No this is the result of about 7 years of on and off hyperfocus and reading a couple k studies before decent LLMs were a thing. Some snippets lifted from my previous comments for convenience.
RCCX = a four-gene block that can tweak immunity, hormones, connective tissue, and gut nerves. As well as making carriers more prone to random epigenetic mutations in response to the environment. That terrain can make folate-receptor antibodies more likely and more harmful. Frye’s “cerebral folate disorder” fits that picture, and folinic acid gives a realistic bypass for the subgroup that tests positive for those antibodies.
The block acts like a four-piece Lego unit. Some people carry extra copies. Some people carry fewer. The pieces can swap bits with nearby look-alike segments. That setup can shift four body systems: immune tone (C4), stress hormones (CYP21A2), connective tissue and joints (TNXB), and signal control in the nucleus (RP/STK19). The gut and autonomic nerves often feel those shifts.
It’s a chimeric region that spits out mutations in response to the environment and is how our genome evolves. Pretty cool right? The stress diathesis in the stress diathesis model of disease.
It is the most complex gene cluster in our genome, and has avoided detection for this very reason. It was recently linked by NIH to the sex biases in autoimmune conditions.
5 years ago now actually 😳 but I’ve been waiting on mainstream sequencing and analysis techniques to catch up. Rccx also has connections to hypermobility via tnxb; known cyp21a2 mutations cause CAH and intersex disorders, milder ones are linked to gender and sexual fluidity (hence why rccx autists are more likely to be trans, although not all - some may even appear hyper-masculine due to the danger wiring).
Dendrites are the little branches on neurons. A dendrite problem means a different class of issue inside the brain’s wiring. RCCX lives in the immune-hormone-matrix space. It can shape brain function through immune and metabolic routes, not through a built-in shape flaw in neurons.
some dumpage:
MHC class III is located on chromosome 6 (6p21.3) in humans. It covers 700 kb and contains 61 genes. making it the most gene-dense region of the human genome. The functions of many genes are yet unknown.
CYP21A2 is closely adjacent in tandem with three other gene(serine/threonine kinase RP, complement C4, and tenascin TNX), forming a genetic module termed RCCX (RP/STK19 - C4 - CYP21* - TNX*). The four-gene module is the most complex gene cluster in the human genome. Which includes overlapping genes and genes within genes . In addition, containing high density retroelements such as human endogenous retrovirus (HERV-K).
The RCCX region consists of chimeric genes which are thought to be critical for driving genome evolution. The RCCX module shows a high similarity between the functional genes (RP1, CYP21A2, and TNXB) and the corresponding pseudogenes (RP2, CYP21A1P, and TNXA), leading to gene conversions and gene deletions due to homologous recombination, which inactivate the functional genes.
These genes make multiple copies of themselves (called copy number variations). Behaving as one unit, instead of as four separate genes - deleted and duplicated together. RCCX is the only place in the human genome where genes travel together in this way.
MECHANISM FOR GENE DELETIONS AND DISEASE ASSOCIATIONS (the RCCX Module) (1999) The burdens are the accompanying genetic or autoimmune diseases such as CAH, systemic lupus erythematosus, and possibly EDS, caused by unequal crossovers and incorporations of deleterious mutations in the constituents of the RCCX.
STK19
(previously RP1)
“The relationship with disease for STK19 are being gradually revealed”
Responsible for gene expression and DNA repair, as part of a ‘RNA Metabolism Surveillance Quartet’,
Established links with melanoma, skin pigmentation, metabolic syndrome and inflammation
Correlated to Sjogren Syndrome, Type 1 diabetes, schizophrenia
C4
Work led by researchers at Harvard Medical School and MIT provides a clear genetic explanation behind the sex bias observed in some diseases. The team’s findings, reported May 11, 2020 in Nature, suggest that greater abundance of an immune-related protein C4 in men protects against lupus and Sjögren’s but heightens vulnerability to schizophrenia.
Responsible for immune-clearance
Established links with ASD, Schizophrenia, Lupus, Sjögren’s
Correlated to CSF/ME via HERV-K over-expression in one preliminary dataset.
The geneticists who linked C4 with schizophrenia called it the mother of all mapping problems in a recent webinar. SNP analysis, WES, WGS won’t get at these mutations without a lot more work due to the massive amount of variation and complex and long range disequilibrium changes. They had to use about 5 different state of the art processes and what they found is highly associated with brain plasticity.
C4 controls developmentally relevant and experience-activated dendritic pruning (perhaps the Sensory-Processing-Sensitivity brain becoming more and more associated with autonomic dysregulation circuits associated with conditioned fear response. This may provide some explanation of why LDN could be helpful in both PTSD and chronic illness as C4 controls phagocytosis of synapses by activated microglia and LDN may decrease microglial activation.
CYP21A2
The common CYP21A2 variants presumably exert the same effect on `hormone levels in the healthy and disease-affected populations. Therefore, they may contribute to complex diseases”
Responsible for variations in hormone levels, with it’s primary function being the encoding of 21-hydroxylase, deficiency of which causes defective conversion of adrenal precursors to cortisol and, in some cases, to aldosterone
Established links with Classic & Non-Classic Congenital Adrenal Hyperplasia
Correlated to Addisons Disease, most mental health issues, higher rates of sexual and gender variance, and psychological vulnerability to stress
CYP21A2 travels in tandem with a psuedogene and the high degree of sequence similarity between them indicates that these two genes are evolving in tandem through intergenic exchange of DNA.
CYP21A2 mutations are also associated with elevated levels of Corticotropin releasing hormone. The combination of corticotropin-releasing hormone (CRH), secreted under stress, together with environmental stimuli could be major contributors to the pathogenesis of immunological disease - as the diathesis in the stress diathesis model of disease.
No this is the result of about 7 years of on and off hyperfocus and reading a couple k studies before decent LLMs were a thing. Some snippets lifted from my previous comments for convenience.
RCCX = a four-gene block that can tweak immunity, hormones, connective tissue, and gut nerves. As well as making carriers more prone to random epigenetic mutations in response to the environment. That terrain can make folate-receptor antibodies more likely and more harmful. Frye’s “cerebral folate disorder” fits that picture, and folinic acid gives a realistic bypass for the subgroup that tests positive for those antibodies.
The block acts like a four-piece Lego unit. Some people carry extra copies. Some people carry fewer. The pieces can swap bits with nearby look-alike segments. That setup can shift four body systems: immune tone (C4), stress hormones (CYP21A2), connective tissue and joints (TNXB), and signal control in the nucleus (RP/STK19). The gut and autonomic nerves often feel those shifts.
It’s a chimeric region that spits out mutations in response to the environment and is how our genome evolves. Pretty cool right? The stress diathesis in the stress diathesis model of disease.
It is the most complex gene cluster in our genome, and has avoided detection for this very reason. It was recently linked by NIH to the sex biases in autoimmune conditions.
https://neurosciencenews.com/genetics-sex-disease-16348/amp/
5 years ago now actually 😳 but I’ve been waiting on mainstream sequencing and analysis techniques to catch up. Rccx also has connections to hypermobility via tnxb; known cyp21a2 mutations cause CAH and intersex disorders, milder ones are linked to gender and sexual fluidity (hence why rccx autists are more likely to be trans, although not all - some may even appear hyper-masculine due to the danger wiring).
Dendrites are the little branches on neurons. A dendrite problem means a different class of issue inside the brain’s wiring. RCCX lives in the immune-hormone-matrix space. It can shape brain function through immune and metabolic routes, not through a built-in shape flaw in neurons.
some dumpage:
MHC class III is located on chromosome 6 (6p21.3) in humans. It covers 700 kb and contains 61 genes. making it the most gene-dense region of the human genome. The functions of many genes are yet unknown.
CYP21A2 is closely adjacent in tandem with three other gene(serine/threonine kinase RP, complement C4, and tenascin TNX), forming a genetic module termed RCCX (RP/STK19 - C4 - CYP21* - TNX*). The four-gene module is the most complex gene cluster in the human genome. Which includes overlapping genes and genes within genes . In addition, containing high density retroelements such as human endogenous retrovirus (HERV-K).
The RCCX region consists of chimeric genes which are thought to be critical for driving genome evolution. The RCCX module shows a high similarity between the functional genes (RP1, CYP21A2, and TNXB) and the corresponding pseudogenes (RP2, CYP21A1P, and TNXA), leading to gene conversions and gene deletions due to homologous recombination, which inactivate the functional genes. These genes make multiple copies of themselves (called copy number variations). Behaving as one unit, instead of as four separate genes - deleted and duplicated together. RCCX is the only place in the human genome where genes travel together in this way.
MECHANISM FOR GENE DELETIONS AND DISEASE ASSOCIATIONS (the RCCX Module) (1999) The burdens are the accompanying genetic or autoimmune diseases such as CAH, systemic lupus erythematosus, and possibly EDS, caused by unequal crossovers and incorporations of deleterious mutations in the constituents of the RCCX.
STK19
(previously RP1) “The relationship with disease for STK19 are being gradually revealed” Responsible for gene expression and DNA repair, as part of a ‘RNA Metabolism Surveillance Quartet’, Established links with melanoma, skin pigmentation, metabolic syndrome and inflammation Correlated to Sjogren Syndrome, Type 1 diabetes, schizophrenia
C4
Work led by researchers at Harvard Medical School and MIT provides a clear genetic explanation behind the sex bias observed in some diseases. The team’s findings, reported May 11, 2020 in Nature, suggest that greater abundance of an immune-related protein C4 in men protects against lupus and Sjögren’s but heightens vulnerability to schizophrenia. Responsible for immune-clearance Established links with ASD, Schizophrenia, Lupus, Sjögren’s Correlated to CSF/ME via HERV-K over-expression in one preliminary dataset.
The geneticists who linked C4 with schizophrenia called it the mother of all mapping problems in a recent webinar. SNP analysis, WES, WGS won’t get at these mutations without a lot more work due to the massive amount of variation and complex and long range disequilibrium changes. They had to use about 5 different state of the art processes and what they found is highly associated with brain plasticity.
C4 controls developmentally relevant and experience-activated dendritic pruning (perhaps the Sensory-Processing-Sensitivity brain becoming more and more associated with autonomic dysregulation circuits associated with conditioned fear response. This may provide some explanation of why LDN could be helpful in both PTSD and chronic illness as C4 controls phagocytosis of synapses by activated microglia and LDN may decrease microglial activation.
CYP21A2
The common CYP21A2 variants presumably exert the same effect on `hormone levels in the healthy and disease-affected populations. Therefore, they may contribute to complex diseases” Responsible for variations in hormone levels, with it’s primary function being the encoding of 21-hydroxylase, deficiency of which causes defective conversion of adrenal precursors to cortisol and, in some cases, to aldosterone
Established links with Classic & Non-Classic Congenital Adrenal Hyperplasia Correlated to Addisons Disease, most mental health issues, higher rates of sexual and gender variance, and psychological vulnerability to stress
CYP21A2 travels in tandem with a psuedogene and the high degree of sequence similarity between them indicates that these two genes are evolving in tandem through intergenic exchange of DNA.
CYP21A2 mutations are also associated with elevated levels of Corticotropin releasing hormone. The combination of corticotropin-releasing hormone (CRH), secreted under stress, together with environmental stimuli could be major contributors to the pathogenesis of immunological disease - as the diathesis in the stress diathesis model of disease.
TNXB
Encodes an extracellular matrix protein.
Established Links : Classical-like Ehlers-Danlos Syndrome (EDS), Vesicoureteral Reflux Correlated to Hypermobile EDS, Hypermobility (Joint-Hypermobiltiy Syndrome, Hypermobility Spectrum Disorder (HSD), juvenile RA.
Holy cow.
I am insanely impressed by your level of knowledge here.
I am going to have to star this and attempt to digest this in chunks, thank you very much for all this info!