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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for EFNA1

check button Gene summary
Gene informationGene symbol

EFNA1

Gene ID

1942

Gene nameephrin A1
SynonymsB61|ECKLG|EFL1|EPLG1|LERK-1|LERK1|TNFAIP4
Cytomap

1q22

Type of geneprotein-coding
Descriptionephrin-A1TNF alpha-induced protein 4eph-related receptor tyrosine kinase ligand 1immediate early response protein B61ligand of eph-related kinase 1tumor necrosis factor, alpha-induced protein 4
Modification date20180523
UniProtAcc

P20827

ContextPubMed: EFNA1 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
EFNA1

GO:0016477

cell migration

10655584

EFNA1

GO:0033628

regulation of cell adhesion mediated by integrin

10655584

EFNA1

GO:0034446

substrate adhesion-dependent cell spreading

10655584

EFNA1

GO:0048013

ephrin receptor signaling pathway

10655584

EFNA1

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

10655584

EFNA1

GO:1902004

positive regulation of amyloid-beta formation

24217950


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Exon skipping events across known transcript of Ensembl for EFNA1 from UCSC genome browser

check buttonSkipped 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.
all structure

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Gene isoform structures and expression levels for EFNA1

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for EFNA1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_113651155103814:155104110:155105978:155106044:155106205:155106256155105978:155106044ENSG00000169242.7ENST00000368407.3,ENST00000474413.1,ENST00000497282.1
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENSG00000169242.7ENST00000469878.1
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENSG00000169242.7ENST00000368406.2

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for EFNA1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_113651155103814:155104110:155105978:155106044:155106205:155106256155105978:155106044ENSG00000169242.7ENST00000368407.3,ENST00000474413.1,ENST00000497282.1
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENSG00000169242.7ENST00000469878.1
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENSG00000169242.7ENST00000368406.2

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for EFNA1

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000368407155105978155106044In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000368407155105978155106044In-frame

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Infer the effects of exon skipping event on protein functional features for EFNA1

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003684071943205155105978155106044907972129151

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003684071943205155105978155106044907972129151

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P20827129151131152Alternative sequenceID=VSP_017543;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
P20827129151125134Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3HEI
P20827129151142147Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3HEI
P2082712915119182ChainID=PRO_0000008353;Note=Ephrin-A1
P2082712915180140Disulfide bondOntology_term=ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:3HEI,ECO:0000269|PubMed:19525919,ECO:0000269|PubMed:20505120;Dbxref=PMID:19525919,PMID:20505120
P2082712915119151DomainNote=Ephrin RBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00884


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P20827129151131152Alternative sequenceID=VSP_017543;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
P20827129151125134Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3HEI
P20827129151142147Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3HEI
P2082712915119182ChainID=PRO_0000008353;Note=Ephrin-A1
P2082712915180140Disulfide bondOntology_term=ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:3HEI,ECO:0000269|PubMed:19525919,ECO:0000269|PubMed:20505120;Dbxref=PMID:19525919,PMID:20505120
P2082712915119151DomainNote=Ephrin RBD;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00884


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SNVs in the skipped exons for EFNA1

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
HCC366_LUNG155105979155106256155106015155106015Missense_MutationGAp.R142K
HCC366_LUNG155105979155106044155106015155106015Missense_MutationGAp.R142K

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for EFNA1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2ACCrs4745chr1:155106227A/T3.76e-05
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2GBMrs4745chr1:155106227A/T4.38e-23
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2CESCrs4745chr1:155106227A/T6.60e-43
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2COADrs4745chr1:155106227A/T8.75e-50
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2BLCArs4745chr1:155106227A/T4.32e-37
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2ESCArs4745chr1:155106227A/T2.26e-41
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2HNSCrs4745chr1:155106227A/T1.34e-94
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2KIRPrs4745chr1:155106227A/T2.66e-37
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2LGGrs4745chr1:155106227A/T7.90e-80
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2KIRCrs4745chr1:155106227A/T2.50e-84
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2LUADrs4745chr1:155106227A/T1.77e-68
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2MESOrs4745chr1:155106227A/T2.54e-13
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2LUSCrs4745chr1:155106227A/T7.31e-75
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2OVrs4745chr1:155106227A/T3.17e-53
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2READrs4745chr1:155106227A/T1.19e-17
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2PCPGrs4745chr1:155106227A/T2.78e-17
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2PAADrs4745chr1:155106227A/T1.30e-34
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2PRADrs4745chr1:155106227A/T2.33e-56
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2SARCrs4745chr1:155106227A/T2.52e-23
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2THYMrs4745chr1:155106227A/T1.66e-16
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2TGCTrs4745chr1:155106227A/T3.47e-11
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2SKCMrs4745chr1:155106227A/T3.45e-20
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2STADrs4745chr1:155106227A/T2.42e-82
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2THCArs4745chr1:155106227A/T5.65e-95
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2UVMrs4745chr1:155106227A/T3.10e-09
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2UCSrs4745chr1:155106227A/T9.53e-06
exon_skip_113691155103814:155104110:155106205:155106256:155106430:155106601155106205:155106256ENST00000368406.2UCECrs4745chr1:155106227A/T2.53e-24
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1ACCrs4745chr1:155106227A/T3.76e-05
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1GBMrs4745chr1:155106227A/T4.38e-23
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1GBMrs4390169chr1:155106054A/G2.47e-22
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1CESCrs4390169chr1:155106054A/G3.14e-43
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1CESCrs4745chr1:155106227A/T6.60e-43
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1COADrs4390169chr1:155106054A/G4.69e-53
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1COADrs4745chr1:155106227A/T8.75e-50
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1BLCArs4390169chr1:155106054A/G8.32e-41
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1BLCArs4745chr1:155106227A/T4.32e-37
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1ESCArs4390169chr1:155106054A/G7.26e-44
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1ESCArs4745chr1:155106227A/T2.26e-41
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1HNSCrs4745chr1:155106227A/T1.34e-94
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1HNSCrs4390169chr1:155106054A/G1.38e-94
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1KIRPrs4745chr1:155106227A/T2.66e-37
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1KIRPrs4390169chr1:155106054A/G1.07e-36
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1LGGrs4390169chr1:155106054A/G1.73e-80
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1LGGrs4745chr1:155106227A/T7.90e-80
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1KIRCrs4390169chr1:155106054A/G2.71e-85
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1KIRCrs4745chr1:155106227A/T2.50e-84
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1LUADrs4745chr1:155106227A/T1.77e-68
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1LUADrs4390169chr1:155106054A/G4.16e-68
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1MESOrs4745chr1:155106227A/T2.54e-13
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1MESOrs4390169chr1:155106054A/G4.11e-13
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1LUSCrs4390169chr1:155106054A/G4.14e-85
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1LUSCrs4745chr1:155106227A/T7.31e-75
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1OVrs4390169chr1:155106054A/G1.60e-53
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1OVrs4745chr1:155106227A/T3.17e-53
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1READrs4745chr1:155106227A/T1.19e-17
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1READrs4390169chr1:155106054A/G1.42e-16
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1PCPGrs4390169chr1:155106054A/G1.09e-17
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1PCPGrs4745chr1:155106227A/T2.78e-17
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1PAADrs4390169chr1:155106054A/G2.73e-35
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1PAADrs4745chr1:155106227A/T1.30e-34
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1PRADrs4390169chr1:155106054A/G2.75e-57
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1PRADrs4745chr1:155106227A/T2.33e-56
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1SARCrs4390169chr1:155106054A/G2.90e-25
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1SARCrs4745chr1:155106227A/T2.52e-23
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1THYMrs4745chr1:155106227A/T1.66e-16
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1THYMrs4390169chr1:155106054A/G3.41e-15
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1TGCTrs4745chr1:155106227A/T3.47e-11
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1TGCTrs4390169chr1:155106054A/G8.41e-11
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1SKCMrs4390169chr1:155106054A/G1.20e-20
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1SKCMrs4745chr1:155106227A/T3.45e-20
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1STADrs4745chr1:155106227A/T2.42e-82
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1STADrs4390169chr1:155106054A/G4.20e-80
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1THCArs4390169chr1:155106054A/G5.55e-97
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1THCArs4745chr1:155106227A/T5.65e-95
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1UVMrs4390169chr1:155106054A/G3.10e-09
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1UVMrs4745chr1:155106227A/T3.10e-09
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1UCSrs4390169chr1:155106054A/G5.44e-06
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1UCSrs4745chr1:155106227A/T9.53e-06
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1UCECrs4390169chr1:155106054A/G2.24e-24
exon_skip_113671155103814:155104110:155105978:155106256:155106430:155106601155105978:155106256ENST00000469878.1UCECrs4745chr1:155106227A/T2.53e-24

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for EFNA1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for EFNA1


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RelatedDrugs for EFNA1

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for EFNA1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
EFNA1C1458155Mammary Neoplasms1CTD_human