ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for HMGCL

Gene summary

Gene information	Gene symbol	HMGCL
	Gene ID	3155
	Gene name	3-hydroxymethyl-3-methylglutaryl-CoA lyase
	Synonyms	HL
	Cytomap	1p36.11
	Type of gene	protein-coding
	Description	hydroxymethylglutaryl-CoA lyase, mitochondrial3-hydroxy-3-methylglutarate-CoA lyase3-hydroxy-3-methylglutaryl-CoA lyase3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyaseHMG-CoA lyasehydroxymethylglutaricaciduriamitochondrial 3-hydroxy-3-methylglutary
	Modification date	20180523
	UniProtAcc	P35914
	Context	PubMed: HMGCL [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
HMGCL	GO:0006629	lipid metabolic process	8027038
HMGCL	GO:0046951	ketone body biosynthetic process	9200711\|22847177\|22865860
HMGCL	GO:0051262	protein tetramerization	12464283

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Exon skipping events across known transcript of Ensembl for HMGCL 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 HMGCL

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 HMGCL

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_23154	1	24128399:24129054:24130889:24131015:24134624:24134705	24130889:24131015	ENSG00000117305.10	ENST00000235958.4,ENST00000436439.2,ENST00000374487.2,ENST00000374490.3,ENST00000374483.4
exon_skip_23162	1	24130889:24131015:24134624:24134705:24143164:24143251	24134624:24134705	ENSG00000117305.10	ENST00000509389.1
exon_skip_23163	1	24130889:24131015:24134624:24134813:24137225:24137289	24134624:24134813	ENSG00000117305.10	ENST00000374487.2,ENST00000374490.3,ENST00000374483.4
exon_skip_23164	1	24130889:24131015:24134624:24134813:24143164:24143251	24134624:24134813	ENSG00000117305.10	ENST00000436439.2
exon_skip_23166	1	24133439:24133530:24133643:24133775:24134624:24134705	24133643:24133775	ENSG00000117305.10	ENST00000496907.1
exon_skip_23169	1	24134624:24134813:24137225:24137289:24140679:24140811	24137225:24137289	ENSG00000117305.10	ENST00000496907.1,ENST00000374487.2,ENST00000374490.3,ENST00000374483.4
exon_skip_23177	1	24137225:24137289:24140679:24140828:24143164:24143251	24140679:24140828	ENSG00000117305.10	ENST00000513148.1,ENST00000374487.2,ENST00000374490.3,ENST00000374483.4
exon_skip_23179	1	24143164:24143260:24143965:24144073:24146999:24147083	24143965:24144073	ENSG00000117305.10	ENST00000509389.1,ENST00000513148.1,ENST00000436439.2,ENST00000374487.2,ENST00000374490.3,ENST00000374483.4
exon_skip_23180	1	24143965:24144073:24146999:24147083:24151845:24151892	24146999:24147083	ENSG00000117305.10	ENST00000509389.1,ENST00000513148.1,ENST00000436439.2
exon_skip_23184	1	24146999:24147083:24152573:24152673:24164553:24165110	24152573:24152673	ENSG00000117305.10	ENST00000374487.2,ENST00000374483.4

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for HMGCL

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_23154	1	24128399:24129054:24130889:24131015:24134624:24134705	24130889:24131015	ENSG00000117305.10	ENST00000374490.3,ENST00000436439.2,ENST00000374487.2,ENST00000374483.4,ENST00000235958.4
exon_skip_23162	1	24130889:24131015:24134624:24134705:24143164:24143251	24134624:24134705	ENSG00000117305.10	ENST00000509389.1
exon_skip_23163	1	24130889:24131015:24134624:24134813:24137225:24137289	24134624:24134813	ENSG00000117305.10	ENST00000374490.3,ENST00000374487.2,ENST00000374483.4
exon_skip_23164	1	24130889:24131015:24134624:24134813:24143164:24143251	24134624:24134813	ENSG00000117305.10	ENST00000436439.2
exon_skip_23166	1	24133439:24133530:24133643:24133775:24134624:24134705	24133643:24133775	ENSG00000117305.10	ENST00000496907.1
exon_skip_23169	1	24134624:24134813:24137225:24137289:24140679:24140811	24137225:24137289	ENSG00000117305.10	ENST00000374490.3,ENST00000374487.2,ENST00000374483.4,ENST00000496907.1
exon_skip_23177	1	24137225:24137289:24140679:24140828:24143164:24143251	24140679:24140828	ENSG00000117305.10	ENST00000374490.3,ENST00000374487.2,ENST00000374483.4,ENST00000513148.1
exon_skip_23179	1	24143164:24143260:24143965:24144073:24146999:24147083	24143965:24144073	ENSG00000117305.10	ENST00000374490.3,ENST00000436439.2,ENST00000374487.2,ENST00000374483.4,ENST00000509389.1,ENST00000513148.1
exon_skip_23180	1	24143965:24144073:24146999:24147083:24151845:24151892	24146999:24147083	ENSG00000117305.10	ENST00000436439.2,ENST00000509389.1,ENST00000513148.1
exon_skip_23184	1	24146999:24147083:24152573:24152673:24164553:24165110	24152573:24152673	ENSG00000117305.10	ENST00000374487.2,ENST00000374483.4

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 HMGCL

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
ENST00000374490	24137225	24137289	Frame-shift
ENST00000374490	24140679	24140828	Frame-shift
ENST00000374490	24130889	24131015	In-frame
ENST00000374490	24134624	24134813	In-frame
ENST00000374490	24143965	24144073	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
ENST00000374490	24137225	24137289	Frame-shift
ENST00000374490	24140679	24140828	Frame-shift
ENST00000374490	24130889	24131015	In-frame
ENST00000374490	24134624	24134813	In-frame
ENST00000374490	24143965	24144073	In-frame

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

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
ENST00000374490	1617	325	24143965	24144073	189	296	48	84
ENST00000374490	1617	325	24134624	24134813	606	794	187	250
ENST00000374490	1617	325	24130889	24131015	795	920	250	292

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
ENST00000374490	1617	325	24143965	24144073	189	296	48	84
ENST00000374490	1617	325	24134624	24134813	606	794	187	250
ENST00000374490	1617	325	24130889	24131015	795	920	250	292

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
P35914	48	84	69	71	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	48	84	28	325	Chain	ID=PRO_0000013478;Note=Hydroxymethylglutaryl-CoA lyase%2C mitochondrial
P35914	48	84	33	300	Domain	Note=Pyruvate carboxyltransferase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01151
P35914	48	84	53	65	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	48	84	83	85	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	48	84	48	48	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P35914	48	84	48	48	Modified residue	Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P38060
P35914	48	84	72	72	Mutagenesis	Note=Loss of activity%2C and reduced affinity for metal cofactor and substrate. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12874287;Dbxref=PMID:12874287
P35914	48	84	48	48	Natural variant	ID=VAR_058441;Note=In HMGCLD%3B abolishes almost all enzymatic activity. K->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17459752;Dbxref=PMID:17459752
P35914	48	84	70	70	Natural variant	ID=VAR_003748;Note=In HMGCLD. V->L;Dbxref=dbSNP:rs121964996
P35914	48	84	75	75	Natural variant	ID=VAR_058442;Note=In HMGCLD. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12746442;Dbxref=dbSNP:rs1357942068,PMID:12746442
P35914	48	84	79	81	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	117	187	Alternative sequence	ID=VSP_047444;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:21952825;Dbxref=PMID:14702039,PMID:21952825
P35914	187	250	188	250	Alternative sequence	ID=VSP_043788;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:21952825;Dbxref=PMID:21952825
P35914	187	250	198	204	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	230	235	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	28	325	Chain	ID=PRO_0000013478;Note=Hydroxymethylglutaryl-CoA lyase%2C mitochondrial
P35914	187	250	33	300	Domain	Note=Pyruvate carboxyltransferase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01151
P35914	187	250	182	194	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	211	224	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	227	229	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	241	250	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	233	233	Metal binding	Note=Divalent metal cation
P35914	187	250	235	235	Metal binding	Note=Divalent metal cation
P35914	187	250	204	204	Mutagenesis	Note=Reduced activity%2C and reduced affinity for metal cofactor and substrate. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12874287;Dbxref=PMID:12874287
P35914	187	250	233	233	Mutagenesis	Note=Loss of activity%2C and reduced proton exchange rate. H->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12874287,ECO:0000269\|PubMed:15122894;Dbxref=PMID:12874287,PMID:15122894
P35914	187	250	192	192	Natural variant	ID=VAR_058445;Note=In HMGCLD%3B activity lower than 5%25 respect to the wild-type. F->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19177531;Dbxref=PMID:19177531
P35914	187	250	200	200	Natural variant	ID=VAR_058446;Note=In HMGCLD%3B activity lower than 5%25 respect to the wild-type. I->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19177531;Dbxref=PMID:19177531
P35914	187	250	201	201	Natural variant	ID=VAR_058447;Note=In HMGCLD. S->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12746442;Dbxref=dbSNP:rs760106433,PMID:12746442
P35914	187	250	203	203	Natural variant	ID=VAR_058448;Note=In HMGCLD%3B complete loss of activity. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16601870;Dbxref=PMID:16601870
P35914	187	250	204	204	Natural variant	ID=VAR_058449;Note=In HMGCLD. D->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12746442;Dbxref=PMID:12746442
P35914	187	250	233	233	Natural variant	ID=VAR_003749;Note=In HMGCLD%3B loss of activity. H->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:19177531,ECO:0000269\|PubMed:8798725,ECO:0000269\|PubMed:9784232;Dbxref=dbSNP:rs727503963,PMID:19177531,PMID:8798725,PMID:97
P35914	187	250	243	243	Sequence conflict	Note=A->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35914	250	292	266	266	Active site	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU10115
P35914	250	292	188	250	Alternative sequence	ID=VSP_043788;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:21952825;Dbxref=PMID:21952825
P35914	250	292	255	259	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	250	292	28	325	Chain	ID=PRO_0000013478;Note=Hydroxymethylglutaryl-CoA lyase%2C mitochondrial
P35914	250	292	33	300	Domain	Note=Pyruvate carboxyltransferase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01151
P35914	250	292	241	250	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	250	292	278	288	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	250	292	275	275	Metal binding	Note=Divalent metal cation
P35914	250	292	266	266	Mutagenesis	Note=Loss of activity. C->A
P35914	250	292	279	279	Mutagenesis	Note=Reduced thermal stability%2C but normal activity. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12874287;Dbxref=PMID:12874287
P35914	250	292	280	280	Mutagenesis	Note=Normal activity. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12874287;Dbxref=PMID:12874287
P35914	250	292	263	263	Natural variant	ID=VAR_058450;Note=In HMGCLD. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9784232;Dbxref=PMID:9784232
P35914	250	292	279	279	Natural variant	ID=VAR_014202;Note=In HMGCLD. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11129331;Dbxref=dbSNP:rs121964998,PMID:11129331

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
P35914	48	84	69	71	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	48	84	28	325	Chain	ID=PRO_0000013478;Note=Hydroxymethylglutaryl-CoA lyase%2C mitochondrial
P35914	48	84	33	300	Domain	Note=Pyruvate carboxyltransferase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01151
P35914	48	84	53	65	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	48	84	83	85	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	48	84	48	48	Modified residue	Note=N6-acetyllysine%3B alternate;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19608861;Dbxref=PMID:19608861
P35914	48	84	48	48	Modified residue	Note=N6-succinyllysine%3B alternate;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P38060
P35914	48	84	72	72	Mutagenesis	Note=Loss of activity%2C and reduced affinity for metal cofactor and substrate. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12874287;Dbxref=PMID:12874287
P35914	48	84	48	48	Natural variant	ID=VAR_058441;Note=In HMGCLD%3B abolishes almost all enzymatic activity. K->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17459752;Dbxref=PMID:17459752
P35914	48	84	70	70	Natural variant	ID=VAR_003748;Note=In HMGCLD. V->L;Dbxref=dbSNP:rs121964996
P35914	48	84	75	75	Natural variant	ID=VAR_058442;Note=In HMGCLD. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12746442;Dbxref=dbSNP:rs1357942068,PMID:12746442
P35914	48	84	79	81	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	117	187	Alternative sequence	ID=VSP_047444;Note=In isoform 2 and isoform 3. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:21952825;Dbxref=PMID:14702039,PMID:21952825
P35914	187	250	188	250	Alternative sequence	ID=VSP_043788;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:21952825;Dbxref=PMID:21952825
P35914	187	250	198	204	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	230	235	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	28	325	Chain	ID=PRO_0000013478;Note=Hydroxymethylglutaryl-CoA lyase%2C mitochondrial
P35914	187	250	33	300	Domain	Note=Pyruvate carboxyltransferase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01151
P35914	187	250	182	194	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	211	224	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	227	229	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	241	250	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	187	250	233	233	Metal binding	Note=Divalent metal cation
P35914	187	250	235	235	Metal binding	Note=Divalent metal cation
P35914	187	250	204	204	Mutagenesis	Note=Reduced activity%2C and reduced affinity for metal cofactor and substrate. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12874287;Dbxref=PMID:12874287
P35914	187	250	233	233	Mutagenesis	Note=Loss of activity%2C and reduced proton exchange rate. H->A;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12874287,ECO:0000269\|PubMed:15122894;Dbxref=PMID:12874287,PMID:15122894
P35914	187	250	192	192	Natural variant	ID=VAR_058445;Note=In HMGCLD%3B activity lower than 5%25 respect to the wild-type. F->S;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19177531;Dbxref=PMID:19177531
P35914	187	250	200	200	Natural variant	ID=VAR_058446;Note=In HMGCLD%3B activity lower than 5%25 respect to the wild-type. I->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:19177531;Dbxref=PMID:19177531
P35914	187	250	201	201	Natural variant	ID=VAR_058447;Note=In HMGCLD. S->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12746442;Dbxref=dbSNP:rs760106433,PMID:12746442
P35914	187	250	203	203	Natural variant	ID=VAR_058448;Note=In HMGCLD%3B complete loss of activity. G->E;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:16601870;Dbxref=PMID:16601870
P35914	187	250	204	204	Natural variant	ID=VAR_058449;Note=In HMGCLD. D->N;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12746442;Dbxref=PMID:12746442
P35914	187	250	233	233	Natural variant	ID=VAR_003749;Note=In HMGCLD%3B loss of activity. H->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:19177531,ECO:0000269\|PubMed:8798725,ECO:0000269\|PubMed:9784232;Dbxref=dbSNP:rs727503963,PMID:19177531,PMID:8798725,PMID:97
P35914	187	250	243	243	Sequence conflict	Note=A->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
P35914	250	292	266	266	Active site	Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU10115
P35914	250	292	188	250	Alternative sequence	ID=VSP_043788;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:21952825;Dbxref=PMID:21952825
P35914	250	292	255	259	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	250	292	28	325	Chain	ID=PRO_0000013478;Note=Hydroxymethylglutaryl-CoA lyase%2C mitochondrial
P35914	250	292	33	300	Domain	Note=Pyruvate carboxyltransferase;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU01151
P35914	250	292	241	250	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	250	292	278	288	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2CW6
P35914	250	292	275	275	Metal binding	Note=Divalent metal cation
P35914	250	292	266	266	Mutagenesis	Note=Loss of activity. C->A
P35914	250	292	279	279	Mutagenesis	Note=Reduced thermal stability%2C but normal activity. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12874287;Dbxref=PMID:12874287
P35914	250	292	280	280	Mutagenesis	Note=Normal activity. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12874287;Dbxref=PMID:12874287
P35914	250	292	263	263	Natural variant	ID=VAR_058450;Note=In HMGCLD. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9784232;Dbxref=PMID:9784232
P35914	250	292	279	279	Natural variant	ID=VAR_014202;Note=In HMGCLD. E->K;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11129331;Dbxref=dbSNP:rs121964998,PMID:11129331

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SNVs in the skipped exons for HMGCL

- 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
UCEC	TCGA-AX-A0IW-01	exon_skip_23154	24130890	24131015	24130916	24130923	Frame_Shift_Del	TGTAGACC	-	p.L281fs
UCEC	TCGA-AX-A0IW-01	exon_skip_23154	24130890	24131015	24130916	24130923	Frame_Shift_Del	TGTAGACC	-	p.V282fs
HNSC	TCGA-CR-7388-01	exon_skip_23169	24137226	24137289	24137224	24137224	Splice_Site	A	C	p.E187_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
NCIH1304_LUNG	24130890	24131015	24130976	24130976	Missense_Mutation	C	T	p.G264R
NCIH2170_LUNG	24134625	24134813	24134671	24134671	Missense_Mutation	T	C	p.H235R
NCIH2170_LUNG	24134625	24134705	24134671	24134671	Missense_Mutation	T	C	p.H235R
SW962_VULVA	24134625	24134813	24134709	24134709	Missense_Mutation	C	A	p.M222I
SW962_VULVA	24134625	24134705	24134709	24134709	Missense_Mutation	C	A	p.M222I
NCIH1651_LUNG	24134625	24134813	24134719	24134719	Missense_Mutation	G	C	p.S219C
PK45H_PANCREAS	24134625	24134813	24134785	24134785	Missense_Mutation	C	T	p.C197Y
EN_ENDOMETRIUM	24137226	24137289	24137279	24137279	Missense_Mutation	A	G	p.C170R
SBC3_LUNG	24140680	24140828	24140724	24140724	Missense_Mutation	G	T	p.D151E
LNCAPCLONEFGC_PROSTATE	24140680	24140828	24140731	24140731	Missense_Mutation	C	A	p.R149M
CHSA0011_BONE	24140680	24140828	24140749	24140749	Missense_Mutation	A	G	p.I143T
NY_BONE	24140680	24140828	24140749	24140749	Missense_Mutation	A	G	p.I143T
DETROIT562_UPPER_AERODIGESTIVE_TRACT	24140680	24140828	24140788	24140788	Missense_Mutation	G	A	p.A130V
22RV1_PROSTATE	24147000	24147083	24147032	24147032	Missense_Mutation	C	T	p.V38I
CADOES1_BONE	24134625	24134813	24134625	24134625	Splice_Site	C	T	p.Q250Q
CADOES1_BONE	24134625	24134705	24134625	24134625	Splice_Site	C	T	p.Q250Q

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

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

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

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

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RelatedDrugs for HMGCL

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 HMGCL

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
HMGCL	C0268601	HMG CoA lyase deficiency	9	CTD_human;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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