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Multiple endocrine neoplasia type-1 occurs due to the mutations in gene MEN-1. This gene encodes for menin protein. Menin prevents the cells from growing and dividing aggressively. Menin is likely involved in cell functions such as copying and repairing DNA and regulating the activity of other genes. Inactivating mutations of both the copies of the MEN1 gene leads to lack of availability of menin to control cell growth and division. This leads to the formation of tumors characteristic of MEN-1 syndrome. Why these tumors preferentially affect endocrine tissues is unclear.

MEN-1 syndrome is inherited in an autosomal dominant fashion. The altered gene is usually inherited from an affected parent. People with this condition are born with one mutated MEN1 gene copy in each cell. New mutations in MEN-1 without a family history can also occur in some patients.

Unlike most other autosomal dominant conditions, in which one altered copy of a gene in each cell is sufficient to cause the disorder, two copies of the MEN1 gene must be altered to trigger tumor formation in multiple endocrine neoplasia type 1. A mutation in the second copy of the MEN1 gene occurs in a small number of cells during a person's lifetime. Almost everyone who is born with one MEN1 mutation acquires a second mutation in certain cells, which can then divide in an unregulated way to form tumors.