ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for GDAP1

Gene summary

Gene information	Gene symbol	GDAP1
	Gene ID	54332
	Gene name	ganglioside induced differentiation associated protein 1
	Synonyms	CMT4\|CMT4A\|CMTRIA
	Cytomap	8q21.11
	Type of gene	protein-coding
	Description	ganglioside-induced differentiation-associated protein 1Charcot-Marie-Tooth neuropathy 4A
	Modification date	20200328
	UniProtAcc	E5RGI2, E7FJF5, Q8TB36,
	Context

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene	GO ID	GO term	PubMed ID
GDAP1	GO:0000266	mitochondrial fission	15772096

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Gene structures and expression levels for GDAP1

Skipped exons in the ROSMAP, MSBB, and Mayo 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.

ENSG00000104381

Differentially expressed gene analysis across multiple brain tissues between AD and control.

Tissue type

DEG direction

Base mean exp.

log2FC(AD/control)

P-value

Adj. p-value

Differentially expressed isoform analysis across multiple brain tissues between AD and control.

Tissue type	DEG direction	ENST	Transcript info.	Base mean exp.	log2FC(AD/control)	P-value	Adjc. p-value
CB	UP	ENST00000524366.5	GDAP1-208:lncRNA:GDAP1	2.282319e+00	9.138487e-01	1.528323e-03	7.372120e-03

Landscape of isoform expressions across multiple brain tissues between AD and control.

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for GDAP1

Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).

All exon skipping events in AD cohorts.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon
exon_skip_162855	chr8	74350434:74350578:74351274:74351466:74360137:74360248	74351274:74351466
exon_skip_176116	chr8	74350444:74350578:74351274:74351321:74360137:74360248	74351274:74351321
exon_skip_211576	chr8	74351298:74351466:74360137:74360310:74361884:74361978	74360137:74360310
exon_skip_240202	chr8	74350444:74350578:74351274:74351466:74360137:74360248	74351274:74351466
exon_skip_240220	chr8	74351274:74351321:74360137:74360310:74361884:74361978	74360137:74360310
exon_skip_244609	chr8	74350444:74350578:74351274:74351466:74361884:74361978	74351274:74351466
exon_skip_285411	chr8	74351426:74351466:74360137:74360310:74361884:74361978	74360137:74360310
exon_skip_30643	chr8	74350434:74350578:74351274:74351321:74360137:74360248	74351274:74351321
exon_skip_94712	chr8	74351274:74351466:74360137:74360310:74361884:74361978	74360137:74360310

Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.

Exon skipping information

Tissue type

Avg(PSIs) in AD

Avg(PSIs) in control

Difference (PSI)

Adj. p-value

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Open reading frame (ORF) annotation in the exon skipping event for GDAP1

Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000220822	74351274	74351466	Frame-shift
ENST00000220822	74360137	74360310	In-frame

Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000220822	74351274	74351466	Frame-shift
ENST00000220822	74360137	74360310	In-frame

Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000220822	74351274	74351466	Frame-shift
ENST00000220822	74360137	74360310	In-frame

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Infer the effects of exon skipping event on protein functional features for GDAP1

p-ENSG00000104381_img4.png
boxplot

Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000220822	3683	358	74360137	74360310	392	564	104	161

Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000220822	3683	358	74360137	74360310	392	564	104	161

Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.

ENST	Length of mRNA	Length of AA seq.	Genomic start	Genomic end	mRNA start	mRNA end	AA start	AA end
ENST00000220822	3683	358	74360137	74360310	392	564	104	161

Lost protein functional features of individual exon skipping events in ROSMAP.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q8TB36	104	161	1	358	Chain	ID=PRO_0000186038;Note=Ganglioside-induced differentiation-associated protein 1
Q8TB36	104	161	24	105	Domain	Note=GST N-terminal
Q8TB36	104	161	153	309	Domain	Note=GST C-terminal
Q8TB36	104	161	116	116	Mutagenesis	Note=Impairment in the ability to induce mitochondrial fragmentation. M->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16172208;Dbxref=PMID:16172208
Q8TB36	104	161	157	157	Mutagenesis	Note=No effect on mitochondrial localization. T->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15772096;Dbxref=PMID:15772096
Q8TB36	104	161	120	120	Natural variant	ID=VAR_078265;Note=In CMT2K%3B dominant form. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26525999;Dbxref=PMID:26525999
Q8TB36	104	161	120	120	Natural variant	ID=VAR_017184;Note=In CMT4A%3B no effect on mitochondrial localization but impairment in the ability to induce mitochondrial fragmentation. R->Q;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12601710,ECO:0000269\|PubMed:1577
Q8TB36	104	161	120	120	Natural variant	ID=VAR_078266;Note=In CMT2K%3B dominant form%3B no effect on mitochondrial localization. R->W;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15772096,ECO:0000269\|PubMed:26525999,ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs104
Q8TB36	104	161	123	123	Natural variant	ID=VAR_078267;Note=In CMT2K%3B dominant form%3B. H->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:26525999,ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs397515442,PMID:26525999,PMID:28244113
Q8TB36	104	161	126	126	Natural variant	ID=VAR_078268;Note=In CMT2K%3B dominant form%3B unknown pathological significance. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs879254005,PMID:28244113
Q8TB36	104	161	156	156	Natural variant	ID=VAR_078269;Note=In CMT2K%3B dominant form. A->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs397515441,PMID:28244113
Q8TB36	104	161	161	161	Natural variant	ID=VAR_017185;Note=In CMT4A%3B no effect on mitochondrial localization but abolishes mitochondrial fission. R->H;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11743579,ECO:0000269\|PubMed:15772096,ECO:0000269\|PubMed:16172208
Q8TB36	104	161	133	133	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305

Lost protein functional features of individual exon skipping events in MSBB.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q8TB36	104	161	1	358	Chain	ID=PRO_0000186038;Note=Ganglioside-induced differentiation-associated protein 1
Q8TB36	104	161	24	105	Domain	Note=GST N-terminal
Q8TB36	104	161	153	309	Domain	Note=GST C-terminal
Q8TB36	104	161	116	116	Mutagenesis	Note=Impairment in the ability to induce mitochondrial fragmentation. M->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16172208;Dbxref=PMID:16172208
Q8TB36	104	161	157	157	Mutagenesis	Note=No effect on mitochondrial localization. T->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15772096;Dbxref=PMID:15772096
Q8TB36	104	161	120	120	Natural variant	ID=VAR_078265;Note=In CMT2K%3B dominant form. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26525999;Dbxref=PMID:26525999
Q8TB36	104	161	120	120	Natural variant	ID=VAR_017184;Note=In CMT4A%3B no effect on mitochondrial localization but impairment in the ability to induce mitochondrial fragmentation. R->Q;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12601710,ECO:0000269\|PubMed:1577
Q8TB36	104	161	120	120	Natural variant	ID=VAR_078266;Note=In CMT2K%3B dominant form%3B no effect on mitochondrial localization. R->W;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15772096,ECO:0000269\|PubMed:26525999,ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs104
Q8TB36	104	161	123	123	Natural variant	ID=VAR_078267;Note=In CMT2K%3B dominant form%3B. H->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:26525999,ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs397515442,PMID:26525999,PMID:28244113
Q8TB36	104	161	126	126	Natural variant	ID=VAR_078268;Note=In CMT2K%3B dominant form%3B unknown pathological significance. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs879254005,PMID:28244113
Q8TB36	104	161	156	156	Natural variant	ID=VAR_078269;Note=In CMT2K%3B dominant form. A->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs397515441,PMID:28244113
Q8TB36	104	161	161	161	Natural variant	ID=VAR_017185;Note=In CMT4A%3B no effect on mitochondrial localization but abolishes mitochondrial fission. R->H;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11743579,ECO:0000269\|PubMed:15772096,ECO:0000269\|PubMed:16172208
Q8TB36	104	161	133	133	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305

Lost protein functional features of individual exon skipping events in Mayo.

UniProt acc.	Start of exon skipping (AA)	End of exon skipping (AA)	Protein feature start (AA)	Protein feature end (AA)	Category of protein feature	Description of feature
Q8TB36	104	161	1	358	Chain	ID=PRO_0000186038;Note=Ganglioside-induced differentiation-associated protein 1
Q8TB36	104	161	24	105	Domain	Note=GST N-terminal
Q8TB36	104	161	153	309	Domain	Note=GST C-terminal
Q8TB36	104	161	116	116	Mutagenesis	Note=Impairment in the ability to induce mitochondrial fragmentation. M->H;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16172208;Dbxref=PMID:16172208
Q8TB36	104	161	157	157	Mutagenesis	Note=No effect on mitochondrial localization. T->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15772096;Dbxref=PMID:15772096
Q8TB36	104	161	120	120	Natural variant	ID=VAR_078265;Note=In CMT2K%3B dominant form. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:26525999;Dbxref=PMID:26525999
Q8TB36	104	161	120	120	Natural variant	ID=VAR_017184;Note=In CMT4A%3B no effect on mitochondrial localization but impairment in the ability to induce mitochondrial fragmentation. R->Q;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12601710,ECO:0000269\|PubMed:1577
Q8TB36	104	161	120	120	Natural variant	ID=VAR_078266;Note=In CMT2K%3B dominant form%3B no effect on mitochondrial localization. R->W;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:15772096,ECO:0000269\|PubMed:26525999,ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs104
Q8TB36	104	161	123	123	Natural variant	ID=VAR_078267;Note=In CMT2K%3B dominant form%3B. H->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:26525999,ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs397515442,PMID:26525999,PMID:28244113
Q8TB36	104	161	126	126	Natural variant	ID=VAR_078268;Note=In CMT2K%3B dominant form%3B unknown pathological significance. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs879254005,PMID:28244113
Q8TB36	104	161	156	156	Natural variant	ID=VAR_078269;Note=In CMT2K%3B dominant form. A->G;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28244113;Dbxref=dbSNP:rs397515441,PMID:28244113
Q8TB36	104	161	161	161	Natural variant	ID=VAR_017185;Note=In CMT4A%3B no effect on mitochondrial localization but abolishes mitochondrial fission. R->H;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11743579,ECO:0000269\|PubMed:15772096,ECO:0000269\|PubMed:16172208
Q8TB36	104	161	133	133	Sequence conflict	Note=M->I;Ontology_term=ECO:0000305;evidence=ECO:0000305

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3'-UTR located exon skipping events that lost miRNA binding sites in GDAP1

3'-UTR exon skipping evnets lost miRNA binding.

Tissue type

ENST

Exon skip start

Exon skip end

microRNA

Binding site by TargetScan

Binding type by TargetScan

Bdinding site by miRanda

Score of miRanda

Energy by miRanda

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SNVs in the skipped exons for GDAP1

- Differential PSIs between mutated versus non-mutated samples.

- Depth of Coverage in the skipped exon of the mutated samples.

- Sashimi plot in the skipped exon of the mutated samples.

- Non-synonymous mutations located in the skipped exons.

Cancer type

Sample

ESID

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample

Skipped exon start

Skipped exon end

Mutation start

Mutation end

Mutation type

Reference seq

Mutation seq

AAchange

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AD stage-associated exon skippint events for GDAP1

Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).

AD stage info

Cohort

Tissue

SE id

Coefficient

P-value

Chromosome

Strand

E1 start

E1 end

Skipped start

Skipped end

E2 start

E2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GDAP1

sQTL information located at the skipped exons.

Tissue type

Exon skip ID

SNP id

Location

P-value

FDR

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Correlation with RNA binding proteins (RBPs) for GDAP1

Correlated RBP and related information.

Tissue type

RBP name

Exon skip ID

Correlation coeifficient

P-value

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RelatedDrugs for GDAP1

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for GDAP1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	3'-UTR located exon skipping events lost miRNA binding sites
	SNVs in the skipped exons with depth of coverage
	AD stage-associated exon skipping events
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Correlation with RNA binding proteins (RBPs)
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for GDAP1

Gene structures and expression levels for GDAP1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for GDAP1

Open reading frame (ORF) annotation in the exon skipping event for GDAP1

Infer the effects of exon skipping event on protein functional features for GDAP1

3'-UTR located exon skipping events that lost miRNA binding sites in GDAP1

SNVs in the skipped exons for GDAP1

AD stage-associated exon skippint events for GDAP1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GDAP1

Correlation with RNA binding proteins (RBPs) for GDAP1

RelatedDrugs for GDAP1

RelatedDiseases for GDAP1