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	lissencephaly 1

Disease ID	1760
Disease	lissencephaly 1
Definition	A genetic disorder caused by mutations in the LIS1, XLIS, or TUBA1A genes. It results in brain malformation characterized by the underdevelopment or absence of gyri or ridges in the cerebral cortex. Signs and symptoms include epilepsy and mental retardation.
Synonym	classic lissencephaly classical lissencephalies classical lissencephaly classical lissencephaly syndrome ils isolated lissencephaly sequence lis1 lissencephalies, classical lissencephalies, type 1 lissencephaly sequence, isolated lissencephaly type 001 lissencephaly type 1 lissencephaly type i lissencephaly, classic lissencephaly, classical lissencephaly, type 1 lissencephaly, type i type 1 lissencephalies type 1 lissencephaly type 1 lissencephaly (disorder) type i lissencephaly
Orphanet	ORPHANET:102009
OMIM	OMIM:607432
UMLS	C0431375
SNOMED-CT	SNOMEDCT_US_2016_09_01:253147000
Comorbidity	UMLS \| Disease \| Sentences' Count(Total Sentences:5) C0266463 \| lissencephaly \| 3 C0006111 \| brain disease \| 1 C0004352 \| autism \| 1 C0023903 \| liver cancer \| 1 C0027765 \| neurological disorder \| 1
Curated Gene	Entrez_id \| Symbol \| Resource(Total Genes:1) 5048 \| PAFAH1B1 \| OMIM;ORPHANET;UNIPROT
Inferring Gene	(Waiting for update.)
Text Mined Gene	(Waiting for update.)
Locus	(Waiting for update.)

Disease ID	1760
Disease	lissencephaly 1
Integrated Phenotype	(Waiting for update.)
Text Mined Phenotype	HPO \| Name \| Sentences' Count(Total Phenotypes:8) HP:0001339 \| Lissencephaly \| 5 HP:0000717 \| Autism \| 1 HP:0001274 \| Absent corpus callosum \| 1 HP:0002282 \| Heterotopias \| 1 HP:0008066 \| Skin bullae \| 1 HP:0002896 \| Liver cancer \| 1 HP:0002539 \| Cortical dysplasia \| 1 HP:0001321 \| Small cerebellum \| 1

Disease ID	1760
Disease	lissencephaly 1
Manually Symptom	(Waiting for update.)
Text Mined Symptom	(Waiting for update.)

Manually Genotype(Total Text Mining Genotypes:0)
(Waiting for update.)

Text Mining Genotype(Total Genotypes:0)
(Waiting for update.)

All Snps(Total Genotypes:3)
snpId	pubmedId	geneId	geneSymbol	diseaseId	sourceId	sentence	score	Year	geneSymbol_dbSNP	CHROMOSOME	POS	REF	ALT
rs28936410	11502906	5048	PAFAH1B1	umls:C0431375	UNIPROT	The authors suggest that the few patients found thus far with missense mutations of LIS1 results from an underascertainment of patients with more subtle malformations and that abnormalities of the LIS1 gene may account for a greater spectrum of neurologic problems in childhood than has previously been appreciated.	0.327328931	2001	NA	NA	NA	NA	NA
rs28936411	14581661	5048	PAFAH1B1	umls:C0431375	UNIPROT	Mosaic mutations of the LIS1 gene cause subcortical band heterotopia.	0.327328931	2003	NA	NA	NA	NA	NA
rs28936689	11502906	5048	PAFAH1B1	umls:C0431375	UNIPROT	The authors suggest that the few patients found thus far with missense mutations of LIS1 results from an underascertainment of patients with more subtle malformations and that abnormalities of the LIS1 gene may account for a greater spectrum of neurologic problems in childhood than has previously been appreciated.	0.327328931	2001	NA	NA	NA	NA	NA

GWASdb Annotation(Total Genotypes:3)
Chr	Pos	SNP_Id	RefGene	EnsemblGene	ENCODE_Factor	ENCODE_TFBS	Chromosome_interaction	GTEx_eQTL	SNP_TFBS_affinity_GWAS3D	SNP_miRNA_target_affinity_PolymiRTS	SNP_splicing_effect_Skippy	SNP_splicing_effect_MutPred_Splice	SNP_ns_protein_effect_dbNSFP	SNP_syn_effect_Silva	SNP_phosphorylation_effect_PhosSNP	PhastCons_score	PhyloP_score	GERP++_RS	Segway_state	Ancestral_allele	ESP_AF	ESP_AFR	ESP_AFR	ESP_EUR	TG_ASN	TG_AMR	TG_AFR	TG_EUR	Type	Consequence	bStatistic	EncH3K27Ac	EncH3K4Me1	EncH3K4Me3	EncNucleo	OMIM	Clinvar
17	2545473	rs8077351	NM_000430,PAFAH1B1	ENST00000451360,ENSG00000007168	ENST00000397195,ENSG00000007168	ENST00000006951,ENSG00000007168	NA	NA	NA	NA	Sfl1-DBD-primary,1.5202	Sut2-primary,1.6034	Ynr063w-primary,2.2647	LM61,2.9484	LM191,4.0633	NA	NA	NA	NA	NA	NA	0.030	0.726	0.988	GE0	A	NA	NA	NA	NA	NA	NA	NA	NA	Transcript	INTRONIC	600
17	2577091	rs2317297	NM_000430,PAFAH1B1	ENST00000451360,ENSG00000007168	ENST00000397195,ENSG00000007168	ENST00000006951,ENSG00000007168	ENST00000397193,ENSG00000007168	ENST00000500520,ENSG00000247061	NA	NA	chr17,2570001,2580000,chr17,2590001,2600000,27,Hi-C	chr17,2570001,2580000,chr17,4440001,4450000,7,Hi-C	chr17,2570001,2580000,chr17,1640001,1650000,10,Hi-C	chr17,2570001,2580000,chr17,2610001,2620000,6,Hi-C	chr17,2570001,2580000,chr17,2610001,2620000,6,Hi-C	chr17,2570001,2580000,chr10,32260001,32270000,7,Hi-C	NA	LM15,1.812	LM43,2.0465	LM67,1.8687	LM78,3.5109	LM81,1.6239	NA	NA	NA	NA	NA	NA	0.130	0.146	1.09	F1	T	NA	NA	NA	NA
17	2578648	rs4790353	NM_000430,PAFAH1B1	ENST00000451360,ENSG00000007168	ENST00000397195,ENSG00000007168	ENST00000006951,ENSG00000007168	ENST00000397193,ENSG00000007168	TFP.CTCF	TFP.RAD21	TFP.SMC3	DRM	NA	chr17,2570001,2580000,chr17,2590001,2600000,27,Hi-C	chr17,2570001,2580000,chr17,4440001,4450000,7,Hi-C	chr17,2570001,2580000,chr17,1640001,1650000,10,Hi-C	chr17,2570001,2580000,chr17,2610001,2620000,6,Hi-C	chr17,2570001,2580000,chr17,2610001,2620000,6,Hi-C	chr17,2570001,2580000,chr10,32260001,32270000,7,Hi-C	NA	LM41,3.4227	LM51,4.0972	LM56,3.0599	LM69,2.1736	LM85,12.564	NA	NA	NA	NA	NA	NA	0.000	-0.055	-0.204	C1	T	NA	NA

GWASdb Snp Trait(Total Genotypes:0)
(Waiting for update.)

Mapped by lexical matching(Total Items:0)
(Waiting for update.)

Mapped by homologous gene(Total Items:0)
(Waiting for update.)

Disease ID	1760
Disease	lissencephaly 1
Case	(Waiting for update.)

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