Persius/hicric huggingface dataset:
MT-TP
Mitochondrially encoded tRNA proline also known as MT-TP is a transfer RNA that in humans is encoded by the mitochondrial MT-TP gene.

# Structure
The MT-TP gene is located on the p arm of the non-nuclear mitochondrial DNA at position 12 and it spans 68 base pairs. The structure of a tRNA molecule is a distinctive folded structure which contains three hairpin loops and resembles a three-leafed clover.

# Function
MT-TP is a small 68 nucleotide RNA (human mitochondrial map position 15956-16023) that transfers the amino acid proline to a growing polypeptide chain at the ribosome site of protein synthesis during translation. MT-TP is responsible for coding the microsomal triglyceride transfer protein, which is required for the synthesis of beta-lipoproteins in the liver and intestine. Beta-lipoproteins are essential in fat, cholesterol, and fat-soluble vitamin transport from the intestine to the bloodstream for absorption.

# Clinical Significance

## Abetalipoproteinemia
Mutations in MT-TP have been associated with Abetalipoproteinemia. Abetalipoproteinemia is an inherited disorder characterized by an impaired absorption of fats and certain vitamins from the diet. Mutations in MT-TP cause an impaired microsomal triglyceride transfer protein and lead to reduced or absent beta-lipoprotein. The dysfunction of the microsomal triglyceride transfer protein then results in 
insufficient levels of fats, cholesterol, and vitamins, which are necessary for growth and development. Therefore, clinical manifestations of abetalipoproteinemia include impaired weight gain and growth, failure to thrive, diarrhea, and steatorrhea. Mutations of GLY865TER, SER590ILE, ASN780TYR, ARG540HIS, IVS9AS, and ARG215TER of the MT-TP gene have been found in patients with the disease.

## Complex I deficiency
MT-TP mutations may result in complex I deficiency of the mitochondrial respiratory chain, which may cause a wide variety of signs and symptoms affecting many organs and systems of the body, particularly the nervous system, the heart, and the muscles used for movement (skeletal muscles). These signs and symptoms can appear at any time from birth to adulthood. Phenotypes of the condition include encephalopathy, epilepsy, dystonia, hypotonia, myalgia, exercise intolerance, and more. A G15975A mutation has been found in a patient with the deficiency. In addition, MT-TP mutations have been associated with late-onset ataxia, retinitis, pigmentosa, deafness, leukoencephalopathy, and complex IV deficiency.
MT-TR
Mitochondrially encoded tRNA arginine also known as MT-TR is a transfer RNA which in humans is encoded by the mitochondrial MT-TR gene.

# Structure
The MT-TR gene is located on the p arm of the non-nuclear mitochondrial DNA at position 12 and it spans 65 base pairs. The structure of a tRNA molecule is a distinctive folded structure which contains three hairpin loops and resembles a three-leafed clover.

# Function
MT-TR is a small 65 nucleotide RNA (human mitochondrial map position 10405-10469) that transfers the amino acid arginine to a growing polypeptide chain at the ribosome site of protein synthesis during translation.

# Clinical significance

## Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS)
Mutations in MT-TR have been associated with mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS).  MELAS is a rare mitochondrial disorder known to affect many parts of the body, especially the nervous system and the brain. Symptoms of MELAS include recurrent severe headaches, muscle weakness (myopathy), hearing loss, stroke-like episodes with a loss of consciousness, seizures, and other problems affecting the nervous system. Mutations in MT-TR associated with the disease have included 10450A-G and 10438A-G.

## Cytochrome c oxidase deficiency
MT-TR mutations have been associated with complex IV deficiency of the mitochondrial respiratory chain, also known as the cytochrome c oxidase deficiency. Cytochrome c oxidase deficiency is a rare genetic condition that can affect multiple parts of the body, including skeletal muscles, the heart, the brain, or the liver. Common clinical manifestations include myopathy, hypotonia, and encephalomyopathy, lactic acidosis, and hypertrophic cardiomyopathy. A 10437 G>A mutation has been found with a patient with the deficiency.
MT-TT
Mitochondrially encoded tRNA threonine also known as MT-TT is a transfer RNA which in humans is encoded by the mitochondrial MT-TT gene.

# Structure
The MT-TT gene is located on the p arm of the non-nuclear mitochondrial DNA at position 12 and it spans 66 base pairs. The structure of a tRNA molecule is a distinctive folded structure which contains three hairpin loops and resembles a three-leafed clover.

# Function
MT-TT is a small 66 nucleotide RNA (human mitochondrial map position 15888-15953) that transfers the amino acid threonine to a growing polypeptide chain at the ribosome site of protein synthesis during translation.

# Clinical significance

## Myoclonic epilepsy with ragged-red fibers (MERRF)
Mutations in MT-TT have been associated with myoclonic epilepsy with ragged-red fibers (MERRF), and cause mitochondrial energy deficiencies and reduced proliferation leading to oxidative phosphorylation. Myoclonic epilepsy with ragged-red fibers (MERRF) is a rare mitochondrial disorder that affects many parts of the body, particularly the muscles and nervous system. In most cases, the signs and symptoms of this disorder appear during childhood or adolescence. The features of MERRF vary widely among affected individuals, even among members of the same family. Common clinical manifestations include myoclonus, myopathy, spasticity,epilepsy, peripheral neuropathy, dementia, ataxia, atrophy and more. In addition, mutations have also been linked to lethal infantile mitochondrial myopathy, Parkinson's disease associated with a 15950G>A mutation, and a 15923A>G mutation found to result in an unconfirmed heart disease.

## Cytochrome c oxidase deficiency
MT-TT mutations result in complex IV deficiency of the mitochondrial respiratory chain, also known as the cytochrome c oxidase deficiency. Cytochrome c oxidase deficiency is a rare genetic condition that can affect multiple parts of the body, including skeletal muscles, the heart, the brain, or the liver. Common clinical manifestations include myopathy, hypotonia, and encephalomyopathy, lactic acidosis, and hypertrophic cardiomyopathy. A 15915G>A mutation was found in a patient with cytochrome c oxidase deficiency with accompany symptoms of seizures, progressive hearing loss and muscle weakness.
MT-TW
Mitochondrially encoded tRNA tryptophan also known as MT-TW is a transfer RNA which in humans is encoded by the mitochondrial MT-TW gene.

# Structure
The MT-TW gene is located on the p arm of the non-nuclear mitochondrial DNA at position 12 and it spans 68 base pairs. The structure of a tRNA molecule is a distinctive folded structure which contains three hairpin loops and resembles a three-leafed clover.

# Function
MT-TW is a small 68 nucleotide RNA (human mitochondrial map position 5512-5579) that transfers the amino acid tryptophan to a growing polypeptide chain at the ribosome site of protein synthesis during translation.

# Clinical significance
Mutations in MT-TW have been associated with Leigh's syndrome. Leigh's syndrome is a severe neurological disorder that usually becomes apparent in the first year of life. This condition is characterized by progressive loss of mental and movement abilities (psychomotor regression) and typically results in death within two to three years, usually due to respiratory failure. A small number of individuals do not develop symptoms until adulthood or have symptoms that worsen more slowly. A patient with the syndrome associated with a mutation of 5537insT in the MT-TW gene exhibited symptoms of hypotonia, nystagmus, optic atrophy and seizures.
Changes in MT-TW which impair oxidate phosphorylation also cause mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS). MELAS is a rare mitochondrial disorder known to affect many parts of the body, especially the nervous system and the brain. Symptoms of MELAS include recurrent severe headaches, muscle weakness (myopathy), hearing loss, stroke-like episodes with a loss of consciousness, seizures, and other problems affecting the nervous system. Variants of the gene which cause the disease have included 5556G-A, 5545C-T, and 5521G-A.
MT-TY
Mitochondrially encoded tRNA tyrosine also known as MT-TY is a transfer RNA which in humans is encoded by the mitochondrial MT-TY gene.

# Structure
The MT-TY gene is located on the p arm of the non-nuclear mitochondrial DNA at position 12 and it spans 66 base pairs. The structure of a tRNA molecule is a distinctive folded structure which contains three hairpin loops and resembles a three-leafed clover.

# Function
MT-TY is a small 66 nucleotide RNA (human mitochondrial map position 5826-5891) that transfers the amino acid tyrosine to a growing polypeptide chain at the ribosome site of protein synthesis during translation.

# Clinical significance
Mutations in MT-TY have been associated with mitochondrial complex III deficiency, a genetic condition that can affect several parts of the body, including the brain, kidneys, liver, heart, and the skeletal muscles.Common clinical manifestations include muscle weakness (myopathy) and extreme tiredness (fatigue), particularly during exercise (exercise intolerance). Additional symptoms may also arise depending on the severity of the condition. A patient with a mutation of the gene exhibited complex III deficiency, characterized by high levels of cytochrome c oxidasedeficient fibers with symptoms of weakness and fatigue. A 5874A-G mutation was also found in a patient with the condition.
Changes in MT-TY may also result in progressive external ophthalmoplegia. Progressive external ophthalmoplegia is characterized by weakness of the eye muscles. Common symptoms of the disorder include hearing loss, loss of sensation in the limbs, ataxia, and neuropathy. A 5885T deletion and 5877G-A substitution have been associated with the disease.
MTCH1
Mitochondrial carrier homolog 1 (MTCH1), also referred to as presenilin 1-associated protein (PSAP), is a protein that in humans is encoded by the MTCH1 gene on chromosome 6. MTCH1 is a proapoptotic mitochondrial protein potentially involved in Alzheimers disease (AD).

# Structure
The protein encoded by this gene is named for its structural resemblance to the members of the mitochondrial carrier protein family. The MTCH1 gene contains 12 exons and produces four isoforms. These isoforms arise from alternative splicing of exon 8 and two potential start codons, which results in the deletion of 17 amino acid residues in the hydrophilic loop between two transmembrane domains of some isoforms. Though they differ in sequence and length, the four isoforms still share a similar topological structure, including six transmembrane domains, one of which is responsible for localization to the outer mitochondrial membrane (OMM), and two N-terminal apoptotic domains. As a result, all four isoforms retain these apoptotic domains and mitochondrial localization, both of which are required for the proteins proapoptotic function.

# Function
MTCH1 is a proapoptotic protein that localizes to the OMM and induces apoptosis independently of BAX and BAK. One possible mechanism proposes that its interactions with the mitochondrial permeability transition pore (MPTP) complex leads to depolarization of the mitochondrial membrane, release of cytochrome C, and activation of caspase-3. Expression of this protein is observed in 16 different tissue types, indicating that the protein may serve a housekeeping function.

# Clinical Significance
MTCH1 may be associated with AD and other neurodegenerative and neuroinflammatory diseases through its close interaction with presenilin. However, more research is required to confirm its clinical involvement.

# Interactions
MTCH1 has been shown to interact with PS1.
MTFMT
Mitochondrial methionyl-tRNA formyltransferase is a protein that in humans is encoded by the MTFMT gene.
The protein encoded by this nuclear gene localizes to the mitochondrion, where it catalyzes the formylation of methionyl-tRNA. Recessive-type mutations in MTFMT have been shown to cause mitochondrial disease.

# Model organisms
Model organisms have been used in the study of MTFMT function. A conditional knockout mouse line, called Mtfmttm1a(KOMP)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists  at the Wellcome Trust Sanger Institute.
Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. Twenty six tests were carried out on mutant mice and two significant abnormalities were observed.  During gestation homozygous mutant embryos displayed lethal growth retardation and oedema. In a separate study, no homozygous animals were observed at weaning. The remaining tests were carried out on adult heterozygous mutant animals, but no further abnormalities were seen.
MTUS1
Mitochondrial tumor suppressor 1 (MTSG1) or Microtubule-Associated Scaffold Protein 1 (MTUS1) is a candidate tumor suppressor protein encoded by the MTUS1 gene in humans. Expression levels of MTUS1 was reported to be lost in various types of human malignancies such as colon, ovarian, head-and-neck, pancreas, breast cancers, bladder, gastric, and lung cancers.

# Proteins encoded by MTUS1
As a result of alternative splicing MTUS1 was shown to encode 5 different protein isoforms as listed as ATIP1, ATIP2, ATIP3a, ATIP3b and ATIP4. ATIP3a and ATIP3b was generally considered as ATIP3 and ATIP1 and ATIP3 is the major splice variants encoded by MTUS1 gene.

# Function
This gene encodes a protein which contains a C-terminal domain able to interact with the angiotensin II receptor type 2 (AT2) and a large coiled-coil region allowing dimerization. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. One of the transcript variants has been shown to encode a mitochondrial protein that acts as a tumor suppressor and participates in AT2 signaling pathways. Other variants may encode nuclear or transmembrane proteins but it has not been determined whether they also participate in AT2 signaling pathways.

# Interactions
MTUS1 has been shown to interact with Angiotensin II receptor type 2.
MUS81
Crossover junction endonuclease MUS81 is an enzyme that in humans is encoded by the MUS81 gene.
In mammalian somatic cells, MUS81 and another structure specific DNA endonuclease,  XPF (ERCC4), play overlapping and essential roles in completion of homologous recombination.  The significant overlap in function between these enzymes is most likely related to processing joint molecules such as D-loops and nicked Holliday junctions.

# Meiosis
MUS81 is a component of a minor chromosomal crossover (CO) pathway in the meiosis of budding yeast, plants and vertebrates.  However, in the protozoan Tetrahymena thermophila, MUS81 appears to be part of an essential (if not the predominant) CO pathway.  The MUS81 pathway also appears to be the predominant CO pathway in the fission yeast Schizosaccharomyces pombe.
The relationship of the CO pathway to the overall process of meiotic recombination is illustrated in the accompanying diagram.  Recombination during meiosis is often initiated by a DNA double-strand break (DSB). During recombination, sections of DNA at the 5' ends of the break are cut away in a process called resection. In the strand invasion step that follows, an overhanging 3' end of the broken DNA molecule "invades" the DNA of an homologous chromosome that is not broken forming a displacement loop (D-loop). After strand invasion, the further sequence of events may follow either of two main pathways, leading to a crossover (CO) or a non-crossover (NCO) recombinant (see Genetic recombination).  The pathway leading to a CO involves a double Holliday junction (DHJ) intermediate. Holliday junctions need to be resolved for CO recombination to be completed.
MU81-MMS4, in the budding yeast Saccharomyces cerevisiae, is a DNA structure-selective endonuclease that cleaves joint DNA molecules formed during homologous recombination in meiosis and mitosis.  The MUS81-MMS4 endonuclease, although a minor resolvase for CO formation in S. cerevisiae, is crucial for limiting chromosome entanglements by suppressing multiple consecutive recombination events from initiating from the same DSB.
Mus81 deficient mice have significant meiotic defects including the failure to repair a subset of DSBs.

# Interactions
MUS81 has been shown to interact with CHEK2.
MUTED
Protein Muted homolog is a protein that in humans is encoded by the MUTED gene.

# Function
This gene encodes a component of BLOC-1 (biogenesis of lysosome-related organelles complex 1). Components of this complex are involved in the biogenesis of organelles such as melanosomes and platelet-dense granules. A mouse model for HermanskyPudlak syndrome is mutated in the murine version of this gene. Some transcripts of the downstream gene TXNDC5 overlap this gene, but they do not contain an open reading frame for this gene.

# Interactions
MUTED has been shown to interact with BLOC1S2, Dysbindin and PLDN.
MXRA5
Matrix-remodelling associated 5 is a protein in humans that is encoded by the MXRA5 gene.

# Function
This gene encodes one of the matrix-remodelling associated proteins. This protein contains 7 leucine-rich repeats and 12 immunoglobulin-like C2-type domains related to perlecan. This gene has a pseudogene on chromosome Y.

# Clinical relevance
Mutations in this gene have been seen frequently mutated in cases of non-small cell lung carcinoma.
MYCBP
C-Myc-binding protein is a protein that in humans is encoded by the MYCBP gene.

# Function
The MYCBP gene encodes a protein that binds to the N-terminal region of MYC (MIM 190080) and stimulates the activation of E box-dependent transcription by MYC.

# Interactions
MYCBP has been shown to interact with AKAP1, C3orf15 and Myc.
MYD88
Myeloid differentiation primary response 88 (MYD88) is a protein that, in humans, is encoded by the MYD88 gene.

# Model organisms
Model organisms have been used in the study of MYD88 function. The gene was originally discovered and cloned by Dan Liebermann and Barbara Hoffman in mice.	In that species it is a universal adapter protein as it is used by almost all TLRs (except TLR 3) to activate the transcription factor NF-B. Mal (also known as TIRAP) is necessary to recruit Myd88 to TLR 2 and TLR 4, and MyD88 then signals through IRAK. It also interacts functionally with amyloid formation and behavior in a transgenic mouse model of Alzheimer's disease.
A conditional knockout mouse line, called Myd88tm1a(EUCOMM)Wtsi was generated as part of the International Knockout Mouse Consortium program  a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion.  Twenty-one tests were carried out on homozygous mutant animals, revealing one abnormality: male mutants had an increased susceptibility to bacterial infection.

# Function
The MYD88 gene provides instructions for making a protein involved in signaling within immune cells. The MyD88 protein acts as an adapter, connecting proteins that receive signals from outside the cell to the proteins that relay signals inside the cell.
The human ortholog MYD88 seems to function similarly to mice, since the  immunological phenotype of human cells deficient in MYD88 is similar to cells  from MyD88 deficient mice. However, available evidence suggests that MYD88 is dispensable for human resistance to common viral infections and to all but a few pyogenic bacterial infections, demonstrating a major difference  between mouse and human immune responses. Mutation in MYD88 at position 265 leading to a change from leucine to proline have been identified in many human lymphomas including ABC subtype of diffuse large B-cell lymphoma and Waldenstrom's macroglobulinemia.

# Interactions
Myd88 has been shown to interact with:
- IRAK1
- IRAK2
- Interleukin 1 receptor, type I
- RAC1
- TLR 4

# Gene polymorphisms
Various single nucleotide polymorphisms (SNPs) of the MyD88 have been identified. and for some of them an association with susceptibility to various infectious diseases and to some autoimmune diseases like ulcerative colitis was found.
MYLIP
Myosin regulatory light chain interacting protein, also known as MYLIP, is a protein that in humans is encoded by the MYLIP gene.
MYLIP is also known as IDOL "Inducible Degrader of the LDL receptor" based on its involvement in cholesterol regulation.  The expression of IDOL is induced by the sterol-activated liver X receptor.
Increased Degradation of LDL Receptor Protein (IDOL) is a ubiquitin ligase that ubiquinates LDL receptors in endosomes and directs the receptors to the lysosomal compartment for degradation. IDOL is transcriptionally up-regulated by LXR/RXR in response to an increase in intracellular cholesterol. Pharmacologic inhibition of IDOL could reduce plasma LDL cholesterol by increasing plasma LDL receptor density.

# Function
The ERM protein family members ezrin, radixin, and moesin are cytoskeletal effector proteins linking actin to membrane-bound proteins at the cell surface. Myosin regulatory light chain interacting protein (MYLIP) is a novel ERM-like protein that interacts with myosin regulatory light chain and inhibits neurite outgrowth.
MYLK2
Myosin light chain kinase 2 also known as MYLK2 is an enzyme which in humans is encoded by the MYLK2 gene.

# Function
This gene encodes a myosin light chain kinase, a calcium / calmodulin dependent enzyme, that is exclusively expressed in adult skeletal muscle.  The MYLK2 gene expresses skMLCK more prevalently in fast twitch muscle fibers as compared to slow twitch muscle fibers.  Calmodulin is composed of two terminal domains (N,C) each containing two E-F hand motifs that bind to Ca2+.  Upon saturation of Ca2+, Calmodulin undergoes a conformation change allowing it to bind with a target protein such as skMLCK.  An image depicting a similar complex (sdCen/skMLCK2) is shown under myosin light chain kinase.    This binding to skMLCK increases the affinity of Ca2+ and ultimately leads to a sustained muscle action.

# Clinical significance
Mutations in the MYLK2 gene have been linked to midventricular hypertrophic cardiomyopathy.
MYLK4
Myosin light chain kinase 4 also known as MYLK4 is an enzyme which in humans is encoded by the MYLK2 gene. MYLK4 is a member of the myosin light-chain kinase family of  serine/threonine-specific protein kinases that phosphorylate the regulatory light chain of myosin II.
This protein acts as an enzyme that catalyzes the following reaction: ATP + a protein -> ADP + a phosphoprotein.
MYLK4 is also involved in protein amino acid phosphorylation meaning that it adds a phosphate group onto the molecule.
Not very much is known about the specific functional characteristics of MLYK4, but it has recently been found that the gene may possibly have a role in having at least one driver mutation for cancer.
MYLK4 may also be involved in transferase activity, ATP binding, protein serine/threonine kinase activity, and also nucleotide binding.
Other names for MYLK4 are CaMLCK like; EG238564; MYLK4; Mylk4; Myosin light chain kinase family, member 4; SgK085; SGK085; Sgk085; Sugen kinase 85; Uncharacterized serine/threonine-protein kinase SgK085.
There are other known myosin light-chain kinase enzymes.