Ehlers-Danlos Syndrome is painful. All over. All of the time.
Rather than looking for a specific spot, injury or motion to relate it to, take a step back and think about laws of physics and joint structure.
Laws of physics dictate that the pull of gravity will keep pulling 'parts' to the center of gravity. In joints without hypermobility this is a good thing as it allows people to stand upright and move through the world.
In people with hypermobile connective tissue, it means that the gravitational pull will put pressure on any tissue/structure between the 'part' and the center of gravity. In the leg for example, the thigh bone will put pressure on the tendons, ligaments, cartilage, bones, skin, muscle, blood vessels, etc between it and the center of gravity depending on the individual's posture. Most of those tissues have nerves in or near them. So the result may be as varied as unexplained bruises or pain.
The nerves are confusing because, oftentimes, while the individual is sitting, for example, the pressure exerted may cut off the nerve's communication with the brain. When the individual stands up, the communication may be restored quickly or slowly, depending on a lot of factors (time sitting, position, quantity of tissue impinged, etc). So it is possible for the individual to get up, walk around and a few minutes later think "Ow, why does my knee/thigh/ankle/hip... hurt?" because they can't connect the pain to a specific trauma/injury.
Repeating that process throughout the body over a period of time creates confusion in the brain as to why these 'illogical' signals of pain keep coming in. The brain responds in a variety of ways. It may become hyper-aware, thus amplifying pain signals for micro traumas; i.e., paper cut, weight of a blanket, clothing seams on the skin,etc... The brain may choose to ignore pain signals unless they last a longer period of time which may lead to more serious injury; i.e., burns, hematomas, collapse, fatigue, etc...
Thus, there are lots of people with EDS/HS with secondary disorders; i.e., Fibromyalgia (FM), Chronic Fatigue Syndrome (CF), Reflex Sympathetic Dystrophy Syndrome (RSD), Complex Regional Pain Syndrome (CRPS), chronic pain and general unexplained neuropathy. There are also a higher proportion of people with EDS/HS that have comorbidities of things like Chiari Malformation, Tethered Cord Syndrome and arthritis than in the non EDS/HS population.
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