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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: EIF2D (NCBI Gene ID:1939)

Gene Summary

Gene Summary

Gene Information	Gene Name: EIF2D
	Gene ID: 1939
	Gene Symbol	EIF2D
	Gene ID	1939
	Gene Name	eukaryotic translation initiation factor 2D
	Synonyms	HCA56\|LGTN
	Cytomap	1q32.1
	Type of Gene	protein-coding
	Description	eukaryotic translation initiation factor 2Dhepatocellular carcinoma-associated antigen 56ligatin
	Modification date	20200313
	UniProtAcc	P41214

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: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	EIF2D	GO:0001731	formation of translation preinitiation complex	20713520
Hgene	EIF2D	GO:0032790	ribosome disassembly	20713520
Hgene	EIF2D	GO:0075522	IRES-dependent viral translational initiation	20713520

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

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Translation Studies in PubMed

We searched PubMed using 'EIF2D[title] AND translation [title] AND human.'

Gene	Title	PMID
EIF2D	A C. elegans model of C9orf72-associated ALS/FTD uncovers a conserved role for eIF2D in RAN translation	34654821

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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
ENST00000271764	206770449	206770545	In-frame
ENST00000271764	206772816	206772966	In-frame
ENST00000271764	206773086	206773190	Frame-shift
ENST00000271764	206775689	206775807	Frame-shift
ENST00000271764	206776304	206776558	Frame-shift
ENST00000271764	206778752	206778860	In-frame
ENST00000271764	206782728	206782812	In-frame

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)
ENST00000271764	206770449	206770545	2111	1502	1597	584	431	462
ENST00000271764	206772816	206772966	2111	1262	1411	584	351	400
ENST00000271764	206778752	206778860	2111	632	739	584	141	176
ENST00000271764	206782728	206782812	2111	457	540	584	82	110

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.

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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

adj.pval

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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

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with EIF2D (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

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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
HNSC	EIF2D	EIF1	-4.13399438210909	0.000228392819053625
BRCA	EIF2D	ABCE1	1.3740626146648	0.000669229587514616
HNSC	EIF2D	DENR	1.63046611861477	0.00106627625814326
LUAD	EIF2D	RPS8	-2.73463137299833	0.00134906742748461
LIHC	EIF2D	ABCE1	1.33775121002715	0.0033398145023608
PRAD	EIF2D	RPS8	1.32957024497066	0.00418162555035067
LIHC	EIF2D	EIF5B	-2.20229681831546	0.00440340335695336
LIHC	EIF2D	EIF1B	-1.52296643222607	0.00467797572102414
HNSC	EIF2D	EIF1B	1.29022554527937	0.00540290265007571
PRAD	EIF2D	EIF1	1.32822648991353	0.00674237731133815
LUSC	EIF2D	RPS8	-1.95298795124964	0.00724217523600344
COAD	EIF2D	EIF5B	-1.84319839410667	0.0101850330829621
HNSC	EIF2D	ABCE1	1.20332081233659	0.0124875666290336
LUAD	EIF2D	RPS4X	-2.43594282676366	0.0163893452361939
BLCA	EIF2D	ABCE1	-4.08863120087471	0.0229873657226562
COAD	EIF2D	RPS13	1.30175825100469	0.0357243716716767
COAD	EIF2D	RPS9	1.18612014402235	0.0381683111190796
UCEC	EIF2D	EIF1B	-5.93208681724707	0.046875
HNSC	EIF2D	RPS25	2.24439018636525	1.07420805761649e-06
KIRC	EIF2D	RPS8	-3.97243608476641	1.19932271980764e-10
PRAD	EIF2D	ABCE1	-2.9089513514626	1.31460603050763e-05
KIRC	EIF2D	RPS4X	-1.64140073680063	1.72010286166321e-07
BRCA	EIF2D	RPS9	1.9331477546349	2.31299392089389e-07
BRCA	EIF2D	RPS4X	-1.55343710903986	3.36588066248297e-09
KIRC	EIF2D	RPS9	-1.32680816440987	6.53264115309597e-07
THCA	EIF2D	RPS4X	1.49777877118816	6.68348444344278e-07
KIRP	EIF2D	RPS8	-1.20432400687215	7.40401446819306e-05
BRCA	EIF2D	EIF5B	2.09894664144155	8.11370754946327e-13

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

PPI interactors with EIF2D

RAD51, CUL3, EIF1B, HARS, DHX15, EIF1, AICDA, GMPPB, PSMC3, CALU, CKAP5, DENR, ELAC2, GCN1L1, KIN, RECQL5, HNRNPR, NAA38, RCC2, WDR5, ZNHIT2, CDC5L, DUSP12, PCBP1, TNIP2, MYC, ATG16L1, BICD2, HSPA8, MKI67, FASN, SLC22A4, C11orf87, PRPS2, CCNF,

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Mutations

Clinically associated variants from ClinVar.

Gene

Chr

Position

RefSeq

VarSeq

RefSeeq

VarType

Pathogenic

Disease

VarInfo

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
EIF2D	LUAD	chr1	206785640	206785640	C	A	Splice_Site	p.R19_splice	6
EIF2D	SKCM	chr1	206778857	206778857	G	A	Silent	p.A142A	3
EIF2D	LIHC	chr1	206769068	206769068	T	-	Splice_Site	p.K503_splice	3
EIF2D	ESCA	chr1	206765123	206765123	G	A	Missense_Mutation	p.P580L	3
EIF2D	KIRP	chr1	206767112	206767112	C	T	Missense_Mutation	p.G514S	3
EIF2D	LIHC	chr1	206769175	206769175	T	-	Frame_Shift_Del	p.K467fs	3
EIF2D	SKCM	chr1	206769163	206769163	G	A	Silent	p.A471A	3
EIF2D	PAAD	chr1	206773132	206773132	C	A	Missense_Mutation	p.S336I	2
EIF2D	ESCA	chr1	206765123	206765123	G	A	Missense_Mutation		2
EIF2D	STAD	chr1	206767100	206767100	A	G	Missense_Mutation	p.Y518H	2
EIF2D	PRAD	chr1	206778810	206778810	G	A	Missense_Mutation	p.T158M	2
EIF2D	SKCM	chr1	206770466	206770466	C	T	Missense_Mutation	p.D458N	2
EIF2D	ESCA	chr1	206776495	206776495	G	C	Silent		2
EIF2D	LUAD	chr1	206784620	206784620	G	A	Missense_Mutation	p.A55V	2
EIF2D	CESC	chr1	206769124	206769124	C	T	Silent		2
EIF2D	SKCM	chr1	206772821	206772821	G	A	Missense_Mutation	p.H400Y	2
EIF2D	ESCA	chr1	206776495	206776495	G	C	Silent	p.L198L	2
EIF2D	SARC	chr1	206772927	206772927	G	A	Silent		2
EIF2D	SKCM	chr1	206772888	206772888	G	A	Silent	p.H377H	2
EIF2D	SKCM	chr1	206772928	206772928	G	A	Missense_Mutation	p.S364F	2
EIF2D	PAAD	chr1	206773132	206773132	C	A	Missense_Mutation		2
EIF2D	SKCM	chr1	206776555	206776555	C	T	Silent	p.R178R	2
EIF2D	LIHC	chr1	206765135	206765135	T	-	Frame_Shift_Del	p.K576fs	2
EIF2D	STAD	chr1	206772933	206772933	C	T	Silent		2
EIF2D	PAAD	chr1	206773158	206773158	C	T	Silent		2
EIF2D	SKCM	chr1	206769134	206769134	G	A	Missense_Mutation	p.P481L	2
EIF2D	ESCA	chr1	206767028	206767028	C	T	Missense_Mutation	p.D542N	2
EIF2D	STAD	chr1	206767100	206767100	A	G	Missense_Mutation		2
EIF2D	PAAD	chr1	206773158	206773158	C	T	Silent	p.E327E	2
EIF2D	LIHC	chr1	206765155	206765155	T	-	Frame_Shift_Del	p.K569fs	2
EIF2D	STAD	chr1	206772933	206772933	C	T	Silent	p.P362P	2
EIF2D	KIRP	chr1	206773178	206773178	G	T	Missense_Mutation		1
EIF2D	THYM	chr1	206765131	206765131	G	T	Silent	p.A577A	1
EIF2D	BLCA	chr1	206772966	206772966	C	T	Silent		1
EIF2D	SKCM	chr1	206767007	206767007	G	A	Nonsense_Mutation	p.Q549*	1
EIF2D	LUAD	chr1	206772426	206772426	C	T	Missense_Mutation	p.G408D	1
EIF2D	KIRP	chr1	206785684	206785684	C	T	Silent		1
EIF2D	UCEC	chr1	206772406	206772406	C	T	Missense_Mutation	p.V415I	1
EIF2D	BLCA	chr1	206782760	206782760	A	C	Silent	p.P100P	1
EIF2D	LIHC	chr1	206772357	206772357	T	-	Splice_Site	p.N431_splice	1
EIF2D	SKCM	chr1	206770521	206770521	T	C	Silent	p.L439L	1
EIF2D	LUAD	chr1	206767018	206767018	T	C	Missense_Mutation	p.Q545R	1
EIF2D	STAD	chr1	206782790	206782790	A	G	Silent	p.P90P	1
EIF2D	LGG	chr1	206760238	206760238	G	A	Silent		1
EIF2D	PRAD	chr1	206782805	206782805	C	T	Silent	p.T85T	1
EIF2D	SKCM	chr1	206770467	206770467	C	T	Nonsense_Mutation	p.W457X	1
EIF2D	UCS	chr1	206773144	206773144	A	G	Missense_Mutation		1
EIF2D	BLCA	chr1	206772966	206772966	C	T	Splice_Site	p.R351R	1
EIF2D	LIHC	chr1	206772934	206772934	G	-	Frame_Shift_Del	p.P362fs	1
EIF2D	SKCM	chr1	206770467	206770467	C	T	Nonsense_Mutation	p.W457*	1
EIF2D	ESCA	chr1	206767028	206767028	C	T	Missense_Mutation		1
EIF2D	STAD	chr1	206773628	206773628	T	A	Missense_Mutation	p.S313C	1
EIF2D	LIHC	chr1	206775771	206775771	T	C	Missense_Mutation		1
EIF2D	READ	chr1	206776509	206776509	C	T	Missense_Mutation	p.D194N	1
EIF2D	SKCM	chr1	206773087	206773087	C	T	Missense_Mutation	p.R351K	1
EIF2D	UCS	chr1	206773144	206773144	A	G	Missense_Mutation	p.V332A	1
EIF2D	LIHC	chr1	206773124	206773124	C	-	Frame_Shift_Del	p.V339fs	1
EIF2D	SKCM	chr1	206772870	206772870	G	A	Silent	p.P383P	1
EIF2D	ESCA	chr1	206784611	206784611	C	A	Missense_Mutation	p.G58V	1
EIF2D	LUAD	chr1	206772944	206772944	C	A	Nonsense_Mutation	p.E359*	1
EIF2D	STAD	chr1	206784635	206784635	A	G	Missense_Mutation	p.I50T	1
EIF2D	LIHC	chr1	206772954	206772954	G	A	Silent		1
EIF2D	SARC	chr1	206778849	206778849	G	T	Missense_Mutation		1
EIF2D	CESC	chr1	206769124	206769124	C	T	Silent	p.K484	1
EIF2D	LIHC	chr1	206784722	206784722	T	-	Frame_Shift_Del	p.K21fs	1
EIF2D	SKCM	chr1	206784693	206784693	G	A	Missense_Mutation	p.P31S	1
EIF2D	LUAD	chr1	206784708	206784708	C	A	Missense_Mutation	p.V26L	1
EIF2D	STAD	chr1	206776401	206776401	G	A	Missense_Mutation	p.H230Y	1
EIF2D	LIHC	chr1	206775799	206775799	C	A	Missense_Mutation	p.D265Y	1
EIF2D	COAD	chr1	206769079	206769079	C	T	Silent	p.A499A	1
EIF2D	LIHC	chr1	206767003	206767003	C	-	Frame_Shift_Del	p.G550fs	1
EIF2D	SKCM	chr1	206784648	206784648	C	T	Missense_Mutation	p.E46K	1
EIF2D	GBM	chr1	206760184	206760184	T	G	Silent		1
EIF2D	LUSC	chr1	206784717	206784717	G	A	Nonsense_Mutation	p.R23*	1
EIF2D	STAD	chr1	206773636	206773637	-	TTATGTCC	Frame_Shift_Ins	p.K310_K311delinsRTX	1
EIF2D	LIHC	chr1	206772954	206772954	G	A	Silent	p.F355F	1
EIF2D	COAD	chr1	206769090	206769090	C	T	Missense_Mutation	p.A496T	1
EIF2D	LIHC	chr1	206773618	206773618	T	-	Splice_Site	p.K316_splice	1
EIF2D	SKCM	chr1	206767083	206767083	G	A	Silent	p.I523I	1
EIF2D	HNSC	chr1	206785672	206785672	G	C	Silent		1
EIF2D	OV	chr1	206772937	206772937	G	T	Missense_Mutation	p.S361Y	1
EIF2D	SARC	chr1	206772927	206772927	G	A	Silent	p.S364S	1
EIF2D	TGCT	chr1	206781611	206781612	CA	-	Frame_Shift_Del		1
EIF2D	SKCM	chr1	206773087	206773087	C	T	Splice_Site	p.R351_splice	1
EIF2D	LIHC	chr1	206767034	206767034	C	-	Frame_Shift_Del	p.A540fs	1
EIF2D	COAD	chr1	206773090	206773090	G	A	Missense_Mutation	p.P350L	1
EIF2D	LIHC	chr1	206781649	206781649	G	-	Frame_Shift_Del	p.P121fs	1
EIF2D	SKCM	chr1	206785667	206785667	G	A	Missense_Mutation	p.S10F	1
EIF2D	HNSC	chr1	206785672	206785672	G	C	Silent	p.V8V	1
EIF2D	TGCT	chr1	206781611	206781612	CA	-	Frame_Shift_Del	p.134_134del	1
EIF2D	SKCM	chr1	206778855	206778855	G	A	Missense_Mutation	p.P143L	1
EIF2D	ACC	chr1	206784680	206784680	G	C	Missense_Mutation	p.T35S	1
EIF2D	LIHC	chr1	206782734	206782734	C	-	Frame_Shift_Del	p.G109fs	1
EIF2D	TGCT	chr1	206781611	206781612	CA	-	Frame_Shift_Del	p.CA133fs	1
EIF2D	SKCM	chr1	206782792	206782792	G	A	Missense_Mutation	p.P90S	1
EIF2D	ACC	chr1	206769135	206769135	G	A	Missense_Mutation	p.P481S	1
EIF2D	LUAD	chr1	206767041	206767041	G	T	Silent	p.A537A	1
EIF2D	KIRP	chr1	206767112	206767112	C	T	Missense_Mutation		1
EIF2D	THYM	chr1	206766977	206766977	G	A	Silent		1
EIF2D	SKCM	chr1	206769095	206769095	G	A	Missense_Mutation	p.T494I	1
EIF2D	BLCA	chr1	206782760	206782760	A	C	Silent		1
EIF2D	ESCA	chr1	206776495	206776495	G	C	Silent	p.L198	1

Copy number variation (CNV) of EIF2D
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across EIF2D
* 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
102857	GBM	TCGA-27-2519-01A	EIF2D	chr1	206769067	-	CHMP1A	chr16	89713739	-
101074	N/A	AF262403	EIF2D	chr1	206764974	-	MACROD2	chr20	14529420	-
25727	Non-Cancer	61N	EIF2D	chr1	206778752	-	MARC2	chr1	220957260	+
90918	N/A	BI907782	EIF2D	chr1	206762080	-	RASSF5	chr1	206762258	+
94175	N/A	AI299201	PEX19	chr1	160248798	+	EIF2D	chr1	206772898	-
94175	N/A	BE159686	RASSF5	chr1	206760374	+	EIF2D	chr1	206760755	-
94179	N/A	BM151033	TRIM9	chr14	51538091	-	EIF2D	chr1	206764974	+

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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

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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

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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