ExonSkipAD: functional annotation of exon skipping event in human

Gene summary for SYNGAP1

Gene summary

Gene information	Gene symbol	SYNGAP1
	Gene ID	8831
	Gene name	synaptic Ras GTPase activating protein 1
	Synonyms	MRD5\|RASA1\|RASA5\|SYNGAP
	Cytomap	6p21.32
	Type of gene	protein-coding
	Description	ras/Rap GTPase-activating protein SynGAPRas GTPase-activating protein SynGAPneuronal RasGAPsynaptic Ras GTPase activating protein 1 homologsynaptic Ras GTPase activating protein, 135kDa
	Modification date	20200313
	UniProtAcc	A0A0A0MQZ2, A0A140T8W4, A0A1B0GU28, A0A1B0GW70, A0A1U9X8L0, A0A2R8Y6T2, A0A2R8YDS2, B7ZCA0, Q96PV0,
	Context

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

Gene

GO ID

GO term

PubMed ID

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Gene structures and expression levels for SYNGAP1

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.

ENSG00000197283

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

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 SYNGAP1

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_103408	chr6	33441743:33441759:33442453:33442494:33442889:33442973	33442453:33442494
exon_skip_119954	chr6	33441711:33441759:33442453:33442494:33442889:33442973	33442453:33442494
exon_skip_147772	chr6	33447843:33447933:33448789:33448868:33451760:33451831	33448789:33448868
exon_skip_153650	chr6	33447843:33447933:33448789:33448868:33451760:33451799	33448789:33448868
exon_skip_161870	chr6	33438775:33438919:33440553:33440965:33441173:33441374	33440553:33440965
exon_skip_203326	chr6	33441581:33441759:33442453:33442494:33442889:33442973	33442453:33442494
exon_skip_253443	chr6	33438775:33438919:33440729:33440965:33441173:33441374	33440729:33440965
exon_skip_264050	chr6	33432685:33432806:33435152:33435305:33435515:33435613	33435152:33435305

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
exon_skip_119954	Mayo_CB	5.674390e-01	7.223377e-01	-1.548986e-01	1.837625e-06

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Open reading frame (ORF) annotation in the exon skipping event for SYNGAP1

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
ENST00000629380	33440729	33440965	In-frame
ENST00000646630	33440729	33440965	In-frame
ENST00000629380	33442453	33442494	In-frame
ENST00000646630	33442453	33442494	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
ENST00000629380	33442453	33442494	In-frame
ENST00000646630	33442453	33442494	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
ENST00000629380	33435152	33435305	Frame-shift
ENST00000646630	33435152	33435305	Frame-shift
ENST00000629380	33440729	33440965	In-frame
ENST00000646630	33440729	33440965	In-frame
ENST00000629380	33442453	33442494	In-frame
ENST00000646630	33442453	33442494	In-frame

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Infer the effects of exon skipping event on protein functional features for SYNGAP1

p-ENSG00000197283_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
ENST00000629380	9879	1343	33440729	33440965	1873	2108	559	637
ENST00000646630	6032	1343	33440729	33440965	1878	2113	559	637
ENST00000629380	9879	1343	33442453	33442494	2491	2531	765	778
ENST00000646630	6032	1343	33442453	33442494	2496	2536	765	778

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
ENST00000629380	9879	1343	33442453	33442494	2491	2531	765	778
ENST00000646630	6032	1343	33442453	33442494	2496	2536	765	778

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
ENST00000629380	9879	1343	33440729	33440965	1873	2108	559	637
ENST00000646630	6032	1343	33440729	33440965	1878	2113	559	637
ENST00000629380	9879	1343	33442453	33442494	2491	2531	765	778
ENST00000646630	6032	1343	33442453	33442494	2496	2536	765	778

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
Q96PV0	559	637	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	559	637	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	559	637	443	635	Domain	Note=Ras-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00167
Q96PV0	559	637	443	635	Domain	Note=Ras-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00167
Q96PV0	559	637	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	559	637	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	559	637	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	559	637	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	559	637	562	562	Natural variant	ID=VAR_069233;Note=In MRD5%3B the disease phenotype consists of intellectual disability and autism%3B the mutant protein is less efficient in inhibiting ERK phosphorylation induced by neuronal activity. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|
Q96PV0	559	637	562	562	Natural variant	ID=VAR_069233;Note=In MRD5%3B the disease phenotype consists of intellectual disability and autism%3B the mutant protein is less efficient in inhibiting ERK phosphorylation induced by neuronal activity. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|
Q96PV0	765	778	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	765	778	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	765	778	766	766	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9QUH6
Q96PV0	765	778	766	766	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9QUH6
Q96PV0	765	778	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	701	1343	Natural variant	ID=VAR_078618;Note=In MRD5%3B moderate%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	701	1343	Natural variant	ID=VAR_078618;Note=In MRD5%3B moderate%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187

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
Q96PV0	765	778	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	765	778	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	765	778	766	766	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9QUH6
Q96PV0	765	778	766	766	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9QUH6
Q96PV0	765	778	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	701	1343	Natural variant	ID=VAR_078618;Note=In MRD5%3B moderate%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	701	1343	Natural variant	ID=VAR_078618;Note=In MRD5%3B moderate%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187

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
Q96PV0	559	637	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	559	637	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	559	637	443	635	Domain	Note=Ras-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00167
Q96PV0	559	637	443	635	Domain	Note=Ras-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00167
Q96PV0	559	637	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	559	637	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	559	637	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	559	637	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	559	637	562	562	Natural variant	ID=VAR_069233;Note=In MRD5%3B the disease phenotype consists of intellectual disability and autism%3B the mutant protein is less efficient in inhibiting ERK phosphorylation induced by neuronal activity. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|
Q96PV0	559	637	562	562	Natural variant	ID=VAR_069233;Note=In MRD5%3B the disease phenotype consists of intellectual disability and autism%3B the mutant protein is less efficient in inhibiting ERK phosphorylation induced by neuronal activity. P->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|
Q96PV0	765	778	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	765	778	1	1343	Chain	ID=PRO_0000056654;Note=Ras/Rap GTPase-activating protein SynGAP
Q96PV0	765	778	766	766	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9QUH6
Q96PV0	765	778	766	766	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9QUH6
Q96PV0	765	778	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	143	1343	Natural variant	ID=VAR_078616;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy%3B unknown pathological significance. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	267	1343	Natural variant	ID=VAR_078617;Note=In MRD5%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	701	1343	Natural variant	ID=VAR_078618;Note=In MRD5%3B moderate%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187
Q96PV0	765	778	701	1343	Natural variant	ID=VAR_078618;Note=In MRD5%3B moderate%3B associated with autistic spectrum disorder and epileptic encephalopathy. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:23708187;Dbxref=PMID:23708187

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3'-UTR located exon skipping events that lost miRNA binding sites in SYNGAP1

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 SYNGAP1

- 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 SYNGAP1

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

CDR

MSBB

IFG

exon_skip_103408

-3.789254e-01

4.675320e-02

chr6

33441743

33441759

33442453

33442494

33442889

33442973

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SYNGAP1

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 SYNGAP1

Correlated RBP and related information.

Tissue type	RBP name	Exon skip ID	Correlation coeifficient	P-value
CB	RBM6	exon_skip_119954	-4.479640e-01	3.204087e-09
HCC	RBM6	exon_skip_119954	-4.453997e-01	1.459368e-14
HCC	RBM6	exon_skip_147772	4.440184e-01	3.140310e-14
HCC	HNRNPF	exon_skip_147772	4.131037e-01	2.407497e-12
TC	RBM6	exon_skip_119954	-4.991059e-01	2.475509e-11
TC	NOVA1	exon_skip_119954	6.352936e-01	3.088780e-19
TC	SRSF2	exon_skip_147772	-4.172392e-01	6.629784e-08
TC	HNRNPH2	exon_skip_147772	-5.009423e-01	3.173033e-11
TC	ESRP1	exon_skip_147772	-5.452629e-01	2.204138e-13
TC	NOVA1	exon_skip_147772	-5.504431e-01	1.174482e-13

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RelatedDrugs for SYNGAP1

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 SYNGAP1

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 SYNGAP1

Gene structures and expression levels for SYNGAP1

Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SYNGAP1

Open reading frame (ORF) annotation in the exon skipping event for SYNGAP1

Infer the effects of exon skipping event on protein functional features for SYNGAP1

3'-UTR located exon skipping events that lost miRNA binding sites in SYNGAP1

SNVs in the skipped exons for SYNGAP1

AD stage-associated exon skippint events for SYNGAP1

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SYNGAP1

Correlation with RNA binding proteins (RBPs) for SYNGAP1

RelatedDrugs for SYNGAP1

RelatedDiseases for SYNGAP1