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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 HCLS1

check button Gene summary
Gene informationGene symbol

HCLS1

Gene ID

3059

Gene namehematopoietic cell-specific Lyn substrate 1
SynonymsCTTNL|HS1|lckBP1|p75
Cytomap

3q13.33

Type of geneprotein-coding
Descriptionhematopoietic lineage cell-specific protein
Modification date20180522
UniProtAcc

P14317

ContextPubMed: HCLS1 [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

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Exon skipping events across known transcript of Ensembl for HCLS1 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 HCLS1

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 HCLS1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3869523121350561:121350829:121350947:121351031:121351178:121351410121350947:121351031ENSG00000180353.6ENST00000314583.3,ENST00000473883.1,ENST00000428394.2
exon_skip_3869533121350947:121351031:121351178:121351410:121351913:121352018121351178:121351410ENSG00000180353.6ENST00000314583.3,ENST00000473883.1,ENST00000428394.2
exon_skip_3869543121355280:121355336:121355992:121356103:121361773:121361828121355992:121356103ENSG00000180353.6ENST00000314583.3,ENST00000473883.1
exon_skip_3869573121355992:121356103:121361773:121361828:121363664:121363775121361773:121361828ENSG00000180353.6ENST00000464274.1,ENST00000314583.3
exon_skip_3869613121363664:121363775:121366165:121366218:121376125:121376199121366165:121366218ENSG00000180353.6ENST00000464274.1
exon_skip_3869633121363664:121363775:121366165:121366295:121376125:121376199121366165:121366295ENSG00000180353.6ENST00000495491.1,ENST00000314583.3,ENST00000481314.1,ENST00000428394.2,ENST00000487290.1
exon_skip_3869653121363664:121363775:121366165:121366329:121376125:121376199121366165:121366329ENSG00000180353.6ENST00000497391.1
exon_skip_3869683121366165:121366295:121376125:121376199:121377110:121377194121376125:121376199ENSG00000180353.6ENST00000495491.1,ENST00000314583.3,ENST00000481314.1,ENST00000428394.2,ENST00000487290.1

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

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Exon skipping events with PSIs in GTEx for HCLS1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3869523121350561:121350829:121350947:121351031:121351178:121351410121350947:121351031ENSG00000180353.6ENST00000314583.3,ENST00000473883.1,ENST00000428394.2
exon_skip_3869533121350947:121351031:121351178:121351410:121351913:121352018121351178:121351410ENSG00000180353.6ENST00000314583.3,ENST00000473883.1,ENST00000428394.2
exon_skip_3869543121355280:121355336:121355992:121356103:121361773:121361828121355992:121356103ENSG00000180353.6ENST00000314583.3,ENST00000473883.1
exon_skip_3869573121355992:121356103:121361773:121361828:121363664:121363775121361773:121361828ENSG00000180353.6ENST00000314583.3,ENST00000464274.1
exon_skip_3869613121363664:121363775:121366165:121366218:121376125:121376199121366165:121366218ENSG00000180353.6ENST00000464274.1
exon_skip_3869633121363664:121363775:121366165:121366295:121376125:121376199121366165:121366295ENSG00000180353.6ENST00000314583.3,ENST00000428394.2,ENST00000495491.1,ENST00000487290.1,ENST00000481314.1
exon_skip_3869653121363664:121363775:121366165:121366329:121376125:121376199121366165:121366329ENSG00000180353.6ENST00000497391.1
exon_skip_3869683121366165:121366295:121376125:121376199:121377110:121377194121376125:121376199ENSG00000180353.6ENST00000314583.3,ENST00000428394.2,ENST00000495491.1,ENST00000487290.1,ENST00000481314.1

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 HCLS1

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
ENST00000314583121351178121351410Frame-shift
ENST00000314583121361773121361828Frame-shift
ENST00000314583121366165121366295Frame-shift
ENST00000314583121376125121376199Frame-shift
ENST00000314583121350947121351031In-frame
ENST00000314583121355992121356103In-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
ENST00000314583121351178121351410Frame-shift
ENST00000314583121361773121361828Frame-shift
ENST00000314583121366165121366295Frame-shift
ENST00000314583121376125121376199Frame-shift
ENST00000314583121350947121351031In-frame
ENST00000314583121355992121356103In-frame

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Infer the effects of exon skipping event on protein functional features for HCLS1

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
ENST000003145832017486121355992121356103547657151188

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
ENST000003145832017486121355992121356103547657151188

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
P14317151188134209Alternative sequenceID=VSP_056429;Note=In isoform 2. SAVGFDYKGEVEKHTSQKDYSRGFGGRYGVEKDKWDKAALGYDYKGETEKHESQRDYAKGFGGQYGIQKDRVDKSA->ITLVALVAGTGWRRINGTKQLWDMTTRERRRNTSPREIMPRALVASMESRRTEWIRALSASMKWRPRPQLIRRRRP;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxr
P143171511881486ChainID=PRO_0000083921;Note=Hematopoietic lineage cell-specific protein
P14317151188116152RepeatNote=Cortactin 2
P14317151188153189RepeatNote=Cortactin 3


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
P14317151188134209Alternative sequenceID=VSP_056429;Note=In isoform 2. SAVGFDYKGEVEKHTSQKDYSRGFGGRYGVEKDKWDKAALGYDYKGETEKHESQRDYAKGFGGQYGIQKDRVDKSA->ITLVALVAGTGWRRINGTKQLWDMTTRERRRNTSPREIMPRALVASMESRRTEWIRALSASMKWRPRPQLIRRRRP;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxr
P143171511881486ChainID=PRO_0000083921;Note=Hematopoietic lineage cell-specific protein
P14317151188116152RepeatNote=Cortactin 2
P14317151188153189RepeatNote=Cortactin 3


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SNVs in the skipped exons for HCLS1

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
LIHCTCGA-DD-A39Y-01exon_skip_386952
121350948121351031121350950121350950Frame_Shift_DelC-p.G441fs
LIHCTCGA-DD-A39Y-01exon_skip_386953
121351179121351410121351194121351194Frame_Shift_DelA-p.S410fs
LIHCTCGA-DD-A39Y-01exon_skip_386953
121351179121351410121351233121351233Frame_Shift_DelC-p.D396fs
LUADTCGA-78-7150-01exon_skip_386953
121351179121351410121351394121351394Frame_Shift_DelG-p.P342fs
LIHCTCGA-G3-A3CJ-01exon_skip_386954
121355993121356103121356057121356057Frame_Shift_DelT-p.K167fs
LIHCTCGA-DD-A1EG-01exon_skip_386963
121366166121366295121366247121366247Frame_Shift_DelC-p.R69fs
LIHCTCGA-DD-A1EG-01exon_skip_386965
121366166121366329121366247121366247Frame_Shift_DelC-p.R69fs
SKCMTCGA-FR-A726-01exon_skip_386957
121361774121361828121361780121361780Nonsense_MutationGAp.Q150*
BRCATCGA-A8-A06X-01exon_skip_386968
121376126121376199121376169121376169Nonsense_MutationCAp.G39*
COADTCGA-AA-A00K-01exon_skip_386968
121376126121376199121376175121376175Nonsense_MutationGAp.R37X
COADTCGA-CA-6717-01exon_skip_386968
121376126121376199121376175121376175Nonsense_MutationGAp.R37X
SKCMTCGA-D3-A5GO-06exon_skip_386952
121350948121351031121351032121351032Splice_SiteCT.
UCECTCGA-AP-A05N-01exon_skip_386953
121351179121351410121351412121351412Splice_SiteTCp.D337_splice

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
HCLS1_121363664_121363775_121366165_121366329_121376125_121376199_TCGA-DD-A1EG-01Sample: TCGA-DD-A1EG-01
Cancer type: LIHC
ESID: exon_skip_386963
Skipped exon start: 121366166
Skipped exon end: 121366295
Mutation start: 121366247
Mutation end: 121366247
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.R69fs
HCLS1_121363664_121363775_121366165_121366329_121376125_121376199_TCGA-DD-A1EG-01Sample: TCGA-DD-A1EG-01
Cancer type: LIHC
ESID: exon_skip_386965
Skipped exon start: 121366166
Skipped exon end: 121366329
Mutation start: 121366247
Mutation end: 121366247
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.R69fs
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check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
HUT102_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE121351179121351410121351293121351294In_Frame_Ins-CTCAGGCTCGGGCTCAGGp.374_375insEPEPEP
HCC2450_LUNG121351179121351410121351209121351209Missense_MutationCGp.E404Q
K2_SKIN121351179121351410121351220121351220Missense_MutationAGp.V400A
CHLA258_BONE121351179121351410121351301121351301Missense_MutationTGp.E373A
SW684_SOFT_TISSUE121355993121356103121356014121356014Missense_MutationCTp.E182K
TTC549_SOFT_TISSUE121355993121356103121356022121356022Missense_MutationCGp.G179A
HSC3_UPPER_AERODIGESTIVE_TRACT121355993121356103121356097121356097Missense_MutationGCp.S154C
NCIH2595_PLEURA121366166121366295121366273121366273Missense_MutationCTp.V61I
NCIH2595_PLEURA121366166121366329121366273121366273Missense_MutationCTp.V61I
MCC13_SKIN121376126121376199121376150121376151Missense_MutationCCATp.G45M
MCC13_SKIN121376126121376199121376150121376150Missense_MutationCAp.G45V
MCC13_SKIN121376126121376199121376151121376151Missense_MutationCTp.G45R
YKG1_CENTRAL_NERVOUS_SYSTEM121355993121356103121356054121356054Nonsense_MutationCTp.W168*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HCLS1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_3869533121350947:121351031:121351178:121351410:121351913:121352018121351178:121351410ENST00000314583.3,ENST00000473883.1,ENST00000428394.2LGGrs150627065chr3:121351315G/GGGCTCAGGCTCA1.22e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HCLS1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HCLS1


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RelatedDrugs for HCLS1

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 HCLS1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
HCLS1C0003873Rheumatoid Arthritis1CTD_human