Disease table of RHIZOMELIC CHONDRODYSPLASIA PUNCTATA OMIM ID: PS215100

Gene-disease associations table

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Gene	Associated with RHIZOMELIC CHONDRODYSPLASIA PUNCTATA in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
AGPS	ClinVar, OMIM, HUMSAVAR	HGNC link	2q31.2	1	PS215100
GNPAT	ClinVar, OMIM, HUMSAVAR	HGNC link	1q42.2	1	PS215100
PEX5	ClinVar, OMIM	HGNC link	12p13.31	2	PS214100, PS215100
PEX7	ClinVar, OMIM, HUMSAVAR	HGNC link	6q23.3	3	PS214100, 266500, PS215100

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Download the disease annotation in CSV format

Relations among genes:

Tandem repeat annotations from DGD

Cytogenetic band analysis

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
AGPS	PEX5	Yes	4	GNPAT, PEX14, SCP2, CCDC8
AGPS	GNPAT	Yes	3	NTRK1, PEX14, PEX5
PEX5	PEX7	Yes	3	ACAA1, PEX14, PEX13
PEX5	GNPAT	Yes	3	AGPS, PEX14, XPO1
AGPS	PEX7	No	2	PEX14, PEX5
PEX7	GNPAT	No	2	PEX14, PEX5

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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
AGPS	PEX5	Yes	binding	2	UBC, GNPAT
AGPS	GNPAT	Yes	binding	2	UBC, PEX5
PEX5	PEX7	Yes	binding	2	PEX14, PEX13
PEX5	GNPAT	Yes	binding	2	UBC, AGPS
AGPS	PEX7	No	-	1	PEX5
PEX7	GNPAT	No	-	1	PEX5

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

Interactions from CORUM

Gene1	Gene2	Direct Interaction	Complexes	Number of shared interactors	Shared genes in interaction
AGPS	GNPAT	Yes	AGPS-GNPAT complex	0

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
Peroxisome	hsa04146	6.34	4	AGPS, GNPAT, PEX7, PEX5

NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Biosynthesis of unsaturated fatty acids (hsa01040)	NEW	8.38	0.002	PEX7, PEX5
alpha-Linolenic acid metabolism (hsa00592)	NEW	8.12	0.004	PEX7, PEX5
Fatty acid degradation (hsa00071)	NEW	7.15	0.014	PEX7, PEX5
Fatty acid metabolism (hsa01212)	NEW	7.07	0.013	PEX7, PEX5
PPAR signaling pathway (hsa03320)	NEW	6.56	0.048	PEX7, PEX5
Peroxisome (hsa04146)	-	6.34	0.0	AGPS, GNPAT, PEX7, PEX5
Lipid metabolism	NEW	4.16	0.003	AGPS, GNPAT, PEX7, PEX5
Transport and catabolism	NEW	3.49	0.001	AGPS, GNPAT, PEX7, PEX5
Cellular Processes	NEW	2.22	0.021	AGPS, GNPAT, PEX7, PEX5

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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
Plasmalogen biosynthesis	R-HSA-75896	10.98	2	AGPS, GNPAT
Peroxisomal lipid metabolism	R-HSA-390918	8.59	2	AGPS, GNPAT
Metabolism of lipids and lipoproteins	R-HSA-556833	3.79	2	AGPS, GNPAT
Metabolism	R-HSA-1430728	2.34	2	AGPS, GNPAT

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
Plasmalogen biosynthesis (R-HSA-75896)	-	10.98	0.0	AGPS, GNPAT
Beta-oxidation of very long chain fatty acids (R-HSA-390247)	NEW	10.4	0.0	PEX7, PEX5
alpha-linolenic acid (ALA) metabolism (R-HSA-2046106)	NEW	9.28	0.001	PEX7, PEX5
alpha-linolenic (omega3) and linoleic (omega6) acid metabolism (R-HSA-2046104)	NEW	9.28	0.001	PEX7, PEX5
Peroxisomal lipid metabolism (R-HSA-390918)	-	8.59	0.0	AGPS, GNPAT, PEX7, PEX5
Metabolism of lipids and lipoproteins (R-HSA-556833)	-	3.79	0.042	AGPS, GNPAT, PEX7, PEX5

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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
peroxisome targeting sequence binding (GO:0000268)	8.13	2	PEX7, PEX5
signal sequence binding (GO:0005048)	6.07	2	PEX7, PEX5
peptide binding (GO:0042277)	4.22	2	PEX7, PEX5
amide binding (GO:0033218)	4.14	2	PEX7, PEX5
enzyme binding (GO:0019899)	2.27	2	PEX7, PEX5
transferase activity (GO:0016740)	1.95	2	AGPS, GNPAT
catalytic activity (GO:0003824)	1.05	2	AGPS, GNPAT
protein binding (GO:0005515)	0.46	4	AGPS, GNPAT, PEX7, PEX5
binding (GO:0005488)	0.18	4	AGPS, GNPAT, PEX7, PEX5

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
peroxisome targeting sequence binding (GO:0000268)	-	8.13	0.0	PEX7, PEX5
oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor (GO:0016634)	NEW	7.54	0.0	PEX7, PEX5
FAD binding (GO:0071949)	NEW	7.03	0.001	AGPS, PEX5
signal sequence binding (GO:0005048)	-	6.07	0.003	PEX7, PEX5
oxidoreductase activity, acting on the CH-CH group of donors (GO:0016627)	NEW	5.66	0.025	PEX7, PEX5
flavin adenine dinucleotide binding (GO:0050660)	NEW	5.41	0.044	AGPS, PEX5
peptide binding (GO:0042277)	-	4.22	0.047	PEX7, PEX5
cofactor binding (GO:0048037)	NEW	4.16	0.0	AGPS, GNPAT, PEX7, PEX5
amide binding (GO:0033218)	-	4.14	0.049	PEX7, PEX5
oxidoreductase activity (GO:0016491)	NEW	3.12	0.013	AGPS, GNPAT, PEX7, PEX5

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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
cellular lipid biosynthetic process (GO:0097384)	8.34	3	AGPS, GNPAT, PEX7
ether lipid biosynthetic process (GO:0008611)	8.34	3	AGPS, GNPAT, PEX7
ether biosynthetic process (GO:1901503)	8.34	3	AGPS, GNPAT, PEX7
glycerol ether biosynthetic process (GO:0046504)	8.34	3	AGPS, GNPAT, PEX7
ether lipid metabolic process (GO:0046485)	7.94	3	AGPS, GNPAT, PEX7
protein import into peroxisome matrix (GO:0016558)	7.43	2	PEX7, PEX5
glycerol ether metabolic process (GO:0006662)	7.33	3	AGPS, GNPAT, PEX7
ether metabolic process (GO:0018904)	7.16	3	AGPS, GNPAT, PEX7
establishment of protein localization to peroxisome (GO:0072663)	7.02	2	PEX7, PEX5
protein localization to peroxisome (GO:0072662)	7.02	2	PEX7, PEX5

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
ether lipid biosynthetic process (GO:0008611)	-	8.34	0.0	AGPS, GNPAT, PEX7, PEX5
glycerol ether biosynthetic process (GO:0046504)	-	8.34	0.0	AGPS, GNPAT, PEX7, PEX5
cellular lipid biosynthetic process (GO:0097384)	-	8.34	0.0	AGPS, GNPAT, PEX7, PEX5
ether biosynthetic process (GO:1901503)	-	8.34	0.0	AGPS, GNPAT, PEX7, PEX5
ether lipid metabolic process (GO:0046485)	-	7.94	0.0	AGPS, GNPAT, PEX7, PEX5
protein import into peroxisome matrix (GO:0016558)	-	7.43	0.0	PEX7, PEX5
glycerol ether metabolic process (GO:0006662)	-	7.33	0.0	AGPS, GNPAT, PEX7, PEX5
ether metabolic process (GO:0018904)	-	7.16	0.0	AGPS, GNPAT, PEX7, PEX5
alpha-linolenic acid metabolic process (GO:0036109)	NEW	7.16	0.002	PEX7, PEX5
fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)	NEW	7.16	0.002	PEX7, PEX5

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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
peroxisomal matrix (GO:0005782)	6.0	4	AGPS, GNPAT, PEX7, PEX5
microbody lumen (GO:0031907)	6.0	4	AGPS, GNPAT, PEX7, PEX5
peroxisomal membrane (GO:0005778)	5.76	3	AGPS, GNPAT, PEX5
microbody membrane (GO:0031903)	5.76	3	AGPS, GNPAT, PEX5
peroxisomal part (GO:0044439)	5.28	4	AGPS, GNPAT, PEX7, PEX5
microbody part (GO:0044438)	5.28	4	AGPS, GNPAT, PEX7, PEX5
peroxisome (GO:0005777)	5.01	4	AGPS, GNPAT, PEX7, PEX5
microbody (GO:0042579)	4.93	4	AGPS, GNPAT, PEX7, PEX5
organelle lumen (GO:0043233)	3.05	4	AGPS, GNPAT, PEX7, PEX5
membrane-enclosed lumen (GO:0031974)	3.05	4	AGPS, GNPAT, PEX7, PEX5

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
peroxisomal matrix (GO:0005782)	-	6.0	0.0	AGPS, GNPAT, PEX7, PEX5
microbody lumen (GO:0031907)	-	6.0	0.0	AGPS, GNPAT, PEX7, PEX5
peroxisomal membrane (GO:0005778)	-	5.76	0.0	AGPS, GNPAT, PEX5
microbody membrane (GO:0031903)	-	5.76	0.0	AGPS, GNPAT, PEX5
peroxisomal part (GO:0044439)	-	5.28	0.0	AGPS, GNPAT, PEX7, PEX5
microbody part (GO:0044438)	-	5.28	0.0	AGPS, GNPAT, PEX7, PEX5
peroxisome (GO:0005777)	-	5.01	0.0	AGPS, GNPAT, PEX7, PEX5
microbody (GO:0042579)	-	4.93	0.0	AGPS, GNPAT, PEX7, PEX5
organelle lumen (GO:0043233)	-	3.05	0.0	AGPS, GNPAT, PEX7, PEX5
membrane-enclosed lumen (GO:0031974)	-	3.05	0.011	AGPS, GNPAT, PEX7, PEX5

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