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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: EIF2S3 (NCBI Gene ID:1968)

Gene Summary

Gene Summary

Gene Information	Gene Name: EIF2S3
	Gene ID: 1968
	Gene Symbol	EIF2S3
	Gene ID	1968
	Gene Name	eukaryotic translation initiation factor 2 subunit gamma
	Synonyms	EIF2\|EIF2G\|EIF2gamma\|MEHMO\|MRXSBRK\|eIF-2gA
	Cytomap	Xp22.11
	Type of Gene	protein-coding
	Description	eukaryotic translation initiation factor 2 subunit 3eIF-2-gamma XeIF-2gXeukaryotic translation initiation factor 2 subunit gamma Xeukaryotic translation initiation factor 2, subunit 3 gamma, 52kDaeukaryotic translation initiation factor 2G
	Modification date	20200313
	UniProtAcc	P41091

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0006417	Regulation of translation
GO:0008135	Translation factor activity, RNA binding
GO:0045727	Positive regulation of translation
GO:0002181	Cytoplasmic translation
GO:0006413	Translational initiation
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	EIF2S3	GO:0006413	translational initiation	10900014

Inferred gene age of translation factor.

Gene	Inferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
EIF2S3	>1119.25

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Translation Studies in PubMed

We searched PubMed using 'EIF2S3[title] AND translation [title] AND human.'

Gene	Title	PMID
EIF2S3	MEHMO syndrome mutation EIF2S3-I259M impairs initiator Met-tRNAiMet binding to eukaryotic translation initiation factor eIF2	30517694

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Exon Skipping Events

Skipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.

Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	ORF
ENST00000253039	24078204	24078299	Frame-shift
ENST00000253039	24080532	24080691	In-frame
ENST00000253039	24082317	24082452	In-frame
ENST00000253039	24084114	24084209	Frame-shift
ENST00000253039	24086080	24086225	Frame-shift
ENST00000253039	24089674	24089844	Frame-shift
ENST00000253039	24091207	24091380	Frame-shift

Exon skipping position in the amino acid sequence.

ENST	Exon skip start (DNA)	Exon Skip end (DNA)	Len(transcript seq)	Exon skip start (mRNA)	Exon Skip end (mRNA)	Len(amino acid seq)	Exon skip start (AA)	Exon Skip end (AA)
ENST00000253039	24080532	24080691	2875	732	890	472	159	212
ENST00000253039	24082317	24082452	2875	891	1025	472	212	257

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc	Exon skip start (AA)	Exon Skip end (AA)	Function feature start (AA)	Function feature end (AA)	Functional feature type	Functional feature desc.
P41091	159	212	2	472	Chain	ID=PRO_0000137438;Note=Eukaryotic translation initiation factor 2 subunit 3
P41091	212	257	2	472	Chain	ID=PRO_0000137438;Note=Eukaryotic translation initiation factor 2 subunit 3
P41091	159	212	39	248	Domain	Note=tr-type G;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01059
P41091	212	257	39	248	Domain	Note=tr-type G;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01059
P41091	159	212	190	193	Nucleotide binding	Note=GTP;Ontology_term=ECO:0000250;evidence=ECO:0000250
P41091	159	212	190	193	Region	Note=G4;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01059
P41091	212	257	225	227	Region	Note=G5;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01059
P41091	212	257	222	222	Natural variant	ID=VAR_077139;Note=In MEHMO%3B decreased interaction with the other eIF2 complex subunits EIF2S1 and EIF2S2. I->T;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23063529;Dbxref=dbSNP:rs886040855,PMID:23063529

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type	Translation factor	FC	adj.pval
LIHC	EIF2S3	-4.62530933210412	0.00154404530385922
ESCA	EIF2S3	-1.31322237574718	0.0419921875

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type

Gene

miRNA

TargetScan binding score (Context++ score percentile)

Coefficient

Pvalue

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through copy number variation of Translation factor

Cancer type	Gene	Coefficient	Pvalue
PAAD	EIF2S3	-0.303408041	0.002265862
SKCM	EIF2S3	-0.031584333	0.038957074

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with EIF2S3 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)

Cancer type	Gene group	Translation factor	Correlated gene	Coefficient	Pvalue
CHOL	Cell metabolism gene	EIF2S3	SLC25A6	0.838706284	6.40E-13
CHOL	IUPHAR	EIF2S3	SLC25A6	0.838706284	6.40E-13
UVM	TSG	EIF2S3	RBMX	0.81050733	8.38E-20

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

Overlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

* Edge colors based on TCGA cancer types.

* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))

Cancer type	Translation factor	Interacting protein coding gene	FC	adj.pval
LIHC	EIF2S3	EIF2B5	-2.17335102876885	0.000112780019881286
KICH	EIF2S3	EIF2B3	2.17795043401278	0.000216901302337646
HNSC	EIF2S3	EIF1	-4.13399438210909	0.000228392819053625
PRAD	EIF2S3	EIF3A	1.13680328391952	0.000363360004697762
THCA	EIF2S3	EIF2B3	-2.27193247701228	0.000372452864704637
BRCA	EIF2S3	EIF5	-1.16704316213885	0.00107943958337404
KICH	EIF2S3	EIF2S2	-1.06278646532411	0.00308787822723389
HNSC	EIF2S3	EIF2B3	-1.66956934127194	0.00459462782941955
KIRP	EIF2S3	EIF3G	-2.4178322962129	0.00471024587750435
BLCA	EIF2S3	EIF3A	-4.45104058307747	0.00532913208007812
PRAD	EIF2S3	EIF1	1.32822648991353	0.00674237731133815
COAD	EIF2S3	EIF2B3	-1.60183733464354	0.00938254594802858
COAD	EIF2S3	EIF2B5	-3.82949281161428	0.011966735124588
CHOL	EIF2S3	EIF2B2	-1.61211785827489	0.02734375
UCEC	EIF2S3	EIF3G	-3.35078334696571	0.03125
BLCA	EIF2S3	EIF3G	-3.07707559649091	0.0323410034179688
LUAD	EIF2S3	EIF3B	-5.80435587546762	1.0542655358657e-09
BRCA	EIF2S3	EIF2S2	-2.57303037687825	1.70212120584918e-09
BRCA	EIF2S3	EIF3G	1.87948385011271	1.9107949115022e-06
KIRC	EIF2S3	EIF3B	-1.56313263784517	2.35252849767166e-12
STAD	EIF2S3	EIF2S2	-2.13186277769467	3.17529775202275e-05
STAD	EIF2S3	EIF3B	-4.7724660972007	3.25962901115418e-08
LIHC	EIF2S3	EIF2B2	-1.75683032348821	4.08414278982391e-05
LUAD	EIF2S3	EIF2B2	-3.96081365689084	4.19177862905507e-09
HNSC	EIF2S3	EIF3B	2.6202554263604	4.48234413852334e-06
KIRP	EIF2S3	EIF3B	-2.7592297042974	4.6566128730774e-09
LIHC	EIF2S3	EIF5	-2.12060405382854	4.66164898670786e-08
BRCA	EIF2S3	EIF2B3	-1.42398409637427	6.27134207487183e-10
BRCA	EIF2S3	EIF3A	-1.218215573148	7.39403582934137e-06

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with EIF2S3

EIF1B, CASP4, DCC, RAD21, NDRG1, HDGF, ELAVL1, CDK2, CAND1, GRK5, EIF2S1, FN1, MAPK6, TARDBP, AIMP1, AIP, DNAJA1, EEF1E1, QARS, RARS, IMPDH2, IQGAP1, CCAR2, PLD3, rev, RNF2, EIF2S2, UNK, ABCF2, GTPBP1, HBS1L, POLR1B, SUB1, RPS4X, WIBG, NTRK1, XPO1, DNAJC7, NOP56, Hsph1, Rrbp1, Bag2, NF2, Ksr1, C1orf131, CDC73, CDH1, CYLD, TRIM25, KRAS, PRPF8, EFTUD2, AAR2, RIOK1, ESR2, AGR2, CDK9, RPS6KB2, KRT17, PHB, NRAS, MAPT, NR2C2, PRMT7, PSMD14, CD74, DDX60, MAB21L2, SNRNP70, ITFG1, BIRC3, STAU1, NFX1, BRD7, TP53, TRIM28, PLEKHA4, N, HCVgp1, ZC3H18, ATRX, M, nsp13, nsp14, nsp4, nsp6, ORF3a, ORF7b, ESR1, NEK4, DUX4, NDN, BRD4, NUPR1, C18orf8, nsp3, Apc2, LGALS9, IFI16, BKRF1, CD274, UFL1, DDRGK1, AKAP1, ANAPC2, DHFRL1, EIF6, LAMTOR1, POLR2C, FZR1, WDR5, NAA40, CDC123, SPRTN, BTF3, FBXW7, FURIN, IFITM1, IFITM3, E, ORF10, ORF6, ORF8, S, CCNF, SQSTM1,

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Mutations

Clinically associated variants from ClinVar.

Gene	Chr	Position	RefSeq	VarSeq	RefSeeq	VarType	Pathogenic	Disease	VarInfo
EIF2S3	chrX	24073090	C	G	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24073091	G	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24073113	C	T	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24073761	C	T	single_nucleotide_variant	Benign	MEHMO_syndrome\|not_specified\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24073785	A	G	single_nucleotide_variant	Benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24073803	T	C	single_nucleotide_variant	Benign/Likely_benign	not_specified\|not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
EIF2S3	chrX	24075532	C	G	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
EIF2S3	chrX	24075534	A	G	single_nucleotide_variant	Likely_benign	not_specified	SO:0001627\|intron_variant	SO:0001627\|intron_variant
EIF2S3	chrX	24075762	G	A	single_nucleotide_variant	Uncertain_significance	Inborn_genetic_diseases	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24075777	C	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24075794	T	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24075812	T	A	single_nucleotide_variant	Uncertain_significance	MEHMO_syndrome	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24075862	A	G	single_nucleotide_variant	Likely_benign	not_specified	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24075867	G	A	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24078238	T	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24078252	C	T	single_nucleotide_variant	Likely_pathogenic	MEHMO_syndrome	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24078254	A	G	single_nucleotide_variant	Likely_pathogenic	MEHMO_syndrome	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24082345	T	C	single_nucleotide_variant	Pathogenic	MEHMO_syndrome	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24082350	A	G	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24082355	A	G	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24084119	T	G	single_nucleotide_variant	Pathogenic	MEHMO_syndrome	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24084139	A	T	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24084162	C	G	single_nucleotide_variant	Likely_pathogenic	MEHMO_syndrome	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24084216	T	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001627\|intron_variant	SO:0001627\|intron_variant
EIF2S3	chrX	24086125	T	C	single_nucleotide_variant	Benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24086142	T	A	single_nucleotide_variant	Uncertain_significance	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24086179	T	C	single_nucleotide_variant	Likely_benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24086216	G	A	single_nucleotide_variant	Likely_pathogenic	not_provided	SO:0001583\|missense_variant	SO:0001583\|missense_variant
EIF2S3	chrX	24091193	A	G	single_nucleotide_variant	Uncertain_significance	MEHMO_syndrome	SO:0001627\|intron_variant	SO:0001627\|intron_variant
EIF2S3	chrX	24091291	C	T	single_nucleotide_variant	Benign	not_specified\|not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24091339	A	G	single_nucleotide_variant	Benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
EIF2S3	chrX	24094873	ACAAT	A	Deletion	Pathogenic/Likely_pathogenic	MEHMO_syndrome\|not_provided	SO:0001589\|frameshift_variant	SO:0001589\|frameshift_variant
EIF2S3	chrX	24094886	C	G	single_nucleotide_variant	Uncertain_significance	MEHMO_syndrome	SO:0001583\|missense_variant	SO:0001583\|missense_variant

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene

Cancer type

Chromosome

Start

End

RefSeeq

MutSeq

Mutation type

AAchange

# samples

Copy number variation (CNV) of EIF2S3
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across EIF2S3
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
95399	N/A	BG774247	EIF2S3	chrX	24095884	-	H19	chr11	2019057	-
98974	N/A	AI830759	EIF2S3	chrX	24095226	+	HNRNPA3	chr2	178087487	+
98844	N/A	BQ371816	EIF2S3	chrX	24093514	+	MAPK10	chr4	87354057	-
90464	N/A	BF858913	EIF2S3	chrX	24094526	-	NR2C2	chr3	14993253	+
78669	STAD	TCGA-CG-5718	EIF2S3	chrX	24078299	+	PRDX4	chrX	23704401	+
78669	STAD	TCGA-CG-5718-01A	EIF2S3	chrX	24078299	+	PRDX4	chrX	23704402	+
101140	N/A	AA460998	FAM213A	chr10	82192088	+	EIF2S3	chrX	24095449	+
101140	N/A	AW580222	GFPT1	chr2	69560231	+	EIF2S3	chrX	24080683	-
101140	Non-Cancer	TCGA-HU-A4GC-11A	MLTK	chr2	174090042	+	EIF2S3	chrX	24095464	+
101140	SARC	TCGA-DX-A1KY-01A	PDK3	chrX	24483678	+	EIF2S3	chrX	24073732	+
101140	N/A	BP430336	TUBA1B	chr12	49522545	-	EIF2S3	chrX	24095269	-
101146	UCEC	TCGA-AX-A3G4	ZFX	chrX	24167911	+	EIF2S3	chrX	24089674	+
101146	UCEC	TCGA-AX-A3G4-01A	ZFX	chrX	24167911	+	EIF2S3	chrX	24089675	+

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type

Translation factor

Coefficent

Hazard ratio

Wald test pval

Likelihool ratio pval

Logrank test pval

# samples

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
GBM	EIF2S3	0.000119044160811642	0.0015
ESCA	EIF2S3	0.00038883853054575	0.0047
MESO	EIF2S3	0.000504050003878022	0.0055
BRCA	EIF2S3	0.000578233543098314	0.0058
LUAD	EIF2S3	0.00168866355477819	0.015
ACC	EIF2S3	0.00350019395854102	0.028
CHOL	EIF2S3	0.00839173144390323	0.059
DLBC	EIF2S3	0.0168326098953598	0.1
COAD	EIF2S3	0.0318457983395009	0.16
LAML	EIF2S3	1.18868734305814e-05	2e-04
SARC	EIF2S3	1.2054221418744e-07	2.5e-06
LGG	EIF2S3	1.28681854560967e-19	3.5e-18
PAAD	EIF2S3	2.03351569452554e-05	0.00033
KIRP	EIF2S3	2.21119153047962e-15	5.7e-14
STAD	EIF2S3	2.61278950217271e-07	5.2e-06
LIHC	EIF2S3	2.98398165297351e-05	0.00045
SKCM	EIF2S3	3.49286799825527e-06	6.3e-05
LUSC	EIF2S3	3.97742951682647e-09	9.1e-08
THCA	EIF2S3	4.26796563240378e-20	1.2e-18
BLCA	EIF2S3	4.99378359125826e-09	1.1e-07
PCPG	EIF2S3	5.85596001714123e-05	0.00082
THYM	EIF2S3	6.46740810705517e-10	1.6e-08
HNSC	EIF2S3	8.1218392446105e-14	2e-12
KIRC	EIF2S3	9.94881730377697e-07	1.9e-05

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
OV	EIF2S3	0.00013352715546737	0.0044
ACC	EIF2S3	0.00211578851493571	0.068

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Related Drugs

Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID	Disease Name	# PubMeds	Disease source
C1846278	MENTAL RETARDATION, EPILEPTIC SEIZURES, HYPOGONADISM AND HYPOGENITALISM, MICROCEPHALY, AND OBESITY (disorder)	4	CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
C0011847	Diabetes	1	GENOMICS_ENGLAND
C0014544	Epilepsy	1	GENOMICS_ENGLAND
C0020619	Hypogonadism	1	GENOMICS_ENGLAND
C0025958	Microcephaly	1	GENOMICS_ENGLAND