Disease table of MITOCHONDRIAL DNA DEPLETION SYNDROME OMIM ID: PS603041

Gene-disease associations table

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Gene	Associated with MITOCHONDRIAL DNA DEPLETION SYNDROME in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
AGK	ClinVar, OMIM	HGNC link	7q34	2	PS116200, PS603041
C10orf2	ClinVar, OMIM, HUMSAVAR	HGNC link	10q24.31	4	PS157640, 607459, PS603041, PS233400
DGUOK	ClinVar, OMIM, HUMSAVAR	HGNC link	2p13.1	1	PS603041
FBXL4	ClinVar, OMIM, HUMSAVAR	HGNC link	6q16.2	1	PS603041
MGME1	ClinVar, OMIM, HUMSAVAR	HGNC link	20p11.23	1	PS603041
MPV17	ClinVar, OMIM, HUMSAVAR	HGNC link	2p23.3	1	PS603041
OPA1	OMIM	HGNC link	3q29	6	PS256300, 210000, PS165500, PS603041, 125250, 606657
POLG	ClinVar, OMIM, HUMSAVAR	HGNC link	15q26.1	4	PS157640, 607459, PS603041, 256000
RRM2B	ClinVar, OMIM, HUMSAVAR	HGNC link	8q22.3	2	PS157640, PS603041
SLC25A4	ClinVar, OMIM	HGNC link	4q35.1	2	PS157640, PS603041

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Download the disease annotation in CSV format

Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

By region

Shared region	Number of genes associated with the disease	Genes associated with the disease
2p1	2	SUCLG1, DGUOK

By arm

Shared arm	Number of genes associated with the disease	Genes associated with the disease
2p	3	SUCLG1, DGUOK, MPV17

By chromosome

Shared chromosome	Number of genes associated with the disease	Genes associated with the disease
2	3	SUCLG1, DGUOK, MPV17

Transcription Factors (TF) annotation from TRRUST

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regulated gene	associated to this disease	# TFs	TFs	# TFs associated with this disease	TFs associated with this disease
TYMP	YES	2	SP1, SP3	0
RRM2B	YES	4	POU2F1, NFKB1, CREB1, TP53	0

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Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
SUCLA2	SUCLG1	Yes	4	S100A16, OXCT1, SDHB, SDHA
AGK	SUCLA2	No	3	NTRK1, AGO4, ICT1
AGK	OPA1	No	3	NTRK1, PARK2, CUL3
AGK	C10orf2	No	2	BMI1, ICT1
AGK	SLC25A4	No	2	PARK2, ICT1
SUCLA2	OPA1	No	3	NTRK1, EGFR, NIT2
SUCLA2	C10orf2	No	1	ICT1
SUCLA2	SLC25A4	No	3	FAF2, UBXN8, ICT1
SUCLA2	RRM2B	No	1	RRM1
SUCLA2	MPV17	No	1	EGFR

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Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from BIOGRID - genetic

Interactions from STRING

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Gene1	Gene2	Direct Interaction	Interaction mode	Number of shared interactors	Shared genes in interaction
SUCLA2	SUCLG1	Yes	binding	2	IDH3A, ACLY
SUCLA2	SLC25A4	No	-	1	UBC
SUCLA2	RRM2B	No	-	1	UBC
SUCLA2	DGUOK	No	-	1	UBC
SLC25A4	RRM2B	No	-	1	UBC
SLC25A4	DGUOK	No	-	1	UBC
RRM2B	DGUOK	No	-	1	UBC

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Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from CORUM

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Gene1	Gene2	Direct Interaction	Complexes	Number of shared interactors	Shared genes in interaction
SUCLA2	SUCLG1	Yes	Succinyl-CoA synthetase, ADP-forming	0

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Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from CENSUS

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
SUCLA2	SUCLG1	Yes	3	S100A16, OXCT1, SDHA
SUCLA2	OPA1	No	1	NIT2
OPA1	MPV17	No	1	NDUFS8

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Direct interactions graph
Interactions graph (direct and indirect interactions, when direct are not available)

Interactions from PDB

Interactions from manually curated literature

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Gene1	Gene2	Direct interaction	More information
C10orf2	POLG	yes, complex	In vitro, C10orf2 forms in combination with POLG, a processive replication machinery, which can use double-stranded DNA (dsDNA) as template to synthesize single-stranded DNA (ssDNA) molecules. [UniProt]

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KEGG pathways annotation: shared terms / NET-GE enrichment

Shared terms

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KEGG term	KEGG term ID	IC	Number of genes with the same term	Genes
Citrate cycle (TCA cycle)	hsa00020	7.86	2	SUCLA2, SUCLG1
Propanoate metabolism	hsa00640	7.81	2	SUCLA2, SUCLG1
Drug metabolism - other enzymes	hsa00983	7.21	2	TYMP, TK2
Carbon metabolism	hsa01200	6.03	2	SUCLA2, SUCLG1
Pyrimidine metabolism	hsa00240	6.01	3	TYMP, RRM2B, TK2
Purine metabolism	hsa00230	5.28	2	RRM2B, DGUOK
Metabolic pathways	hsa01100	2.49	8	TK2, AGK, TYMP, POLG, SUCLA2, DGUOK, SUCLG1, RRM2B

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Citrate cycle (TCA cycle) (hsa00020)	-	7.86	0.04	SUCLA2, SUCLG1
Propanoate metabolism (hsa00640)	-	7.81	0.029	SUCLA2, SUCLG1
Pyrimidine metabolism (hsa00240)	-	6.01	0.014	TYMP, RRM2B, TK2
Nucleotide metabolism	NEW	5.05	0.005	RRM2B, DGUOK, TYMP, TK2
Metabolic pathways (hsa01100)	-	2.49	0.04	TK2, AGK, TYMP, C10orf2, POLG, SUCLA2, DGUOK, SUCLG1, RRM2B
Global and overview maps	NEW	2.47	0.001	TK2, AGK, TYMP, C10orf2, POLG, SUCLA2, DGUOK, SUCLG1, RRM2B
Metabolism	NEW	2.06	0.01	SUCLG1, TYMP, POLG, AGK, SUCLA2, DGUOK, TK2, RRM2B

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REACTOME pathways annotation: shared terms / NET-GE enrichment

Shared terms

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REACTOME term	REACTOME term ID	IC	Number of genes with the same term	Genes
Pyrimidine salvage reactions	R-HSA-73614	9.81	2	TYMP, TK2
Citric acid cycle (TCA cycle)	R-HSA-71403	8.73	2	SUCLA2, SUCLG1
Pyrimidine metabolism	R-HSA-73848	8.4	2	TYMP, TK2
Pyruvate metabolism and Citric Acid (TCA) cycle	R-HSA-71406	7.56	2	SUCLA2, SUCLG1
Metabolism of nucleotides	R-HSA-15869	6.7	4	RRM2B, DGUOK, TYMP, TK2
The citric acid (TCA) cycle and respiratory electron transport	R-HSA-1428517	5.71	2	SUCLA2, SUCLG1
Metabolism	R-HSA-1430728	2.34	7	SLC25A4, SUCLG1, TYMP, SUCLA2, DGUOK, TK2, RRM2B

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Pyrimidine salvage reactions (R-HSA-73614)	-	9.81	0.007	TYMP, TK2
Pyrimidine catabolism (R-HSA-73621)	NEW	9.4	0.013	TYMP, SUCLA2
Citric acid cycle (TCA cycle) (R-HSA-71403)	-	8.73	0.005	SUCLA2, SUCLG1
Pyrimidine metabolism (R-HSA-73848)	-	8.4	0.008	TYMP, TK2
Pyruvate metabolism and Citric Acid (TCA) cycle (R-HSA-71406)	-	7.56	0.026	SUCLA2, SUCLG1
Metabolism of nucleotides (R-HSA-15869)	-	6.7	0.001	RRM2B, DGUOK, TYMP, TK2
Metabolism (R-HSA-1430728)	-	2.34	0.047	TK2, SLC25A4, AGK, TYMP, C10orf2, SUCLA2, DGUOK, SUCLG1, RRM2B

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GO - molecular function annotation: shared terms / NET-GE enrichment

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GO	IC	Number of genes with the same GO	Genes
succinate-CoA ligase (ADP-forming) activity (GO:0004775)	9.05	2	SUCLA2, SUCLG1
succinate-CoA ligase activity (GO:0004774)	8.64	2	SUCLA2, SUCLG1
deoxynucleoside kinase activity (GO:0019136)	8.35	2	DGUOK, TK2
CoA-ligase activity (GO:0016405)	7.54	2	SUCLA2, SUCLG1
nucleoside kinase activity (GO:0019206)	7.1	2	DGUOK, TK2
acid-thiol ligase activity (GO:0016878)	6.74	2	SUCLA2, SUCLG1
ligase activity, forming carbon-sulfur bonds (GO:0016877)	6.05	2	SUCLA2, SUCLG1
nucleobase-containing compound kinase activity (GO:0019205)	5.85	2	DGUOK, TK2
exonuclease activity (GO:0004527)	5.33	2	MGME1, POLG
nuclease activity (GO:0004518)	4.33	2	MGME1, POLG

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
succinate-CoA ligase (ADP-forming) activity (GO:0004775)	-	9.05	0.0	SUCLA2, SUCLG1
succinate-CoA ligase activity (GO:0004774)	-	8.64	0.001	SUCLA2, SUCLG1
deoxynucleoside kinase activity (GO:0019136)	-	8.35	0.001	DGUOK, TK2
CoA-ligase activity (GO:0016405)	-	7.54	0.002	SUCLA2, SUCLG1
nucleoside kinase activity (GO:0019206)	-	7.1	0.01	DGUOK, TK2
acid-thiol ligase activity (GO:0016878)	-	6.74	0.01	SUCLA2, SUCLG1
ligase activity, forming carbon-sulfur bonds (GO:0016877)	-	6.05	0.027	SUCLA2, SUCLG1
purine ribonucleoside triphosphate binding (GO:0035639)	-	2.22	0.026	TK2, OPA1, AGK, C10orf2, SUCLA2, DGUOK, SUCLG1
ribonucleoside binding (GO:0032549)	-	2.22	0.028	TK2, OPA1, AGK, C10orf2, SUCLA2, DGUOK, SUCLG1
purine ribonucleoside binding (GO:0032550)	-	2.22	0.027	TK2, OPA1, AGK, C10orf2, SUCLA2, DGUOK, SUCLG1

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GO - biological process annotation: shared terms / NET-GE enrichment

Shared terms

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GO	IC	Number of genes with the same GO	Genes
succinyl-CoA metabolic process (GO:0006104)	8.12	2	SUCLA2, SUCLG1
deoxyribonucleoside metabolic process (GO:0009120)	7.78	2	DGUOK, TK2
deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)	7.78	2	DGUOK, TK2
mitochondrial DNA replication (GO:0006264)	7.53	3	MGME1, RRM2B, POLG
deoxyribonucleoside monophosphate metabolic process (GO:0009162)	7.43	2	DGUOK, TK2
succinate metabolic process (GO:0006105)	7.43	2	SUCLA2, SUCLG1
pyrimidine nucleoside salvage (GO:0043097)	7.24	2	TYMP, TK2
pyrimidine-containing compound salvage (GO:0008655)	7.24	2	TYMP, TK2
mitochondrial genome maintenance (GO:0000002)	7.16	5	TYMP, MGME1, SLC25A4, OPA1, MPV17
mitochondrial DNA metabolic process (GO:0032042)	7.09	3	MGME1, RRM2B, POLG

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
succinyl-CoA metabolic process (GO:0006104)	-	8.12	0.003	SUCLA2, SUCLG1
deoxyribonucleoside metabolic process (GO:0009120)	-	7.78	0.004	DGUOK, TK2
deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)	-	7.78	0.004	DGUOK, TK2
mitochondrial DNA replication (GO:0006264)	-	7.53	0.0	RRM2B, TK2, MGME1, POLG, C10orf2
deoxyribonucleoside monophosphate metabolic process (GO:0009162)	-	7.43	0.021	DGUOK, TK2
succinate metabolic process (GO:0006105)	-	7.43	0.021	SUCLA2, SUCLG1
pyrimidine nucleoside salvage (GO:0043097)	-	7.24	0.032	TYMP, TK2
pyrimidine-containing compound salvage (GO:0008655)	-	7.24	0.032	TYMP, TK2
mitochondrial genome maintenance (GO:0000002)	-	7.16	0.0	MGME1, SLC25A4, TYMP, MPV17
mitochondrial DNA metabolic process (GO:0032042)	-	7.09	0.0	RRM2B, MGME1, TK2, POLG, C10orf2

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GO - cellular component annotation: shared terms / NET-GE enrichment

Shared terms

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GO	IC	Number of genes with the same GO	Genes
mitochondrial intermembrane space (GO:0005758)	5.51	2	FBXL4, OPA1
organelle envelope lumen (GO:0031970)	5.41	2	FBXL4, OPA1
myelin sheath (GO:0043209)	4.76	2	SUCLA2, SLC25A4
mitochondrial outer membrane (GO:0005741)	4.76	2	OPA1, AGK
organelle outer membrane (GO:0031968)	4.63	2	OPA1, AGK
outer membrane (GO:0019867)	4.6	2	OPA1, AGK
axon part (GO:0033267)	4.4	2	OPA1, POLG
mitochondrial matrix (GO:0005759)	4.03	4	SUCLA2, DGUOK, TK2, SUCLG1
mitochondrial inner membrane (GO:0005743)	3.65	4	OPA1, SLC25A4, SUCLG1, MPV17
organelle inner membrane (GO:0019866)	3.56	4	SLC25A4, SUCLG1, MPV17, OPA1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
mitochondrial nucleoid (GO:0042645)	NEW	6.02	0.025	C10orf2, POLG
nucleoid (GO:0009295)	NEW	5.97	0.025	C10orf2, POLG
mitochondrial matrix (GO:0005759)	-	4.03	0.0	SLC25A4, SUCLG1, C10orf2, SUCLA2, DGUOK, TK2
mitochondrial inner membrane (GO:0005743)	-	3.65	0.0	TK2, OPA1, SLC25A4, MPV17, SUCLA2, POLG, C10orf2, SUCLG1
organelle inner membrane (GO:0019866)	-	3.56	0.0	TK2, OPA1, SLC25A4, MPV17, SUCLA2, POLG, C10orf2, SUCLG1
mitochondrial membrane (GO:0031966)	-	3.31	0.0	MPV17, TK2, OPA1, SLC25A4, AGK, C10orf2, POLG, SUCLA2, SUCLG1
intracellular organelle lumen (GO:0070013)	-	3.05	0.042	SUCLA2, DGUOK, TK2, SUCLG1
membrane-enclosed lumen (GO:0031974)	-	3.05	0.0	OPA1, SLC25A4, TK2, C10orf2, SUCLA2, FBXL4, SUCLG1, DGUOK
mitochondrial part (GO:0044429)	-	2.92	0.0	MPV17, TK2, SLC25A4, AGK, SUCLG1, C10orf2, POLG, SUCLA2, FBXL4, OPA1, DGUOK
mitochondrion (GO:0005739)	-	2.42	0.0	MPV17, SLC25A4, AGK, MGME1, SUCLG1, C10orf2, POLG, SUCLA2, DGUOK, OPA1

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