. Full gene screens for implicated mt genes 3. Nuclear based eye panel

Question 28

3 common LHON variants

Answer 28

m.11778G>A (MT-ND4) m.3460G>A (MT-ND1) m.14484T>C (MT-ND6)

Question 29

Why are urine samples used for mtDNA testing?

Answer 29

Variant heteroplasmy in urinary epithelial cells often comparable to skeletal muscle allowing non-invasive testing of mtDNA variants likely not detectable in blood Especially good for m.3243A>G in MELAS

Question 30

What are the phenotypes of MELAS and associated mt variant?

Answer 30

Myopathy Encephalopathy Lactic acidosis Stroke like episodes MT-TL1 m.3243A>G

Question 31

Name a syndrome associated with mitochondrial gene deletions. 3 features

Answer 31

Pearson syndrome Pancytopenia, lactic acidosis, pancreatic failure in children

Question 32

How can mtDNA be used in cancer diagnostics?

Answer 32

mtDNA mutations occur early in carcinogenesis due to the Warburg effect (preferential use of glycolysis to produce ATP causing defects in OXPHOS chain) mtDNA has high copy number that may be used as an early biomarker for cancer

Question 33

3 considerations for mitochondrial disorder testing

Answer 33

Muscle is best source of mtDNA but not always possible Negative blood result must be caveated and further tissue requested if clin suspcioun is high 80-95% of clinically suspected mito disease have no detectable mtDNA variant. Test nuclear DNA.

Question 34

3 techniques for mtDNA analysis

Answer 34

mtDNA rearrangements by long range PCR inc deletions Common mtDNA SNVs by seq Whole mt genome sequencing by NGS