. 2016 Mar 18;23(6):915–926. doi: 10.1038/cdd.2015.172

Table 3. Components of the autophagic machinery and their association with inflammatory and autoimmune diseases.

Molecule	Confirmed pathway(s)	Associated Disease(s)	References
NOX2	LAP	CGD, Alzheimer's disease, Creuzfeldt–Jakob disease	^{165, 166, 167}
Rubicon	LAP	Ataxia	¹⁶⁸
Beclin1	Autophagy LAP	Ovarian cancer, breast cancer, lung cancer, cystic fibrosis, Alzheimer's disease, RA	^{169, 170, 171, 172, 173, 174}
VPS34	Autophagy LAP	Schizophrenia	¹⁷⁵
UVRAG	Autophagy LAP	Stomach cancer, non-segmental vitiligo, colorectal cancer, cardiomyopthay	^{85, 176, 177, 178}
ATG5	Autophagy LAP	Airway inflammation, SLE/systemic autoimmunity, MS/EAE, RA, Alzheimer's disease, atherosclerosis	^{179, 180, 181, 182, 183, 184}
ATG16L	Autophagy LAP	Crohn's disease, atheroclerosis	^{185, 186}
ATG7	Autophagy LAP	SLE/systemic autoimmunity, MS/EAE, type I diabetes, RA, Alzheimer's disease, cardiomyopathy	^{187, 188, 189, 190}
ATG4	Autophagy LAP	Otoconia	¹⁹¹
LC3	Autophagy LAP	Nasu-Hakola disease	¹⁹²
LAMP2	Autophagy LAP	Danon disease, type II diabetes	¹⁹³
ULK1	Autophagy	Crohn's disease	¹⁹⁴
FIP200	Autophagy	Inflammatory skin disorders	¹⁹⁵
p62	Autophagy	Huntingtin's disease	¹⁹⁶
EPG5	Autophagy	Vici syndrome	¹⁹⁷
IRGM	Autophagy	Crohn's disease, MS/EAE	¹⁹⁸
SMURF1	Autophagy	Ulcerative colitis	¹⁹⁹
WDR45	Autophagy	Encephalopathy	²⁰⁰
Parkin	Mitophagy	Parkinson's disease	²⁰¹
PINK1	Mitophagy	Parkinson's disease	²⁰²

Abbreviations: ATG, autophagy-related gene; CGD, chronic granulomatous disease; EAE, experimental autoimmune encephalitis; LAP, LC3-associated phagocytosis; MS, Multiple sclerosis; RA, rheumatoid arthritis; SLE, systemic lupus erythematosus

Confirmed activity in autophagy, LAP, and/or mitophagy is indicated