Involved in GABAergic but not glutamatergic transmission (PubMed:29395912). Binds and traps GABAA receptors in the endoplasmic reticulum (ER) (PubMed:29395912). Modulates postsynaptic GABAergic transmission, and therefore inhibitory neurotransmission, by reducing the plasma membrane expression of these receptors (PubMed:29395912). Altered GABAergic signaling is one among many causes of cleft palate (PubMed:29395912). Might function as a lipid scramblase, translocating lipids in membranes from one leaflet to the other one (By similarity). Required for efficient glycosylphosphatidylinositol (GPI) inositol deacylation in the ER, which is a crucial step to switch GPI-anchored proteins (GPI-APs) from protein folding to transport states (By similarity). May play a role in T-cell development (PubMed:9218588). Widely expressed (PubMed:9218588, PubMed:9828125). Expressed by subcapsular and outer cortical thymic cells (PubMed:9218588). Ubiquitously expressed in mouse embryo. Mice overexpressing Clptm1 exhibit an aberrant development of thymocytes. Belongs to the CLPTM1 family.