Disease table of LISSENCEPHALY OMIM ID: PS607432

Gene-disease associations table

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Gene	Associated with LISSENCEPHALY in	Link to HGNC	Cytogenetic band	Number of associated diseases	Associated diseases
APOC3	ClinVar, OMIM, HUMSAVAR	HGNC link	11q23.3	1	PS607432
ARX	ClinVar, OMIM, HUMSAVAR	HGNC link	Xp21.3	5	PS607432, PS309510, 300004, PS308350, PS309530
CDK5	ClinVar, OMIM	HGNC link	7q36.1	1	PS607432
DCX	ClinVar, OMIM, HUMSAVAR	HGNC link	Xq23	1	PS607432
KATNB1	ClinVar, OMIM, HUMSAVAR	HGNC link	16q21	1	PS607432
LAMB1	ClinVar, OMIM	HGNC link	7q31.1	1	PS607432
PAFAH1B1	ClinVar, OMIM, HUMSAVAR	HGNC link	17p13.3	1	PS607432
RELN	ClinVar, OMIM	HGNC link	7q22.1	2	PS600512, PS607432
TUBA1A	ClinVar, OMIM, HUMSAVAR	HGNC link	12q13.12	1	PS607432

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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
7q3	2	LAMB1, CDK5

By arm

Shared arm	Number of genes associated with the disease	Genes associated with the disease
7q	3	RELN, LAMB1, CDK5

By chromosome

Shared chromosome	Number of genes associated with the disease	Genes associated with the disease
7	3	RELN, LAMB1, CDK5
X	2	DCX, ARX

Transcription Factors (TF) annotation from TRRUST

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TF	associated to this disease	# regulated genes	Regulated genes	# regulated genes associated with this disease	Regulated genes associated with this disease
ARX	YES	1	KDM5C	0

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regulated gene	associated to this disease	# TFs	TFs
RELN	YES	4	HDAC1, DNMT1, TBR1, MECP2
APOC3	YES	10	SP1, PPARGC1A, NR2F6, NR2F1, SMAD4, JUN, SMAD3, ATF2, PPARA, HNF4A
LAMB1	YES	2	SSB, NANOG

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Interactions from BIOGRID - physical

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Gene1	Gene2	Direct Interaction	Number of shared interactors	Shared genes in interaction
TUBA1A	PAFAH1B1	Yes	7	NDEL1, PAFAH1B1, HSP90AA1, MAPRE1, IQCB1, CLIP1, NTRK1
KATNB1	PAFAH1B1	Yes	5	DYNC1H1, KATNB1, NDEL1, KATNA1, PAFAH1B1
DCX	PAFAH1B1	Yes	3	NTRK1, DCX, PAFAH1B1
TUBA1A	KATNB1	No	3	SSX2IP, NDEL1, PAFAH1B1
TUBA1A	RELN	No	1	SQSTM1
TUBA1A	DCX	No	2	NTRK1, PAFAH1B1
TUBA1A	LAMB1	No	4	NTRK1, UBC, TMEM25, FBXO6
TUBA1A	CDK5	No	12	CDKN1A, NDEL1, EGFR, MAPT, PARK2, TP53, HSP90AA1, HSP90AB1, NTRK1, UCHL1, TLN1, HTRA2
KATNB1	DCX	No	1	PAFAH1B1
KATNB1	CDK5	No	1	NDEL1

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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
ARX	TUBA1A	Yes	binding	0
TUBA1A	PAFAH1B1	Yes	binding	79	CEP76, TUBGCP5, CDK1, CDK5RAP2, CEP57, CSNK1E, SSNA1, ACTR1A, YWHAE, CEP152, FGFR1OP, CEP78, ALMS1, CSNK1D, TUBG2, PLK1, TUBG1, TUBA4A, TUBGCP6, PRKACA, TUBA1B, CEP135, CLASP2, SFI1, DCTN2, CEP250, DYNLL1, TUBGCP2, MAPRE1, TUBA1C, TUBB4A, DYNC1H1, OFD1, DYNC1I2, SDCCAG8, CLIP1, YWHAG, ARL6, CEP164, NEDD1, AJUBA, CEP63, DNAH17, CCP110, DCTN3, CKAP5, AZI1, PRKAR2B, MAPRE3, HSP90AA1, ODF2, CENPJ, NINL, KIF19, CEP70, PPP2R1A, DNAH11, BORA, TUBGCP3, CEP290, DNAH9, HAUS2, DYNC1I1, KIF18B, TUBB4B, AURKA, CLASP1, NEK2, CNTRL, TUBGCP4, CEP72, PCM1, DYNC2H1, CEP192, UBC, ARL3, PCNT, PLK4, NDE1
RELN	PAFAH1B1	Yes	activation, binding	6	PAFAH1B2, MAP1B, VLDLR, DAB1, AURKB, PAFAH1B3
DCX	PAFAH1B1	Yes	binding	0
DCX	CDK5	Yes	binding, ptmod	2	JUN, CDH2
ARX	PAFAH1B1	No	-	1	TUBA1A
ARX	CDK5	No	-	2	MEF2C, MEF2A
TUBA1A	RELN	No	-	1	PAFAH1B1
TUBA1A	APOC3	No	-	1	PPARA
TUBA1A	DCX	No	-	1	PAFAH1B1

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

Interactions from CORUM

Interactions from CENSUS

Interactions from PDB

Interactions from manually curated literature

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
ECM-receptor interaction	hsa04512	6.09	2	LAMB1, RELN
Focal adhesion	hsa04510	4.92	2	LAMB1, RELN
PI3K-Akt signaling pathway	hsa04151	4.21	2	LAMB1, RELN

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NET-GE enrichment

Term	New enriched term	IC	P value	Genes
Toxoplasmosis (hsa05145)	NEW	5.71	0.005	LAMB1, TUBA1A, RELN, CDK5

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
Loss of Nlp from mitotic centrosomes	R-HSA-380259	7.03	2	TUBA1A, PAFAH1B1
Loss of proteins required for interphase microtubule organizationÂ from the centrosome	R-HSA-380284	7.03	2	TUBA1A, PAFAH1B1
Recruitment of mitotic centrosome proteins and complexes	R-HSA-380270	6.68	2	TUBA1A, PAFAH1B1
Centrosome maturation	R-HSA-380287	6.68	2	TUBA1A, PAFAH1B1
Regulation of PLK1 Activity at G2/M Transition	R-HSA-2565942	6.66	2	TUBA1A, PAFAH1B1
Anchoring of the basal body to the plasma membrane	R-HSA-5620912	6.51	2	TUBA1A, PAFAH1B1
L1CAM interactions	R-HSA-373760	6.19	3	LAMB1, TUBA1A, DCX
Resolution of Sister Chromatid Cohesion	R-HSA-2500257	6.18	2	TUBA1A, PAFAH1B1
Mitotic Prometaphase	R-HSA-68877	6.08	2	TUBA1A, PAFAH1B1
G2/M Transition	R-HSA-69275	6.06	2	TUBA1A, PAFAH1B1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
DARPP-32 events (R-HSA-180024)	NEW	8.4	0.029	CDK5, PAFAH1B1
L1CAM interactions (R-HSA-373760)	-	6.19	0.004	DCX, LAMB1, TUBA1A, PAFAH1B1, CDK5
RHO GTPases Activate Formins (R-HSA-5663220)	-	6.01	0.034	TUBA1A, CDK5, PAFAH1B1
Axon guidance (R-HSA-422475)	-	3.93	0.018	DCX, LAMB1, TUBA1A, CDK5

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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
lipoprotein particle receptor binding (GO:0070325)	6.65	2	APOC3, RELN
dynein binding (GO:0045502)	6.44	2	KATNB1, PAFAH1B1
microtubule binding (GO:0008017)	4.42	3	KATNB1, DCX, PAFAH1B1
tubulin binding (GO:0015631)	4.1	3	KATNB1, DCX, PAFAH1B1
protein serine/threonine kinase activity (GO:0004674)	3.64	2	CDK5, DCX
protein kinase binding (GO:0019901)	3.44	2	CDK5, DCX
kinase binding (GO:0019900)	3.32	2	CDK5, DCX
protein kinase activity (GO:0004672)	3.27	3	CDK5, RELN, DCX
structural molecule activity (GO:0005198)	3.1	2	LAMB1, TUBA1A
nucleoside-triphosphatase activity (GO:0017111)	3.09	2	TUBA1A, KATNB1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
histone kinase activity (GO:0035173)	NEW	6.79	0.016	TUBA1A, CDK5
lipoprotein particle receptor binding (GO:0070325)	-	6.65	0.004	APOC3, RELN
dynein binding (GO:0045502)	-	6.44	0.018	KATNB1, PAFAH1B1
microtubule binding (GO:0008017)	-	4.42	0.01	DCX, TUBA1A, KATNB1, PAFAH1B1, CDK5
tubulin binding (GO:0015631)	-	4.1	0.026	DCX, TUBA1A, KATNB1, PAFAH1B1, CDK5
protein complex binding (GO:0032403)	NEW	3.09	0.046	DCX, LAMB1, KATNB1, PAFAH1B1

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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
cerebral cortex tangential migration (GO:0021800)	7.78	2	RELN, ARX
layer formation in cerebral cortex (GO:0021819)	7.24	4	DCX, CDK5, RELN, PAFAH1B1
positive regulation of dendritic spine morphogenesis (GO:0061003)	7.09	2	RELN, PAFAH1B1
protein localization to synapse (GO:0035418)	6.96	2	CDK5, RELN
central nervous system projection neuron axonogenesis (GO:0021952)	6.73	2	DCX, PAFAH1B1
central nervous system neuron axonogenesis (GO:0021955)	6.51	2	DCX, PAFAH1B1
cerebral cortex cell migration (GO:0021795)	6.36	2	RELN, ARX
regulation of dendritic spine morphogenesis (GO:0061001)	6.33	3	CDK5, RELN, PAFAH1B1
dendrite morphogenesis (GO:0048813)	6.26	2	CDK5, DCX
central nervous system neuron development (GO:0021954)	6.26	2	CDK5, DCX

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
cerebral cortex tangential migration (GO:0021800)	-	7.78	0.0	TUBA1A, RELN, PAFAH1B1, ARX
layer formation in cerebral cortex (GO:0021819)	-	7.24	0.0	CDK5, RELN, PAFAH1B1
protein localization to synapse (GO:0035418)	-	6.96	0.024	CDK5, RELN
cell proliferation in forebrain (GO:0021846)	NEW	6.96	0.001	TUBA1A, PAFAH1B1, ARX
central nervous system projection neuron axonogenesis (GO:0021952)	-	6.73	0.004	CDK5, DCX, PAFAH1B1
central nervous system neuron axonogenesis (GO:0021955)	-	6.51	0.009	CDK5, DCX, PAFAH1B1
cerebral cortex cell migration (GO:0021795)	-	6.36	0.0	TUBA1A, RELN, PAFAH1B1, ARX, CDK5
regulation of dendritic spine morphogenesis (GO:0061001)	-	6.33	0.038	CDK5, RELN
dendrite morphogenesis (GO:0048813)	-	6.26	0.0	DCX, TUBA1A, CDK5, PAFAH1B1
axon extension (GO:0048675)	-	6.12	0.014	CDK5, DCX, PAFAH1B1

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

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GO	IC	Number of genes with the same GO	Genes
cytoplasmic microtubule (GO:0005881)	5.74	2	TUBA1A, PAFAH1B1
growth cone (GO:0030426)	4.89	3	KATNB1, CDK5, PAFAH1B1
site of polarized growth (GO:0030427)	4.85	3	KATNB1, CDK5, PAFAH1B1
microtubule associated complex (GO:0005875)	4.79	3	KATNB1, DCX, PAFAH1B1
microtubule cytoskeleton (GO:0015630)	4.78	2	KATNB1, PAFAH1B1
spindle (GO:0005819)	4.52	2	KATNB1, PAFAH1B1
axon (GO:0030424)	4.15	3	KATNB1, CDK5, PAFAH1B1
proteinaceous extracellular matrix (GO:0005578)	4.01	2	LAMB1, RELN
dendrite (GO:0030425)	3.92	3	CDK5, DCX, RELN
neuronal cell body (GO:0043025)	3.9	3	KATNB1, CDK5, PAFAH1B1

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NET-GE enrichment

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Term	New enriched term	IC	P value	Genes
low-density lipoprotein particle (GO:0034362)	NEW	7.16	0.013	APOC3, PAFAH1B1
protein-lipid complex (GO:0032994)	NEW	6.11	0.002	APOC3, CDK5, PAFAH1B1
cell leading edge (GO:0031252)	NEW	6.04	0.033	CDK5, PAFAH1B1
cytoplasmic microtubule (GO:0005881)	-	5.74	0.023	TUBA1A, PAFAH1B1
growth cone (GO:0030426)	-	4.89	0.002	KATNB1, CDK5, PAFAH1B1
site of polarized growth (GO:0030427)	-	4.85	0.002	KATNB1, CDK5, PAFAH1B1
microtubule associated complex (GO:0005875)	-	4.79	0.0	DCX, TUBA1A, KATNB1, PAFAH1B1, CDK5
neuronal cell body (GO:0043025)	-	3.9	0.021	KATNB1, CDK5, PAFAH1B1
microtubule (GO:0005874)	-	3.81	0.001	DCX, TUBA1A, KATNB1, PAFAH1B1, CDK5
cell body (GO:0044297)	-	3.74	0.033	KATNB1, CDK5, PAFAH1B1

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