OTOF Gene

The official name of OTOF gene is “otoferlin". The OTOF gene provides instructions for making a protein called otoferlin. This protein is present in the brain and the cochlea, which is a snail-shaped structure in the inner ear that helps process sound. Although the exact function of otoferlin is uncertain, it appears to be essential for normal hearing. Researchers believe that otoferlin may play a role in releasing chemical signals (neurotransmitters) from nerve cells that are involved in hearing. This process is dependent on the concentration of calcium within the cell. The otoferlin protein has several regions called C2 domains that bind to calcium and use it to interact with other molecules.

Location:

OTOF Gene is present in human chromosome 2 and its coded from region 26,533,574 to 26,635,069 base pairs with 47 exons, the cytogenetic location 2p23.1.

Disease

Mutations in OTOF gene causes  nonsyndromic deafness     At least 16 mutations in the OTOF gene have been identified in people with a form of nonsyndromic deafness (hearing loss without related signs and symptoms affecting other parts of the body) called DFNB9. People with these mutations have a type of hearing loss called auditory neuropathy, which occurs when sound is not transmitted properly from the inner ear to the brain.

    Some mutations in the OTOF gene result in the production of an abnormally small, nonfunctional version of otoferlin or prevent cells from making any of this protein. Other genetic changes probably alter the 3-dimensional structure of otoferlin, which impairs its ability to bind to calcium.

    A particular OTOF mutation is a common cause of nonsyndromic deafness in the Spanish population. This mutation replaces one amino acid building block, glutamine, with a signal that stops protein production prematurely at position 829 in the otoferlin protein (written as Gln829Ter or Q829X). The Q829X mutation causes an abnormally short version of otoferlin to be made, which disrupts the protein's function and leads to hearing loss.

NR4A2 gene

The official name of NR4A2 gene is “nuclear receptor subfamily 4, group A, member 2". The MSH6 gene provides instructions for making a member of steroid-thyroid hormone-retinoid receptor superfamily. that may plays a role as a Trascription factor. This protein found in the brain and the adrenal gland (the hormone-producing gland located on top of each kidney). In the brain, the NR4A2 protein plays a key role in prompting certain nerve cells to specialize (differentiate) and produce a chemical messenger called dopamine. Dopamine transmits messages that help the brain control physical movement and emotional behavior.

NR4A2 prot direct interactions

image coursey: Oliver Brun
Location:

NR4A2 gene is present in human chromosome 2 and its coded from region 156,889,194 to 156,897,445 base pairs with 8 exons, the cytogenetic location 2q22-q23.

Disease

Mutations in this gene have been associated with disorders related to dopaminergic dysfunction, including Parkinson disease, schizophernia, and manic depression. Misregulation of this gene may be associated with rheumatoid arthritis. Alternatively spliced transcript variants have been described, but their biological validity has not been determined.

MSH6 Gene

The official name of MSH2 gene is “mutS homolog 6 (E. coli)". The MSH6 gene provides instructions for making a protein that plays an essential role in repairing DNA. This protein fixes mistakes that are made when DNA is copied (DNA replication) in preparation for cell division. The MSH6 protein joins with another protein, the MSH2 protein, to form an active protein complex. This active protein complex identifies places on the DNA where mistakes have been made during DNA replication. Another group of proteins, the MLH1-PMS2 protein complex, then takes over to help with the actual repair. The MSH6 gene is a member of a set of genes known as the mismatch repair (MMR) genes.

Location:

MSH2 gene is present in human chromosome 2 and its coded from region 47,863,789 to 47,887,595 base pairs with 16 exons, the cytogenetic location 2p16.

Disease

Mutations in the MSH6 gene have been reported in about 10 percent of families with Lynch syndrome that have an identified gene mutation. All of these mutations cause the production of an abnormally short, nonfunctional MSH6 protein or a partially active version of the protein. When the MSH6 protein is absent or ineffective, the number of mistakes that are left unrepaired during cell division increases substantially. If the cells continue to divide, errors accumulate in DNA; the cells become unable to function properly and may form a tumor in the colon or another part of the body. People with mutations in the MSH6 gene also have an increased risk of developing cancers of the ovary, stomach, small intestine, liver, gallbladder duct, upper urinary tract, brain, and skin.

MSH2 Gene

The official name of MSH2 gene is “mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)". TThe MSH2 gene provides instructions for making a protein that plays an essential role in DNA repair. This protein fixes mistakes that are made when DNA is copied (DNA replication) in preparation for cell division. The MSH2 protein joins with one of two other proteins, the MSH6 protein or the MSH3 protein, to form an active protein complex. This active protein complex identifies places on the DNA where mistakes have been made during DNA replication. Another group of proteins, the MLH1-PMS2 protein complex, then takes over to help with the actual repair. The MSH2 gene is a member of a set of genes known as the mismatch repair (MMR) genes.

Location:

MSH2 gene is present in human chromosome 2 and its coded from region 47,483,766 to 47,563,863 base pairs with 16 exons, the cytogenetic location 2p22-p21.

Disease

Mutations in this gene causes increases the risk of Lynch syndrome, About 40 percent of all cases of Lynch syndrome with an identified gene mutation are associated with mutations in the MSH2 gene. Several hundred MSH2 mutations that predispose people to colorectal cancer and other HNPCC-associated cancers have been found. These mutations may cause the production of an abnormally short or inactivated MSH2 protein that cannot perform its normal function. When the MSH2 protein is absent or ineffective, the number of mistakes that are left unrepaired during cell division increases substantially. If the cells continue to divide, errors accumulate in DNA; the cells become unable to function properly and may form a tumor in the colon or another part of the body. People with mutations in the MSH2 gene have an increased risk of developing several other types of cancer, including cancers of the endometrium (lining of the uterus), ovary, stomach, small intestine, liver, gallbladder duct, upper urinary tract, brain, and skin. Some mutations in the MSH2 gene increase the likelihood of several uncommon skin tumors occurring in addition to colorectal cancer, a combination called Muir-Torre syndrome. These rare skin tumors include sebaceous adenomas and carcinomas, which occur in skin glands (sebaceous glands) that produce an oily substance called sebum. Multiple, rapidly growing skin tumors called keratoacanthomas may also occur, usually on sun-exposed areas.

ASPM Gene

Definition:

ASPM is a human gene whose defective forms are associated with autosomal recessive primary microcephaly."ASPM" is an acronym for "Abnormal Spindle-like, Microcephaly-associated", which reflects its being an ortholog to the Drosophila melanogaster "abnormal spindle" (asp) gene.

Chromsome: Chromosome 1


Location :1q31

Size of gene:62291bp (195319997 to195382287 complementary)

No Exons :28

No Introns:27

Description:The ASPM gene is the human ortholog of the Drosophila melanogaster 'abnormal spindle' gene (asp), which is essential for normal mitotic spindle function in embryonic neuroblasts.

Evolutionary significance:

A new allele (version) of ASPM appeared sometime between 14,100 and 500 years ago with a mean estimate of 5,800 years ago. The new allele has a frequency of about 50 percent in populations of the Middle East and Europe, it is less frequent in East Asia, and has low frequencies among Sub-Saharan African populations.

The mean estimated age of the ASPM allele of 5,800 years ago, roughly correlates with the development of written language, spread of agriculture and development of cities. Currently, two alleles of this gene exist: the older (pre-5,800 years ago) and the newer (post-5,800 years ago). About 10% of humans have two copies of the new ASPM allele, while about 50% have two copies of the old allele. The other 40% of humans have one copy of each. Of those with an instance of the new allele, 50% of them are an identical copy suggesting a highly rapid spread from the original mutation. According to a hypothesis called a "selective sweep", the rapid spread of a mutation (such as the new ASPM) through the population indicates that the mutation is somehow advantageous to the individual. As of today, there is no evidence to support the notion that the new ASPM allele increases intelligence, and some researchers dispute whether the spread of the allele even demonstrates selection. They suggest that the current distribution of the alleles could be explained by a founder effect, following an out of Africa dispersal. However, statistical analysis has shown that the older forms of the gene are found more heavily in populations that speak tonal languages like Chinese.

Protein Sequence:Asp (abnormal spindle)-like, microcephaly associated [Homo sapiens].

ACADM Gene

Defintion:
ACADM (acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain) is a gene that provides instructions for making an enzyme called acyl-coenzyme
Chromosome: Chromosome 1

Location: 1p31 (75962870 to 76001771)

Size Of Gene: 38902 bp

Locus :RP4-682C21.1

Number of Exons: 12

Number Of Introns : 11

Description: A dehydrogenase that is important for breaking down (degrading) a certain group of fats called medium-chain fatty acids. These fatty acids are found in foods such as milk and certain oils, and they are also stored in the body's fat tissue. Medium-chain fatty acids are also produced when larger fatty acids are degraded. The acyl-coenzyme A dehydrogenase for medium-chain fatty acids (ACADM) enzyme is essential for converting these particular fatty acids to energy, especially during periods without food (fasting). The ACADM enzyme functions in mitochondria, the energy-producing centers within cells. It is found in the mitochondria of several types of tissues, particularly the liver.

Related conditions

Medium-chain acyl-coenzyme A dehydrogenase deficiency can be caused by mutations in the ACADM gene. More than 30 ACADM gene mutations that cause medium-chain acyl-coenzyme A dehydrogenase deficiency have been identified. Many of these mutations switch an amino acid building block in the ACADM enzyme. The most common amino acid substitution replaces lysine with glutamic acid at position 304 in the enzyme's chain of amino acids (also written as Lys304Glu or K304E). This mutation and other amino acid substitutions alter the enzyme's structure, reducing or abolishing its activity. Other mutations delete or duplicate part of the ACADM gene, which leads to an unstable enzyme that cannot function.

With a shortage (deficiency) of functional ACADM enzyme, medium-chain fatty acids cannot be degraded and processed. As a result, these fats are not converted into energy, which can lead to characteristic symptoms of this disorder, such as lack of energy (lethargy) and low blood sugar. Levels of medium-chain fatty acids or partially degraded fatty acids may build up in tissues and can damage the liver and brain, causing more serious complications.

Protein Coded:NP_000007

"ACADM." Wikipedia, The Free Encyclopedia. 30 Aug 2008, 20:53 UTC. 14 Oct 2008 <http://en.wikipedia.org/w/index.php?title=ACADM&oldid=235248417>.

HADHB Gene

The official name of HADHB gene is hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme. The HADHB gene provides instructions for making part of an enzyme complex called mitochondrial trifunctional protein. This enzyme complex functions in mitochondria, the energy-producing centers within cells. It is found in the mitochondrimitochondrial trifunctional proteina of several tissues, particularly the heart, liver, muscles, and the part of the eye that detects light and color (the retina).Mitochondrial trifunctional protein is required to break down (metabolize) a group of fats called long-chain fatty acids. Long-chain fatty acids are found in foods such as milk and certain oils, and they are also stored in the body's fat tissues. Mitochondrial trifunctional protein is essential for converting long-chain fatty acids to the major source of energy used by the heart and muscles. During periods without food (fasting), this energy source is also important for the liver and other tissues.

Function:

As the name suggests, mitochondrial trifunctional protein performs three functions. It has three enzyme activities that are essential for fatty acid oxidation, which is the multistep process that metabolizes fats and converts them to energy. The beta subunit performs one of the enzyme activities, known as long-chain 3-keto-acyl-coenzyme A thiolase. The alpha subunit carries out the other two enzyme activities.

Location:

HADHA gene is present in human chromosome 2 and its coded from region 26321120 to 26366837 base pairs with 20 exons, the cytogenetic location 2p23.

Disease

Mutations in this gene causes mitochondrial trifunctional protein deficiency.

In mitochondrial trifunctional protein deficiency Researchers have identified at least 20 HADHB gene mutations that reduce all three enzyme activities of mitochondrial trifunctional protein. Most mutations change one of the building blocks (amino acids) used to make the protein's beta subunit. A change in amino acids probably alters the subunit's structure, which disrupts all three activities of the enzyme complex. Some mutations produce abnormally small, unstable beta subunits, which leads to a decreased amount of mitochondrial trifunctional protein. With a loss of mitochondrial trifunctional protein activity, long-chain fatty acids cannot be metabolized and processed. As a result, these fatty acids are not converted to energy, which can lead to the characteristic features of this disorder, such as lethargy and low blood sugar. Long-chain fatty acids or partially metabolized fatty acids may build up in tissues and damage the liver, heart, and muscles, causing more serious complications.

Carnitine palmitoyltransferase II

Definition
Carnitine palmitoyltransferase II, also known as CPT2, is a human gene also known has CPTASE

Chromosome: Chromosome 1

Position:1p32

Size Of Gene:  17767 bp (53434689..53452455)

No Exons 5

Description

Carnitine palmitoyltransferase II precursor (CPT2) is a nuclear protein which is transported to the mitochondrial inner membrane. CPT2 together with carnitine palmitoyltransferase I oxidizes long-chain fatty acids in the mitochondria. Defects in this gene are associated with mitochondrial long-chain fatty-acid (LCFA) oxidation disorders and carnitine palmitoyltransferase II deficiency.[

Disease:

Carnitine palmitoyltransferase II deficiency is a condition that prevents the body from converting certain fats called long-chain fatty acids into energy, particularly during periods without food (fasting),three main types of carnitine palmitoyltransferase II deficiency are: a lethal neonatal form; a severe infantile form that affects the liver, heart, and muscles (hepatocardiomuscular form); and a less severe form that affects only the muscles (myopathic form). Infants with the lethal neonatal form of this disorder usually experience respiratory failure, liver failure, seizures, and an irregular heart beat (arrythmia) leading to cardiac arrest. In many cases, the brain and kidneys are also abnormal. Usually, affected infants do not survive their first year.

COL11A1 Gene

Definition:

Collagen, type XI, alpha 1, also known as COL11A1, is a human gene.

Chromosome:Chromosome 1

Location: 1p21

Size of gene: 232030 bp (5001..237030)

No Exons:67

Description:

This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Three transcript variants encoding different isoforms have been identified for this gene.

Disease:Stickler syndrome - caused by mutations in the COL11A1 gene

Mutations in the COL11A1 gene have been identified in some people with Stickler syndrome. Some mutations change one of the protein building blocks (amino acids) used to make the pro-alpha1(XI) chain. Other mutations cause segments of DNA to be skipped when the protein is being made, resulting in an abnormally short pro-alpha1(XI) chain. These alterations of type XI collagen impair its function, which can lead hearing loss, a tearing of the lining of the eye (retinal detachment), and abnormalities of the bones and joints.

Mutations in the COL11A1 gene are also responsible for some cases of Marshall syndrome, a disorder that is very similar to Stickler syndrome. In most mutations that cause this syndrome, a segment of DNA is skipped when the protein is made, resulting in an abnormally small pro-alpha1(XI) chain. This shortened protein hinders the formation of mature type XI collagen, which results in the features of Marshall syndrome. Whether Marshall syndrome represents a variant form of Stickler syndrome or a separate disorder is controversial.



Protein:

1464 amino acids. The a1 (I) chains of the type I collagen are synthesised as procollagen molecules containing amino and carboxy-terminal propeptides, wich are removed by site-specific endopeptidase. The central triple helical domain is formed by 338 repeats of a Gly-X-Y triplet where X and Y are often a proline.

Type I collagen is the most abundant protein in vertebrates and a constituent of the extra cellular matrix in connective tissue of bone, skin, tendon, ligament and dentine. It is mostly produced and secreted by fibroblasts and osteoblasts.

HADHA Gene

The official name of HADHA gene is hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit. The HADHA gene provides instructions for making part of an enzyme complex called mitochondrial trifunctional protein. This enzyme complex functions in mitochondria, the energy-producing centers within cells. It is found in the mitochondria of several tissues, particularly the heart, liver, muscles, and the part of the eye that detects light and color (the retina).

Function:

Mitochondrial trifunctional protein is required to break down (metabolize) a group of fats called long-chain fatty acids. Long-chain fatty acids are found in foods such as milk and certain oils, and they are also stored in the body's fat tissues. Mitochondrial trifunctional protein is essential for converting long-chain fatty acids to the major source of energy used by the heart and muscles. During periods without food (fasting), this energy source is also important for the liver and other tissues.Mitochondrial trifunctional protein is made of eight subunits. Four subunits called alpha are produced by the HADHA gene, and four subunits called beta are produced by the HADHB gene. As the name suggests, mitochondrial trifunctional protein performs three functions. It has three enzyme activities that are essential for fatty acid oxidation, which is the multistep process that metabolizes fats and converts them to energy. The alpha subunit performs two of the enzyme activities, known as long-chain 3-hydroxyacyl-coenzyme A dehydrogenase and long-chain 2-enoyl-coenzyme A hydratase. The beta subunit carries out the third enzyme activity.

Location:

HADHA gene is present in human chromosome 2 and its coded from region 26267008 to 26321098 base pairs with 20 exons, the cytogenetic location 2p23.

Disease

Mutations in this gene causes long-chain 3-hydroxyacyl-coenzyme A dehydrogenase deficiency(LCAD defiency) and Mitochondrial trifunctional protein deficiency

In LCAD defiency Researchers have identified several HADHA gene mutations that decrease the long-chain 3-hydroxyacyl-coenzyme A dehydrogenase enzyme activity of the mitochondrial trifunctional protein. (The protein's other enzyme activities remain normal or near normal.) Many of the HADHA mutations change one of the building blocks (amino acids) used to make the protein's alpha subunit. The most common mutation replaces the amino acid glutamic acid with the amino acid glutamine at position 474 in the alpha subunit. This mutation is written as Glu474Gln or E474Q. The Glu474Gln mutation and other amino acid replacements probably alter the structure of the alpha subunit, preventing it from functioning normally. Other types of HADHA mutations produce an abnormally small, unstable alpha subunit, which is unable to function. With a shortage (deficiency) of functional alpha subunits, long-chain fatty acids cannot be metabolized and processed. As a result, these fatty acids are not converted to energy, which can lead to the characteristic features of long-chain 3-hydroxyacyl-coenzyme A dehydrogenase deficiency, such as lack of energy (lethargy) and low blood sugar. Long-chain fatty acids or partially metabolized fatty acids may build up in tissues and damage the liver, heart, and retina, causing more serious complications.

In mitochondrial trifunctional protein deficiency Researchers have identified several HADHA gene mutations that reduce all three enzyme activities of the mitochondrial trifunctional protein. Some mutations produce abnormally small, unstable alpha subunits, which leads to a decreased level of mitochondrial trifunctional protein. Other mutations replace one amino acid with another amino acid in the alpha subunit, which probably alters the subunit's structure and disrupts all three functions of the enzyme complex. With a loss of mitochondrial trifunctional protein activity, long-chain fatty acids cannot be metabolized and processed. As a result, these fatty acids are not converted to energy, which can lead to the characteristic features of this disorder, such as lethargy and low blood sugar. Long-chain fatty acids or partially metabolized fatty acids may build up in tissues and damage the liver, heart, and muscles, causing more serious complications.

COL5A2 Gene

The official name of COL5A2 gene is collagen, type V, alpha 2. The COL5A2 gene provides instructions for making a component of collagen. Collagens form a family of proteins that strengthen and support many tissues in the body, including skin, ligaments, bones, tendons, muscles, and the space between cells and tissues called the extracellular matrix.

Function:

The COL5A2 gene produces a component of type V collagen, called the pro-alpha2(V) chain. One pro-alpha2(V) chain combines with two pro-alpha1(V) chains (produced by the COL5A1 gene) to form type V procollagen. These triple-stranded, rope-like procollagen molecules must be processed by enzymes outside the cell. Once these molecules are processed, they arrange themselves into long, thin fibrils that cross-link to one another in the spaces around cells. The cross-links result in the formation of very strong, mature type V collagen fibers. Type V collagen also plays a role in assembling other types of collagen into fibrils within many connective tissues.

Location:

COL5A2 gene is present in human chromosome 2 and its coded from region 189604886 to 189752850 base pairs with 54 exons, the cytogenetic location 2q14-q32.

Disease

Mutations in this gene causes Ehlers-Danlos syndrome,Mutations in the COL5A2 gene have been identified in a small number of patients with classic Ehlers-Danlos syndrome. These mutations change the structure and function of the pro-alpha2(V) chain. As a result, type V collagen fibrils in the skin that are assembled with the altered protein are large and irregular. Researchers believe that these changes in collagen structure cause the signs and symptoms of classic Ehlers-Danlos syndrome.

COL4A3 Gene

The official name of COL4A3 gene is collagen, type IV, alpha 3 (Goodpasture antigen). COL4A3 gene provides instructions for making one component of type IV collagen. which is a flexible protein that forms complex networks. Specifically, this gene makes the alpha3(IV) chain of type IV collagen. This chain combines with two other types of alpha (IV) chains (the alpha4 and alpha5 chains) to make a complete collagen molecule. Type IV collagen networks make up a large portion of basement membranes, which are thin sheet-like structures that separate and support cells in many tissues. This specific type IV collagen network plays an especially important role in the basement membranes of the kidney, inner ear, and eye.

Function:

Type IV collagen, the major structural component of basement membranes, is a multimeric protein composed of 3 alpha subunits. These subunits are encoded by 6 different genes, alpha 1 through alpha 6, each of which can form a triple helix structure with 2 other subunits to form type IV collagen. This gene encodes alpha 3.In the Goodpasture syndrome, autoantibodies bind to the collagen molecules in the basement membranes of alveoli and glomeruli. The epitopes that elicit these autoantibodies are localized largely to the non-collagenous C-terminal domain of the protein.

Collagen

Location:

COL4A3 gene is present in human chromosome 2 and its coded from region 227,737,524 to base pair 227,887,750 with 52 exons, the cytogenetic location 2q36-q37

Disease

Mutations in this gene causes Alport syndrome,The autosomal recessive form of Alport syndrome results when two copies of the COL4A3 gene in each cell are mutated. Most of the mutations identified in this gene cause a change in the sequence of amino acids (the building blocks of proteins) in a region of the alpha3(IV) collagen chain that is critical for combining with other type IV collagen chains. Other mutations severely decrease or prevent the production of any alpha3(IV) chains in the basement membranes of the kidney, inner ear and eye. In the kidney, other types of collagen accumulate in the basement membranes, eventually leading to scarring of the kidneys and kidney failure. Mutations in this gene can also lead to abnormal function in the inner ear, resulting in hearing loss.

COL3A1 Gene

The official name of COL3A1 gene is collagen, type III, alpha 1. COL3A1 gene provides instructions for making a component of collagen. Collagens form a family of proteins that strengthen and support many tissues in the body. Type III collagen is found in tissues such as the skin, lungs, intestinal walls, and the walls of blood vessels. The COL3A1 gene produces the components of type III collagen, called pro-alpha1(III) chains.Three copies of this chain combine to make a molecule of type III procollagen. These triple-stranded, rope-like procollagen molecules must be processed by enzymes outside the cell to remove extra protein segments from their ends. Once these molecules are processed, the collagen molecules arrange themselves into long, thin fibrils. Within these fibrils, the individual collagen molecules are cross-linked to one another. These cross-links result in the formation of very strong mature type III collagen fibrils, which are found in the spaces around cells.

Function

Collagen protein strengthens and supports tissues

Location:

COL3A1 gene is present in human chromosome 2 and its coded from region189,547,343 to 189,585,716 with 51 exons, the cytogenetic location 2q31

Disease

Mutations in this gene causes Ehlers-Danlos syndrome,Researchers have identified more than 320 mutations mutations that cause the vascular type of Ehlers-Danlos syndrome have been identified in the COL3A1 gene. Only a few of these mutations have been seen in more than one family. The mutations alter the structure and production of type III procollagen molecules. As a result, a large percentage of type III collagen molecules are assembled incorrectly, or the amount of type III collagen is greatly reduced. Researchers believe that these changes affect tissues that are normally rich in this type of collagen, such as the skin, blood vessels, and internal organs. Lack of sufficient type III collagen causes the signs and symptoms of vascular Ehlers-Danlos syndrome.