Disease table of PONTOCEREBELLAR HYPOPLASIA OMIM ID: PS607596

Gene-disease associations table

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Gene	Associated with PONTOCEREBELLAR HYPOPLASIA in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
AMPD2	ClinVar, OMIM, HUMSAVAR	HGNC link	1p13.3	2	PS607596, PS303350
CHMP1A	ClinVar, OMIM	HGNC link	16q24.3	1	PS607596
CLP1	ClinVar, OMIM, HUMSAVAR	HGNC link	11q12.1	1	PS607596
EXOSC3	ClinVar, OMIM, HUMSAVAR	HGNC link	9p13.2	1	PS607596
KCNT1	ClinVar, OMIM, HUMSAVAR	HGNC link	9q34.3	3	PS600513, PS607596, PS308350
PCLO	ClinVar, OMIM	HGNC link	7q21.11	1	PS607596
RARS2	ClinVar, OMIM	HGNC link	6q15	1	PS607596
SEPSECS	ClinVar, OMIM, HUMSAVAR	HGNC link	4p15.2	1	PS607596
TSEN2	ClinVar, OMIM, HUMSAVAR	HGNC link	3p25.2	1	PS607596
TSEN34	ClinVar, OMIM, HUMSAVAR	HGNC link	19q13.42	1	PS607596

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Download the disease annotation in CSV format

Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

By chromosome

Shared chromosome	Number of genes associated with the disease	Genes associated with the disease
9	2	KCNT1, EXOSC3
17	2	TSEN54, VPS53

Transcription Factors (TF) annotation from TRRUST

Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
TSEN34	TSEN2	Yes	3	TSEN15, TSEN54, CLP1
TSEN34	CLP1	Yes	4	TSEN2, TSEN15, TSEN54, CLP1
TSEN34	TSEN54	Yes	3	TSEN2, TSEN15, CLP1
TSEN2	CLP1	Yes	4	TSEN54, TSEN34, TSEN15, CLP1
TSEN2	TSEN54	Yes	4	TSEN34, ZNRF1, TSEN15, CLP1
CLP1	TSEN54	Yes	5	TSEN2, AMMECR1, TSEN34, TSEN15, CLP1
VRK1	CLP1	No	1	SNW1
VRK1	VPS53	No	1	VPS52
TSEN2	CHMP1A	No	1	USP8
CLP1	EXOSC3	No	1	APP

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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
TSEN2	CLP1	Yes	binding	0
TSEN2	TSEN54	Yes	binding	1	TSEN15
VRK1	CLP1	No	-	2	UBC, HNRNPA1
VRK1	AMPD2	No	-	1	UBC
VRK1	VPS53	No	-	1	UBC
VRK1	EXOSC3	No	-	1	UBC
VRK1	CHMP1A	No	-	1	UBC
CLP1	AMPD2	No	-	1	UBC
CLP1	TSEN54	No	-	1	TSEN2
CLP1	VPS53	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
TSEN34	TSEN2	Yes	tRNA splicing endonuclease	3	TSEN15, TSEN54, CLP1
TSEN34	CLP1	Yes	tRNA splicing endonuclease	3	TSEN2, TSEN15, TSEN54
TSEN34	TSEN54	Yes	tRNA splicing endonuclease	3	TSEN2, TSEN15, CLP1
TSEN2	CLP1	Yes	RNA endonuclease (SEN2deltaEx8, SEN54, CLP1);tRNA splicing endonuclease	3	TSEN34, TSEN15, TSEN54
TSEN2	TSEN54	Yes	RNA endonuclease (SEN2deltaEx8, SEN54, CLP1);tRNA splicing endonuclease	3	TSEN34, TSEN15, CLP1
CLP1	TSEN54	Yes	RNA endonuclease (SEN2deltaEx8, SEN54, CLP1);tRNA splicing endonuclease	3	TSEN2, TSEN34, TSEN15

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

Interactions from CENSUS

Interactions from PDB

Interactions from manually curated literature

KEGG pathways annotation: shared terms / NET-GE enrichment

Shared terms

KEGG term	KEGG term ID	IC	Number of genes with the same term	Genes
Aminoacyl-tRNA biosynthesis	hsa00970	7.31	2	SEPSECS, RARS2

NET-GE enrichment

Term	New enriched term	IC	P value	Genes
Aminoacyl-tRNA biosynthesis (hsa00970)	-	7.31	0.01	SEPSECS, RARS2

REACTOME pathways annotation: shared terms (no NET-GE enrichment)

Shared terms

REACTOME term	REACTOME term ID	IC	Number of genes with the same term	Genes
Gene Expression	R-HSA-74160	2.72	3	RARS2, EXOSC3, CLP1

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

Shared terms

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GO	IC	Number of genes with the same GO	Genes
tRNA-intron endonuclease activity (GO:0000213)	8.35	3	TSEN2, TSEN34, TSEN54
endoribonuclease activity, producing 3'-phosphomonoesters (GO:0016892)	7.34	3	TSEN2, TSEN34, TSEN54
tRNA-specific ribonuclease activity (GO:0004549)	6.97	3	TSEN2, TSEN34, TSEN54
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters (GO:0016894)	6.74	3	TSEN2, TSEN34, TSEN54
endoribonuclease activity (GO:0004521)	5.58	3	TSEN2, TSEN34, TSEN54
ribonuclease activity (GO:0004540)	5.04	4	TSEN2, TSEN34, TSEN54, EXOSC3
endonuclease activity (GO:0004519)	4.78	3	TSEN2, TSEN34, TSEN54
lyase activity (GO:0016829)	4.53	2	TSEN2, TSEN34
nuclease activity (GO:0004518)	4.33	4	TSEN2, TSEN34, TSEN54, EXOSC3
hydrolase activity, acting on ester bonds (GO:0016788)	3.1	4	TSEN2, TSEN34, TSEN54, EXOSC3

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
tRNA-intron endonuclease activity (GO:0000213)	-	8.35	0.0	TSEN2, TSEN34
endoribonuclease activity, producing 3'-phosphomonoesters (GO:0016892)	-	7.34	0.002	TSEN2, TSEN34
tRNA-specific ribonuclease activity (GO:0004549)	-	6.97	0.0	TSEN2, TSEN34, CLP1
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 3'-phosphomonoesters (GO:0016894)	-	6.74	0.0	TSEN2, TSEN34, CLP1
endoribonuclease activity (GO:0004521)	-	5.58	0.003	TSEN2, TSEN34, CLP1
ribonuclease activity (GO:0004540)	-	5.04	0.002	TSEN2, TSEN34, EXOSC3, CLP1
nuclease activity (GO:0004518)	-	4.33	0.034	TSEN2, TSEN34, EXOSC3, CLP1

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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
tRNA-type intron splice site recognition and cleavage (GO:0000379)	8.63	3	TSEN2, TSEN34, TSEN54
tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	7.02	4	TSEN2, TSEN34, TSEN54, CLP1
RNA splicing, via endonucleolytic cleavage and ligation (GO:0000394)	6.96	4	TSEN2, TSEN34, TSEN54, CLP1
RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	5.41	3	TSEN2, TSEN34, TSEN54
RNA 3'-end processing (GO:0031123)	5.15	2	EXOSC3, CLP1
tRNA processing (GO:0008033)	4.96	4	TSEN2, TSEN34, TSEN54, CLP1
RNA phosphodiester bond hydrolysis (GO:0090501)	4.83	5	TSEN2, TSEN34, EXOSC3, TSEN54, CLP1
tRNA metabolic process (GO:0006399)	4.52	7	SEPSECS, RARS2, TSEN54, TSEN34, CLP1, EXOSC3, TSEN2
vacuolar transport (GO:0007034)	4.18	2	CHMP1A, VPS53
establishment of organelle localization (GO:0051656)	4.15	2	CHMP1A, PCLO

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	-	7.02	0.0	TSEN2, TSEN34, TSEN54, CLP1
RNA splicing, via endonucleolytic cleavage and ligation (GO:0000394)	-	6.96	0.0	TSEN2, TSEN34, TSEN54, CLP1
RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	-	5.41	0.024	TSEN2, TSEN34, CLP1
tRNA processing (GO:0008033)	-	4.96	0.004	TSEN2, TSEN34, TSEN54, CLP1
RNA phosphodiester bond hydrolysis (GO:0090501)	-	4.83	0.013	TSEN2, TSEN34, EXOSC3, CLP1
tRNA metabolic process (GO:0006399)	-	4.52	0.0	SEPSECS, RARS2, TSEN54, TSEN34, CLP1, TSEN2
RNA splicing (GO:0008380)	-	3.85	0.02	TSEN2, TSEN34, TSEN54, CLP1
ncRNA processing (GO:0034470)	-	3.77	0.007	TSEN2, TSEN54, TSEN34, EXOSC3, CLP1
ncRNA metabolic process (GO:0034660)	-	3.44	0.0	SEPSECS, RARS2, TSEN54, TSEN34, CLP1, EXOSC3, TSEN2
mRNA metabolic process (GO:0016071)	-	3.33	0.015	TSEN2, TSEN54, TSEN34, CLP1, EXOSC3

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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
tRNA-intron endonuclease complex (GO:0000214)	8.42	4	TSEN2, TSEN34, TSEN54, CLP1
endoribonuclease complex (GO:1902555)	6.76	4	TSEN2, TSEN34, TSEN54, CLP1
endosome membrane (GO:0010008)	3.83	2	CHMP1A, VPS53
endosomal part (GO:0044440)	3.73	2	CHMP1A, VPS53
vacuolar membrane (GO:0005774)	3.45	2	CHMP1A, VPS53
microtubule organizing center (GO:0005815)	3.42	2	TSEN2, CHMP1A
vacuolar part (GO:0044437)	3.26	2	CHMP1A, VPS53
endosome (GO:0005768)	3.25	2	CHMP1A, VPS53
nucleolus (GO:0005730)	3.06	5	TSEN2, TSEN34, EXOSC3, VRK1, TSEN54
Golgi apparatus part (GO:0044431)	3.0	2	VRK1, VPS53

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
tRNA-intron endonuclease complex (GO:0000214)	-	8.42	0.0	TSEN2, TSEN34, CLP1
endoribonuclease complex (GO:1902555)	-	6.76	0.0	TSEN2, TSEN34, CLP1
non-membrane-bounded organelle (GO:0043228)	-	1.76	0.036	CHMP1A, TSEN54, TSEN34, PCLO, EXOSC3, TSEN2, VRK1
intracellular non-membrane-bounded organelle (GO:0043232)	-	1.76	0.036	CHMP1A, TSEN54, TSEN34, PCLO, EXOSC3, TSEN2, VRK1

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