TABLE 3.

Effects of mutations in CLN genes on the expression of autophagy-related genes.

Gene	Model organism	Autophagy-related gene	Protein	Protein function	Transcriptional effect
TPP1	M. musculus	Rab7b	Ras-related protein Rab7b	GTPase that regulates endosome-trans-Golgi network vesicular trafficking	Upregulated
		Atg9b	Autophagy-related gene 9B	Regulates lipid transport and autophagy
		Ctsc	Cathepsin C	Cysteine protease
		Ctsd	Cathepsin D
		Ctsh	Cathepsin H
		Ctss	Cathepsin S
		Ctsw	Cathepsin W
		Ctsz	Cathepsin Z
		Pik3cg	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma	Phosphoinositide kinase	Downregulated
		Plcb2	1-phosphtidylinositol 4,5-bisphosphate phospodiesterase beta-2	Phospholipase
		Plcl2	Inactive phopholipase C-like protein 2
		Plcg2	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2
		Plch2	1-phosphatidylinositol 4,5-biphosphate phosphodiesterase eta-2
CLN3	S. pombe	atg3	Autophagy-related gene 3	Ubiquitin-like transferase	Upregulated
		atg8	Autophagy-related gene 8	Phophatidylethanolamine binding protein
		sst2	Ubiquitin specific protease	Peptidase	Downregulated
		vps28	ESCRTI complex subunit Vps28	Vesicular trafficking regulator
		fis1	Putative mitochondrial fission protein Fis1	Mitochondrial and outer membrane fission
		mcs4	Response regulator Mcs4	Oxidative stress signal- transducing protein
		pek1	MAP kinase Pek1	Kinase
DNAJC5	C. elegans	E3 ubiquitin ligase	E3 ubiquitin ligase	Ubiquitin-tagging protein	Downregulated
CLN6	M. musculus	Ctsa	Cathepsin A	Cysteine protease	Downregulated
		Ctsb	Cathepsin B
		Ctsd	Cathepsin D
		Tpp1	Tripeptidyl peptidase 1	Serine protease	Downregulated
	O. aries	LAMP1	LAMP1	Lysosome biogenesis	No change
MFSD8	M. musculus	Ctsd	Cathepsin D	Cysteine protease	Downregulated
		Ctss	Cathepsin S		Upregulated
CTSD	M. musculus	p62	p62	Autophagic and ubiquitin-proteasome system receptor	Upregulated
GRN	M. musculus	Gabarap	Gamma-aminobutyric acid receptor-associated protein-like 1	Gamma-aminobutyric acid receptor	Upregulated
		Tom1	Target of Myb1 membrane trafficking protein	Protein trafficking
		Tfeb	Transcription factor EB	Lysosome biogenesis and autophagy regulating protein
		Atg7	Ubiquitin-like modifier-activating enzyme ATG7	Ubiquitin-like modifier activating protein	Upregulated (with GRN addition)
ATP13A2	H. sapiens	SYT11	Synaptotagmin 11	Calcium membrane trafficking and ubiquitin substrate protein	Downregulated