ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for DMGDH

Gene summary

Gene information	Gene symbol	DMGDH
	Gene ID	29958
	Gene name	dimethylglycine dehydrogenase
	Synonyms	DMGDHD\|ME2GLYDH
	Cytomap	5q14.1
	Type of gene	protein-coding
	Description	dimethylglycine dehydrogenase, mitochondrial
	Modification date	20180523
	UniProtAcc	Q9UI17
	Context	PubMed: DMGDH [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

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.

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Gene isoform structures and expression levels for DMGDH

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for DMGDH

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENSG00000132837.10	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1
exon_skip_442894	5	78329061:78329231:78338105:78338304:78340126:78340375	78338105:78338304	ENSG00000132837.10	ENST00000380311.4,ENST00000255189.3,ENST00000523732.1,ENST00000518477.1
exon_skip_442900	5	78329061:78329231:78359435:78359610:78365342:78365449	78359435:78359610	ENSG00000132837.10	ENST00000540686.1,ENST00000517853.1
exon_skip_442902	5	78340126:78340375:78347109:78347314:78350006:78350063	78347109:78347314	ENSG00000132837.10	ENST00000255189.3,ENST00000523732.1
exon_skip_442909	5	78340126:78340375:78351632:78351727:78365342:78365449	78351632:78351727	ENSG00000132837.10	ENST00000521052.1
exon_skip_442915	5	78340126:78340375:78359435:78359610:78365342:78365449	78359435:78359610	ENSG00000132837.10	ENST00000380311.4,ENST00000518477.1
exon_skip_442920	5	78347109:78347314:78350006:78350171:78351632:78351727	78350006:78350171	ENSG00000132837.10	ENST00000524206.1,ENST00000255189.3
exon_skip_442926	5	78350006:78350171:78351632:78351731:78359435:78359610	78351632:78351731	ENSG00000132837.10	ENST00000255189.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for DMGDH

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENSG00000132837.10	ENST00000255189.3,ENST00000523732.1,ENST00000518477.1,ENST00000380311.4,ENST00000517853.1,ENST00000540686.1,ENST00000523201.1
exon_skip_442894	5	78329061:78329231:78338105:78338304:78340126:78340375	78338105:78338304	ENSG00000132837.10	ENST00000255189.3,ENST00000523732.1,ENST00000518477.1,ENST00000380311.4
exon_skip_442900	5	78329061:78329231:78359435:78359610:78365342:78365449	78359435:78359610	ENSG00000132837.10	ENST00000517853.1,ENST00000540686.1
exon_skip_442902	5	78340126:78340375:78347109:78347314:78350006:78350063	78347109:78347314	ENSG00000132837.10	ENST00000255189.3,ENST00000523732.1
exon_skip_442920	5	78347109:78347314:78350006:78350171:78351632:78351727	78350006:78350171	ENSG00000132837.10	ENST00000255189.3,ENST00000524206.1
exon_skip_442926	5	78350006:78350171:78351632:78351731:78359435:78359610	78351632:78351731	ENSG00000132837.10	ENST00000255189.3

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000255189	78324255	78324473	Frame-shift
ENST00000255189	78338105	78338304	Frame-shift
ENST00000255189	78347109	78347314	Frame-shift
ENST00000255189	78350006	78350171	In-frame
ENST00000255189	78351632	78351731	In-frame

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

ENST	Start of skipped exon	End of skipped exon	ORF
ENST00000255189	78324255	78324473	Frame-shift
ENST00000255189	78338105	78338304	Frame-shift
ENST00000255189	78347109	78347314	Frame-shift
ENST00000255189	78350006	78350171	In-frame
ENST00000255189	78351632	78351731	In-frame

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

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

Loci of skipped exons in TCGA 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
ENST00000255189	3114	866	78351632	78351731	306	404	92	125
ENST00000255189	3114	866	78350006	78350171	405	569	125	180

Loci of skipped exons in GTEx 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
ENST00000255189	3114	866	78351632	78351731	306	404	92	125
ENST00000255189	3114	866	78350006	78350171	405	569	125	180

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 feature	Description of feature
Q9UI17	92	125	19	398	Alternative sequence	ID=VSP_056960;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9UI17	92	125	101	103	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	92	125	51	866	Chain	ID=PRO_0000010767;Note=Dimethylglycine dehydrogenase%2C mitochondrial
Q9UI17	92	125	105	123	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	92	125	114	114	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9DBT9
Q9UI17	92	125	109	109	Natural variant	ID=VAR_011505;Note=In DMGDHD%3B shows 10 fold lower catalytic efficiency due to lower cofactor saturation and reduced thermal stability. H->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11231903,ECO:0000269\|PubMed:27486859;Dbxref=dbS
Q9UI17	92	125	87	95	Nucleotide binding	Note=FAD;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5L46,ECO:0000269\|PubMed:27486859;Dbxref=PMID:27486859
Q9UI17	125	180	19	398	Alternative sequence	ID=VSP_056960;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9UI17	125	180	134	138	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	157	159	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	162	164	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	51	866	Chain	ID=PRO_0000010767;Note=Dimethylglycine dehydrogenase%2C mitochondrial
Q9UI17	125	180	141	154	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	166	170	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	148	148	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9DBT9
Q9UI17	125	180	148	148	Modified residue	Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9DBT9
Q9UI17	125	180	168	168	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9DBT9

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 feature	Description of feature
Q9UI17	92	125	19	398	Alternative sequence	ID=VSP_056960;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9UI17	92	125	101	103	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	92	125	51	866	Chain	ID=PRO_0000010767;Note=Dimethylglycine dehydrogenase%2C mitochondrial
Q9UI17	92	125	105	123	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	92	125	114	114	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9DBT9
Q9UI17	92	125	109	109	Natural variant	ID=VAR_011505;Note=In DMGDHD%3B shows 10 fold lower catalytic efficiency due to lower cofactor saturation and reduced thermal stability. H->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11231903,ECO:0000269\|PubMed:27486859;Dbxref=dbS
Q9UI17	92	125	87	95	Nucleotide binding	Note=FAD;Ontology_term=ECO:0000244,ECO:0000269;evidence=ECO:0000244\|PDB:5L46,ECO:0000269\|PubMed:27486859;Dbxref=PMID:27486859
Q9UI17	125	180	19	398	Alternative sequence	ID=VSP_056960;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q9UI17	125	180	134	138	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	157	159	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	162	164	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	51	866	Chain	ID=PRO_0000010767;Note=Dimethylglycine dehydrogenase%2C mitochondrial
Q9UI17	125	180	141	154	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	166	170	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:5L46
Q9UI17	125	180	148	148	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9DBT9
Q9UI17	125	180	148	148	Modified residue	Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9DBT9
Q9UI17	125	180	168	168	Modified residue	Note=N6-acetyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q9DBT9

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SNVs in the skipped exons for DMGDH

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

- Differential PSIs between mutated versus non-mutated samples.

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

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-DD-A1EG-01	exon_skip_442894	78338106	78338304	78338150	78338150	Frame_Shift_Del	C	-	p.G383fs
LIHC	TCGA-DD-A3A0-01	exon_skip_442920	78350007	78350171	78350040	78350040	Frame_Shift_Del	A	-	p.I169fs
LIHC	TCGA-DD-A39Y-01	exon_skip_442920	78350007	78350171	78350125	78350125	Frame_Shift_Del	G	-	p.P141fs
LIHC	TCGA-DD-A3A0-01	exon_skip_442915 exon_skip_442900	78359436	78359610	78359601	78359601	Frame_Shift_Del	T	-	p.K37fs
LIHC	TCGA-BC-A112-01	exon_skip_442889	78324256	78324473	78324312	78324313	Frame_Shift_Ins	-	T	p.Q659fs
COAD	TCGA-AA-3510-01	exon_skip_442894	78338106	78338304	78338269	78338269	Nonsense_Mutation	G	A	p.R344X
HNSC	TCGA-CV-5970-01	exon_skip_442894	78338106	78338304	78338269	78338269	Nonsense_Mutation	G	A	p.R344*
BRCA	TCGA-EW-A1J5-01	exon_skip_442920	78350007	78350171	78350099	78350099	Nonsense_Mutation	G	A	p.Q150*
SKCM	TCGA-W3-A824-06	exon_skip_442915 exon_skip_442900	78359436	78359610	78359490	78359490	Nonsense_Mutation	T	A	p.R30*
HNSC	TCGA-CN-A6V1-01	exon_skip_442915 exon_skip_442900	78359436	78359610	78359574	78359574	Nonsense_Mutation	C	T	p.W46*
BLCA	TCGA-K4-A3WS-01	exon_skip_442915 exon_skip_442900	78359436	78359610	78359611	78359611	Splice_Site	C	G	p.G34_splice

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- 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
HEC251_ENDOMETRIUM	78324256	78324473	78324342	78324342	Missense_Mutation	A	G	p.L649P
MEWO_SKIN	78324256	78324473	78324457	78324457	Missense_Mutation	C	T	p.A611T
MEWO_SKIN	78338106	78338304	78338140	78338140	Missense_Mutation	C	T	p.G387R
SNU1040_LARGE_INTESTINE	78338106	78338304	78338197	78338197	Missense_Mutation	C	T	p.V368I
NCIH1792_LUNG	78347110	78347314	78347289	78347289	Missense_Mutation	C	G	p.G189A
SR786_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78350007	78350171	78350033	78350033	Missense_Mutation	T	C	p.M172V
EN_ENDOMETRIUM	78350007	78350171	78350041	78350041	Missense_Mutation	A	T	p.I169N
HSC2_UPPER_AERODIGESTIVE_TRACT	78350007	78350171	78350090	78350090	Missense_Mutation	G	A	p.R153W
NCIH1573_LUNG	78350007	78350171	78350090	78350090	Missense_Mutation	G	A	p.R153W
NCIH1355_LUNG	78350007	78350171	78350114	78350114	Missense_Mutation	C	T	p.D145N
LU65_LUNG	78350007	78350171	78350140	78350140	Missense_Mutation	C	A	p.R136I
SNU1040_LARGE_INTESTINE	78359436	78359610	78359564	78359564	Missense_Mutation	C	T	p.A50T
HEC108_ENDOMETRIUM	78324256	78324473	78324382	78324382	Nonsense_Mutation	G	A	p.Q636*
GP2D_LARGE_INTESTINE	78350007	78350171	78350171	78350171	Splice_Site	C	A	p.V126L
GP5D_LARGE_INTESTINE	78350007	78350171	78350171	78350171	Splice_Site	C	A	p.V126L

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

sQTL information located at the skipped exons.

Exon skip ID	Chromosome	Three exons	Skippped exon	ENST	Cancer type	SNP id	Location	DNA change (ref/var)	P-value
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1	KIRP	rs1805074	chr5:78324352	A/G	2.94e-04
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1	KIRP	rs1805074	chr5:78324352	A/G	1.23e-03
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1	LGG	rs1805074	chr5:78324352	A/G	2.19e-04
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1	LGG	rs1805074	chr5:78324352	A/G	4.41e-04
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1	KIRC	rs1805074	chr5:78324352	A/G	1.21e-05
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1	KIRC	rs1805074	chr5:78324352	A/G	4.41e-05
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1	THCA	rs1805074	chr5:78324352	A/G	1.95e-04
exon_skip_442889	5	78322258:78322404:78324255:78324473:78325726:78325857	78324255:78324473	ENST00000380311.4,ENST00000255189.3,ENST00000523201.1,ENST00000540686.1,ENST00000517853.1,ENST00000523732.1,ENST00000518477.1	THCA	rs1805074	chr5:78324352	A/G	2.44e-04

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

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

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RelatedDrugs for DMGDH

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

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for DMGDH

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
DMGDH	C1853892	Dimethylglycine Dehydrogenase Deficiency	1	CTD_human;ORPHANET;UNIPROT

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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