Although anion channel activities have been demonstrated in sarcoplasmic reticulum/endoplasmic reticulum (SR/ER), their molecular identities and functions remain unclear. Here, we link rare variants of CLCC1 (Chloride Channel CLIC Like 1) to ALS (amyotrophic lateral sclerosis). We demonstrate that CLCC1 is a pore-forming component of an ER anion channel and that ALS-associated mutations impair the channel activity. CLCC1 unitary conductance is inhibited by luminal Ca2+ but facilitated by phosphatidylinositol 4,5-bisphosphate (PIP2). We identified a conserved lysine 298 (K298) in CLCC1 intraluminal loop as the critical PIP2-sensing residue. CLCC1 maintains steady-state [Cl-]ER and morphology and regulates ER Ca2+ homeostasis including steady-state [Ca2+]ER and efficiency of internal Ca2+ release. ALS-associated mutant CLCC1 increase steady-state [Cl-]ER and impair ER Ca2+ homeostasis. Phenotypic comparisons of multiple Clcc1 mutant alleles, including ALS-associated mutations, reveal a CLCC1 dosage-dependence in severity of disease phenotypes in vivo. Conditional knockout of Clcc1 cell-autonomously causes motor neuron loss and ER stress, misfolded protein accumulation, and characteristic ALS pathologies in the spinal cord. Thus, we argue that disruption of ER ion homeostasis maintained by CLCC1 underlies etiology of neurodegenerative diseases.