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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 MCPH1

check button Gene summary
Gene informationGene symbol

MCPH1

Gene ID

79648

Gene namemicrocephalin 1
SynonymsBRIT1|MCT
Cytomap

8p23.1

Type of geneprotein-coding
DescriptionmicrocephalinBRCT-repeat inhibitor of TERT expression 1truncated microcephalin
Modification date20180519
UniProtAcc

Q8NEM0

ContextPubMed: MCPH1 [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
MCPH1

GO:0000122

negative regulation of transcription by RNA polymerase II

12837246

MCPH1

GO:0071850

mitotic cell cycle arrest

24633962


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Exon skipping events across known transcript of Ensembl for MCPH1 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 MCPH1

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 MCPH1

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_48102086272285:6272404:6289019:6289107:6293568:62936836289019:6289107ENSG00000147316.8ENST00000522905.1,ENST00000344683.5,ENST00000519480.1
exon_skip_48102186289019:6289107:6293568:6293683:6296473:62966176293568:6293683ENSG00000147316.8ENST00000344683.5,ENST00000519480.1
exon_skip_48102286293568:6293683:6296473:6296617:6299587:62996776296473:6296617ENSG00000147316.8ENST00000344683.5,ENST00000519480.1
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENSG00000147316.8ENST00000344683.5
exon_skip_48102986312722:6312773:6335114:6335152:6338234:63383976335114:6335152ENSG00000147316.8ENST00000344683.5
exon_skip_48103486357372:6357450:6478974:6479212:6500514:65008916478974:6479212ENSG00000147316.8ENST00000344683.5
exon_skip_48103786478974:6479212:6500200:6500360:6500514:65008916500200:6500360ENSG00000147316.8ENST00000521175.1

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

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Exon skipping events with PSIs in GTEx for MCPH1

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_48102086272285:6272404:6289019:6289107:6293568:62936836289019:6289107ENSG00000147316.8ENST00000344683.5,ENST00000519480.1,ENST00000522905.1
exon_skip_48102186289019:6289107:6293568:6293683:6296473:62966176293568:6293683ENSG00000147316.8ENST00000344683.5,ENST00000519480.1
exon_skip_48102286293568:6293683:6296473:6296617:6299587:62996776296473:6296617ENSG00000147316.8ENST00000344683.5,ENST00000519480.1
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENSG00000147316.8ENST00000344683.5
exon_skip_48102986312722:6312773:6335114:6335152:6338234:63383976335114:6335152ENSG00000147316.8ENST00000344683.5
exon_skip_48103486357372:6357450:6478974:6479212:6500514:65008916478974:6479212ENSG00000147316.8ENST00000344683.5
exon_skip_48103786478974:6479212:6500200:6500360:6500514:65008916500200:6500360ENSG00000147316.8ENST00000521175.1

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 MCPH1

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

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

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Infer the effects of exon skipping event on protein functional features for MCPH1

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

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

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


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


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SNVs in the skipped exons for MCPH1

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
ESCATCGA-L5-A4OI-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.I104fs
ESCATCGA-L5-A4OI-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
ESCATCGA-L5-A8NN-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
LGGTCGA-DU-A76K-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
LGGTCGA-HT-7601-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
LIHCTCGA-G3-A25Y-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
LIHCTCGA-G3-A3CJ-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
PRADTCGA-HC-7212-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
THCATCGA-FY-A3R9-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
UCECTCGA-D1-A17M-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K105fs
UCSTCGA-N7-A4Y0-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.I104fs
UCSTCGA-N7-A4Y0-01exon_skip_481020
6289020628910762890996289099Frame_Shift_DelA-p.K107fs
COADTCGA-AA-3663-01exon_skip_481027
6301914630306863026396302639Frame_Shift_DelA-p.G417fs
COADTCGA-CK-5916-01exon_skip_481034
6478975647921264790676479067Frame_Shift_DelC-p.S769fs
ESCATCGA-L5-A88Z-01exon_skip_481020
6289020628910762890986289099Frame_Shift_Ins-Ap.R107fs
LUADTCGA-69-7978-01exon_skip_481021
6293569629368362936376293638Frame_Shift_Ins-Tp.*131fs
SKCMTCGA-EE-A3AH-06exon_skip_481027
6301914630306863025156302516Frame_Shift_Ins-Tp.R376fs
SKCMTCGA-EE-A3AH-06exon_skip_481027
6301914630306863025156302516Frame_Shift_Ins-Tp.RF424fs
UCECTCGA-B5-A0JV-01exon_skip_481027
6301914630306863026386302639Frame_Shift_Ins-Ap.G465fs
UCECTCGA-B5-A0K2-01exon_skip_481027
6301914630306863026386302639Frame_Shift_Ins-Ap.G465fs
KIRPTCGA-BQ-7059-01exon_skip_481029
6335115633515263351326335133Frame_Shift_Ins-Ap.D652fs
KIRPTCGA-BQ-7059-01exon_skip_481029
6335115633515263351326335133Frame_Shift_Ins-Ap.V651fs
STADTCGA-BR-8591-01exon_skip_481034
6478975647921264790666479067Frame_Shift_Ins-Cp.S769fs
STADTCGA-BR-8591-01exon_skip_481034
6478975647921264790676479068Frame_Shift_Ins-Cp.S769fs
LUSCTCGA-85-6561-01exon_skip_481020
6289020628910762890336289033Nonsense_MutationGTp.G83*
ESCATCGA-LN-A49M-01exon_skip_481020
6289020628910762890886289088Nonsense_MutationCGp.S101*
ESCATCGA-JY-A6F8-01exon_skip_481027
6301914630306863023376302337Nonsense_MutationCAp.S365X
UCECTCGA-AX-A0J1-01exon_skip_481027
6301914630306863028526302852Nonsense_MutationGTp.G537*
HNSCTCGA-CV-7568-01exon_skip_481027
6301914630306863030356303035Nonsense_MutationGTp.E598*
ESCATCGA-2H-A9GF-01exon_skip_481021
6293569629368362935686293568Splice_SiteGT.
ESCATCGA-2H-A9GF-01exon_skip_481021
6293569629368362935686293568Splice_SiteGTe5-1

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
GP2D_LARGE_INTESTINE6293569629368362936696293669Frame_Shift_DelA-p.Q141fs
GP5D_LARGE_INTESTINE6293569629368362936696293669Frame_Shift_DelA-p.Q141fs
WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6293569629368362936696293669Frame_Shift_DelA-p.Q141fs
GCT_SOFT_TISSUE6301914630306863020826302085Frame_Shift_DelTCAC-p.FT280fs
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM6301914630306863026396302639Frame_Shift_DelA-p.K467fs
NCIH2461_PLEURA6301914630306863027286302728Frame_Shift_DelT-p.T495fs
DU145_PROSTATE6289020628910762890986289099Frame_Shift_Ins-Ap.K105fs
MFE319_ENDOMETRIUM6289020628910762890986289099Frame_Shift_Ins-Ap.K105fs
RKO_LARGE_INTESTINE6289020628910762890986289099Frame_Shift_Ins-Ap.K105fs
CACO2_LARGE_INTESTINE6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
CHAGOK1_LUNG6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HCC1569_BREAST6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HCC364_LUNG6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HEC59_ENDOMETRIUM6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HMCB_SKIN6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HPAC_PANCREAS6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HS578T_BREAST6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HS695T_SKIN6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HS766T_PANCREAS6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HT1376_URINARY_TRACT6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
HUPT3_PANCREAS6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
IPC298_SKIN6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
ISTMES1_PLEURA6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
K562_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
KNS60_CENTRAL_NERVOUS_SYSTEM6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
KP3_PANCREAS6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
KPNYN_AUTONOMIC_GANGLIA6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
KYSE270_OESOPHAGUS6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
LN319_CENTRAL_NERVOUS_SYSTEM6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
MDAMB453_BREAST6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
MDAMB468_BREAST6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
NCIH2077_LUNG6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
NCIH1373_LUNG6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
NCIH1666_LUNG6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
NCIH1734_LUNG6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
NCIH2171_LUNG6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
NCIH508_LARGE_INTESTINE6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
OVCAR4_OVARY6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
PANC1_PANCREAS6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
PC14_LUNG6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
SCABER_URINARY_TRACT6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
SLR23_KIDNEY6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
SNU182_LIVER6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
T24_URINARY_TRACT6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
TOLEDO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
TOV21G_OVARY6301914630306863026386302639Frame_Shift_Ins-Ap.K466fs
SKMEL24_SKIN6289020628910762890426289042Missense_MutationAGp.I86V
TMK1_STOMACH6293569629368362935896293589Missense_MutationACp.K114N
HT115_LARGE_INTESTINE6293569629368362936176293617Missense_MutationGTp.D124Y
MEC1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6293569629368362936806293680Missense_MutationCGp.L145V
TT_OESOPHAGUS6296474629661762965986296598Missense_MutationGTp.R187S
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6296474629661762966036296603Missense_MutationATp.N189I
HEC265_ENDOMETRIUM6301914630306863020646302064Missense_MutationTCp.I274T
HCC2814_LUNG6301914630306863020936302093Missense_MutationGTp.D284Y
MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863021436302143Missense_MutationAGp.I300M
CW2_LARGE_INTESTINE6301914630306863021626302162Missense_MutationGAp.A307T
BONNA12_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863021816302181Missense_MutationCTp.P313L
KO52_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863022176302217Missense_MutationCGp.T325R
ATN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863022396302239Missense_MutationGTp.L332F
NCIH1563_LUNG6301914630306863022416302241Missense_MutationCTp.S333F
DEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863022616302261Missense_MutationAGp.K340E
MUGCHOR1_BONE6301914630306863023436302343Missense_MutationCTp.P367L
A427_LUNG6301914630306863024066302406Missense_MutationGTp.C388F
SKUT1_SOFT_TISSUE6301914630306863024126302412Missense_MutationCTp.S390L
SNUC5_LARGE_INTESTINE6301914630306863026636302663Missense_MutationAGp.T474A
KMS26_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6301914630306863027776302777Missense_MutationCGp.Q512E
LNCAPCLONEFGC_PROSTATE6301914630306863027956302795Missense_MutationGAp.A518T
UACC257_SKIN6301914630306863028736302873Missense_MutationCGp.P544A
UACC257_SKIN6301914630306863028736302874Missense_MutationCCGTp.P544V
UACC257_SKIN6301914630306863028746302874Missense_MutationCTp.P544L
IGROV1_OVARY6301914630306863029026302902Missense_MutationATp.K553N
H2369_PLEURA6301914630306863029276302927Missense_MutationCGp.Q562E
NCIH64_LUNG6478975647921264790376479037Missense_MutationGTp.Q759H
SNU1040_LARGE_INTESTINE6478975647921264790606479060Missense_MutationCTp.A767V
AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE6478975647921264790716479071Missense_MutationCGp.P771A
COLO800_SKIN6478975647921264791526479152Missense_MutationGAp.G798R
MHHES1_BONE6478975647921264791526479152Missense_MutationGAp.G798R
SKMEL24_SKIN6478975647921264792066479206Missense_MutationGCp.V816L
OC316_OVARY6301914630306863027776302777Nonsense_MutationCTp.Q512*
OC314_OVARY6301914630306863027776302777Nonsense_MutationCTp.Q512*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MCPH1

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5GBMrs930557chr8:6302183G/C4.48e-04
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5KIRPrs930557chr8:6302183G/C5.40e-04
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5LGGrs930557chr8:6302183G/C4.06e-08
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5LGGrs2083914chr8:6302154G/T1.15e-04
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5KIRCrs2920676chr8:6302671A/G1.19e-03
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5KIRCrs930557chr8:6302183G/C2.23e-03
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5LUSCrs2083914chr8:6302154G/T7.45e-05
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5LUSCrs930557chr8:6302183G/C2.64e-03
exon_skip_48102786299587:6299677:6301913:6303068:6312663:63127736301913:6303068ENST00000344683.5THCArs930557chr8:6302183G/C1.92e-05

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MCPH1


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MCPH1


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RelatedDrugs for MCPH1

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 MCPH1

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
MCPH1C1855081MICROCEPHALY, PRIMARY AUTOSOMAL RECESSIVE, 11CTD_human;ORPHANET;UNIPROT