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com/ejhg/journ
al/v11/n5/pdf/5200968a.pdf%3Forigin%3Dppub&ved=2ahUKEwj9wpGs-
frZAhXMGZQKHfK3CkQQFjADegQIABAB&usg=AOvVaw0z91mh7__-TqrTwsexQh8a

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wse/silent_mutation&ved=2ahUKEwj9wpGs-
frZAhXMGZQKHfK3CkQQFjAGegQIBRAB&usg=AOvVaw1HU2UPdtIhGD7xDqO0mtNM

RESEARCH ARTICLE
Different outcome of sarcoglycan missense
mutation between human and mouse
Sara F. Henriques, Cécile Patissier, Nathalie Bourg,Chiara Fecchio, Doriana
Sandona, Justine Marsolier,Isabelle Richard
 Abstract

Sarcoglycanopathies are rare autosomic limb girdle muscular

dystrophies caused by mutations in one of the genes coding
for sarcoglycan (α, β, δ, and γ-sarcoglycans). Sarcoglycans
form a complex, which is an important part of the dystrophin-
associated glycoprotein complex that protects sarcolemma
against muscle contraction-induced damages. Absence of one
of the sarcoglycan at the plasma membrane induces the
disappearance of the whole complex and perturbs muscle fiber
membrane integrity. We previously demonstrated that point
mutations in the human sarcoglycan genes affects the folding
of the corresponding protein, which is then retained in the
endoplasmic reticulum by the protein quality control and
prematurely degraded by the proteasome. Interestingly,
modulation of the quality control using pharmacological
compounds allowed the rescue of the membrane localization
of the mutated sarcoglycan. Two previously generated mouse
models, knock-in for the most common sarcoglycan mutant,
R77C α-sarcoglycan, failed in reproducing the dystrophic
phenotype observed in human patients. Based on these results
and the need to test therapies for these fatal diseases, we
decided to generate a new knock-in mouse model carrying the
missense mutation T151R in the β-sarcoglycan gene since this
is the second sarcoglycan protein with the most frequently
reported missense mutations. Muscle analysis, performed at
the age of 4 and 9-months, showed the presence of the
mutated β-sarcoglycan protein and of the other components of
the dystrophin-associated glycoprotein complex at the muscle
membrane. In addition, these mice did not develop a
dystrophic phenotype, even at a late stage or in condition of
stress-inducing exercise. We can speculate that the absence of
phenotype in mouse may be due to a higher tolerance of the
endoplasmic reticulum quality control for amino-acid changes
in mice compared to human.

BRCA1/2 germline missense mutations: a systematic review

Hereditary breast and ovarian cancer is an inherited syndrome associated

with BRCA1/2germline defects. The identified mutations are classified as missense, large
deletion, insertion, nonsense and splice-site variants with a deleterious impact
on BRCA1/2 function. Part of these forms the well-documented truncating mutations, and
missense variants represent a clinical dilemma as the pathogenic role is yet to be clearly shown.
In this systematic review, we collected these missense variations with a documented deleterious
function. We focused on English language articles from MEDLINE. This study included
all BRCA1/2 germline missense mutations identified in breast andovarian cancer patients. The
method of this study followed the ‘PRISMA statement for reporting systematic reviews and meta-
analyses’. A total of 61 BRCA1/2 germline and pathogenic missense mutations were identified:
70.5% affected BRCA1 and 29.5% BRCA2, respectively. In BRCA1, the majority of mutations
were located in the BRCA C-terminus (48.8%), leading to a disruption of function. Conversely, no
specific associations were verified between mutations and the BRCA2gene. The European
population was the most affected by BRCA1 and the Asian population byBRCA2 mutant
patterns. The identification of novel BRCA1/2 missense mutations requires specific genetic tests
to assess pathogenicity. With this systematic review, we are, to the best of our knowledge, the
first to collect the overall amount of data on these pathogenic mutants with the aim of improving
the management of carriers and their kindred.
 https://www.google.com.ph/url?sa=t&source=web&rct=j&url=https://journals.lww.com/eurjcancer
prev/Abstract/publishahead/BRCA1_2_germline_missense_mutations___a_systematic.99351.aspx&
ved=2ahUKEwjriYbW_vrZAhXHGJQKHdh8DAY4ChAWMAJ6BAgIEAE&usg=AOvVaw0uIN_qAG4JVSUXg
eaU7ug_ (upper article)

When Silent Mutations Provide Evolutionary Advantages

Joseph Caspermeyer

Molecular Biology and Evolution, Volume 33, Issue 6, 1 June 2016, Pages
1639,https://doi.org/10.1093/molbev/msw078

Published:

02 May 2016

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Until recently, most biologists believed that so-called silent mutations, created
by ‘synonymous’ DNA changes—those that do not affect the protein-coding
sequence—had very weak effects on the evolution of organisms.

However, a new study by an international team of scientists has shown that a

different set of DNA codes specifying the same product can have major effects
on the survival and evolution of bacteria. Moreover, they have now shown
that single highly beneficial synonymous mutations can allow organisms to
rapidly evolve and adapt to their environment.
Working on the bacteriumMethylobacterium extorquens , the group created
several variants of a gene called fae, a metabolic enzyme essential for survival
and growth in an environment where the only source of carbon comes from
methanol or methylamine. Under such restrictive conditions, bacteria undergo
strong selection for retaining the fae gene function. When grown in conditions
where methanol was provided as the sole carbon source, all bacterial
populations with the “synonymous” fae gene variants performed poorly when
compared with bacteria carrying the normal gene.

However, when bacterial populations carrying these variants of fae were

grown over a long period of time with methanol being the only carbon
source—described as “strong selection conditions,” an interesting
phenomenon was observed. Within 100–200 generations, these bacterial
populations began to regain their fitness through additional mutations to the
gene variants. Many of these mutations were again synonymous. Furthermore,
these mutations occurred at single points within the gene, were highly
beneficial, and they seemed to recur in multiple experiments.

“What is surprising about our results is that the beneficial mutations we see
are highly repeatable in specific gene variants—you can think of this process
with an analogy to climbers—different climbers who start independently
from the bottom of a hill are using the exact same strategy to reach the top,”
said Agashe, from the National Centre for Biological Sciences, Bangalore, and
lead author of the publication, published in the early online edition of the
journal Molecular Biology and Evolution . The new study is not only critical to
understanding the genetic basis of adaptation, but also, the development of
antibiotic resistance.

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le/33/6/1639/2579832&ved=2ahUKEwj9wpGs-
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 Identification of novel mutations in congenital afibrinogenemia
patients and molecular modeling of missense mutations in
Pakistani population

 Arshi NazEmail authorView ORCID ID profile,

 Arijit Biswas,
 Tehmina Nafees Khan,
 Anne Goodeve,
 Nisar Ahmed,
 Nazish Saqlain,
 Shariq Ahmed,
 Ikram Din Ujjan,
 Tahir S Shamsi and
 Johannes Oldenburg

Thrombosis Journal201715:24
https://doi.org/10.1186/s12959-017-0143-3
© The Author(s). 2017
Received: 9 November 2016
Accepted: 28 June 2017
Published: 12 September 2017

Abstract
Background

Congenital afibrinogenemia (OMIM #202400) is a rare coagulation disorder that

was first described in 1920. It is transmitted as an autosomal recessive trait that
is characterized by absent levels of fibrinogen (factor I) in plasma. Consanguinity
in Pakistan and its neighboring countries has resulted in a higher number of
cases of congenital fibrinogen deficiency in their respective populations. This
study focused on the detection of mutations in fibrinogen genes using DNA
sequencing and molecular modeling of missense mutations in all three genes
[Fibrinogen gene alpha (FGA), beta (FGB) and gamma (FGG)] in Pakistani
patients.

Methods

This descriptive and cross sectional study was conducted in Karachi and Lahore
and fully complied with the Declaration of Helsinki. Patients with fibrinogen
deficiency were screened for mutations in the Fibrinogen alpha (FGA), beta (FGB)
and gamma (FGG) genes by direct sequencing. Molecular modeling was
performed to predict the putative structure functional impact of the missense
mutations identified in this study.
 Results

Ten patients had mutations in FGAfollowed by three mutations in FGB and three
mutations in FGG, respectively. Twelve of these mutations were novel. The
missense mutations were predicted to result in a loss of stability because they
break ordered regions and cause clashes in the hydrophobic core of the protein.

Conclusions

Congenital afibrinogenemia is a rapidly growing problem in regions where

consanguinity is frequently practiced. This study illustrates that mutations
inFGA are relatively more common in Pakistani patients and molecular modeling
of the missense mutations has shown damaging protein structures which has
profounding effect on phenotypic bleeding manifestations in these patients.

Discussion

Fibrinogen deficiency is a rare inherited bleeding disorder that is characterized

by two subtypes of either reduced or completely absent levels of fibrinogen in
the blood [18]. FGA is documented as the most affected gene in literature [19,20].
We have found the larger chunk of mutations in FGA gene in our set of data. A
total of 169 mutations in fibrinogen are reported on the Human Gene Mutation
Database (http://www.hgmd.cf.ac.uk/ac/index.php) date accessed August 12,
2014). Consanguinity involving first and second cousin marriages is accelerating
the spread of disease in areas such as Pakistan, Iran, the Middle East, China and
the far Middle East, including Turkey, in societies where consanguinity is
frequent. The spectrum of causative mutations for afibrinogenemia is interesting
as FGAappears to stand out from the two other fibrinogen genes [21]. The
predominant inheritance pattern was homozygous with a high proportion of
nonsense mutations followed by missense mutations in our study results. A
frame shift mutation (p.Glu262AspfsX158) in FGA exon 5 reported in one study is
predicted as truncated polypeptide. It is associated with exceptionally long
stretch of abnormal residues in homozygous patient with congenital
afibrinogenemia [22]. Frameshift mutation (p.Gln282Thr fsx83*) and (p. Lys
(AAA) 48Arg fs9*) are the novel compound heterozygous mutations which have
manifested deletions along with frameshift defects. The bleeding phenotype is
severe as these mutations worsen the symptoms due to combined effect of
compound mutation and truncation of polypeptide chain.

Three missense mutations (Pro302Ala, Thr305Ala and Thr331Ala) in the alpha

chain reside on short helices surrounding a central beta sheet core. All these
mutations are non-conservative in nature, i.e., the Pro302Ala substitution results
in the replacement of a rigid imino group with a smaller, more flexible residue,
and the Thr305Ala and Thr302Ala substitutions result in the replacement of
polar side chains by smaller but hydrophobic side chains. In addition, the
introduction of alanine in these regions will most likely disrupt some of the intra-
helical hydrogen bonds, thereby breaking the helical structure surrounding the
central core. Because these short helices provide order and stability around an
otherwise disordered coiled-coil region, their disruption might result in a loss of
stability for this region and the alpha chain. The third mutation in this chain,
Ser325Gly, is also non-conservative, i.e., it results in the substitution of a polar
residue to a very small and flexible Gly residue. Because the wild-type residue
already lies on the flexible loop, the introduction of a small residue will make this
region more disordered and therefore unstable. Moreover, because all four
missense mutations belong to a fold of the alpha chain that might be interacting
with Factor XIII (this fold also contains the Lys and Gln residues that participate
in interchain cross linking and cross linking to alpha 2- antiplasmin),
conformational changes induced by these mutations on this fold might interfere
with the interaction of fibrinogen alpha chain with Factor XIII. The one beta chain
missense mutation resides on a highly conserved region of the beta chain, most
likely because many of the residues of this region contribute to the stability of its
densely packed hydrophobic core. The p.Trp432Arg substitution occurs in the
middle of the hydrophobic core. The introduction of a large polar, positively
charged residue instead of a hydrophobic aromatic one would destabilize the
hydrophobic core of this region. Thus, the mutation affects the stability of the
beta chain by disrupting its C-terminal hydrophobic core.
Background

Hemostasis is the normal physiological response that prevents blood loss

following vascular injury. It is dependent on an intricate series of events
involving platelets and specific coagulation factors. Inherited bleeding disorders
can be grouped into abnormalities of primary and secondary hemostasis.
Fibrinogen (Factor I) deficiency can originate from congenital or acquired causes.
Congenital afibrinogenemia (OMIM #202400) is a rare coagulation disorder that
was first described in 1920 [1]. It is as a recessive autosomal inherited trait
characterized by the absence of fibrinogen (factor I) in plasma [2]. The disease
has a worldwide prevalence of 1–2 per million in the general population [3].
Fibrinogen is a 340 KDa hexameric protein of hepatic origin with multiple
functions including roles in platelet aggregation and platelet plug formation and
is an acute phase reactant [4]. It is secreted as zymogen similar to all other
clotting factors and needs to be activated prior to its participation in the
coagulation cascade. It consist of three pairs (Aα, Bβ and Gγ) of polypeptide
chains [5] encoded by three genes (FGA, FGB and FGG) clustered in a region of
approximately 50 kb on chromosome 4q28-q31 [6, 7]. The normal plasma levels
of fibrinogen are 4 g/l [8, 9] and its half-life is approximately 100 h/4 days [10].
The main role of fibrinogen in hemostasis is to strengthen the platelet plug by
converting into its polymeric insoluble form called fibrin by thrombin [11]. The
fibrin meshwork traps red blood cells and platelets to form a plug which stops
bleeding from site of injury. The absence of fibrinogen may result in excessive
blood loss after a trauma. Moreover spontaneous bleeding events can occur.
Fibrinogen defects are classified as quantitative (Hypofibrinogenemia and
Afibrinogenemia, depending upon the partial or complete absence of fibrinogen)
or qualitative (Dysfibrinogenemia and Hypodysfibrinogenemia) [12]. The most
common symptom associated with fibrinogen deficiency is umbilical stump
bleeding with other secondary bleeding manifestations including epistaxis, gum
bleeding, cutaneous bleeding, muscle hematoma and haemarthrosis [13].
Congenital fibrinogen deficiency is considered as rare coagulation disorder but
its incidence is growing higher in those regions where consanguineous
partnerships are common [14, 15]. Pakistan is the country with high ratio of
consanguinity resulting in increasing numbers of rare inherited bleeding
disorders including congenital afibrinogenemia. Our focus was to identify the
mutations, assess the possible structure functional impact of affected protein by
using molecular modeling/silico analysis tools. In addition to this, the study also
encompasses the insight for possible mutational spectrum in frequently involved
fibrinogen gene which may contribute for future prenatal diagnosis of carriers of
these defects in Pakistani population.

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7DSs4FBAWMAV6BAgAEAE&usg=AOvVaw3svjMs21lFbuA6l9vdUW2C