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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 MCM3AP

check button Gene summary
Gene informationGene symbol

MCM3AP

Gene ID

8888

Gene nameminichromosome maintenance complex component 3 associated protein
SynonymsGANP|MAP80|SAC3
Cytomap

21q22.3

Type of geneprotein-coding
Descriptiongerminal-center associated nuclear protein80 kDa MCM3-associated proteinMCM3 acetylating proteinMCM3 acetyltransferaseMCM3 import proteinMCM3 minichromosome maintenance deficient 3 associated proteingerminal center-associated nuclear proteingermina
Modification date20180519
UniProtAcc

O60318

ContextPubMed: MCM3AP [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 MCM3AP 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 MCM3AP

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 MCM3AP

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3628762147660724:47660931:47662715:47662845:47663378:4766363647662715:47662845ENSG00000160294.6ENST00000397708.1,ENST00000496607.1,ENST00000467026.1,ENST00000486937.1,ENST00000291688.1
exon_skip_3628792147664720:47665111:47666220:47666800:47671442:4767159647666220:47666800ENSG00000160294.6ENST00000486937.1
exon_skip_3628812147666220:47666318:47666541:47666800:47671442:4767159647666541:47666800ENSG00000160294.6ENST00000397708.1,ENST00000496607.1,ENST00000467026.1,ENST00000291688.1
exon_skip_3628842147666694:47666800:47671442:47671596:47674305:4767444047671442:47671596ENSG00000160294.6ENST00000397708.1,ENST00000496607.1,ENST00000467026.1,ENST00000486937.1,ENST00000291688.1
exon_skip_3628882147671442:47671596:47674305:47674440:47674689:4767475847674305:47674440ENSG00000160294.6ENST00000397708.1,ENST00000496607.1,ENST00000481113.1,ENST00000467026.1,ENST00000486937.1,ENST00000291688.1
exon_skip_3628902147676702:47676900:47678852:47679005:47680706:4768082047678852:47679005ENSG00000160294.6ENST00000397708.1,ENST00000496607.1,ENST00000486937.1,ENST00000291688.1
exon_skip_3628922147681193:47681325:47684030:47684131:47685234:4768543747684030:47684131ENSG00000160294.6ENST00000397708.1,ENST00000496607.1,ENST00000486937.1,ENST00000291688.1
exon_skip_3628962147685234:47685437:47685838:47686080:47686895:4768705647685838:47686080ENSG00000160294.6ENST00000397708.1,ENST00000486937.1,ENST00000291688.1
exon_skip_3629002147686895:47687056:47690314:47690477:47692474:4769253747690314:47690477ENSG00000160294.6ENST00000397708.1,ENST00000291688.1
exon_skip_3629032147690314:47690477:47692474:47692743:47693301:4769349947692474:47692743ENSG00000160294.6ENST00000397708.1,ENST00000291688.1
exon_skip_3629042147692474:47692743:47693301:47693499:47695099:4769523947693301:47693499ENSG00000160294.6ENST00000397708.1,ENST00000291688.1
exon_skip_3629072147699906:47700051:47700410:47700489:47703528:4770375247700410:47700489ENSG00000160294.6ENST00000397708.1,ENST00000291688.1

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

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Exon skipping events with PSIs in GTEx for MCM3AP

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_3628762147660724:47660931:47662715:47662845:47663378:4766363647662715:47662845ENSG00000160294.6ENST00000467026.1,ENST00000496607.1,ENST00000486937.1,ENST00000397708.1,ENST00000291688.1
exon_skip_3628792147664720:47665111:47666220:47666800:47671442:4767159647666220:47666800ENSG00000160294.6ENST00000486937.1
exon_skip_3628812147666220:47666318:47666541:47666800:47671442:4767159647666541:47666800ENSG00000160294.6ENST00000467026.1,ENST00000496607.1,ENST00000397708.1,ENST00000291688.1
exon_skip_3628842147666694:47666800:47671442:47671596:47674305:4767444047671442:47671596ENSG00000160294.6ENST00000467026.1,ENST00000496607.1,ENST00000486937.1,ENST00000397708.1,ENST00000291688.1
exon_skip_3628882147671442:47671596:47674305:47674440:47674689:4767475847674305:47674440ENSG00000160294.6ENST00000467026.1,ENST00000496607.1,ENST00000486937.1,ENST00000397708.1,ENST00000291688.1,ENST00000481113.1
exon_skip_3628902147676702:47676900:47678852:47679005:47680706:4768082047678852:47679005ENSG00000160294.6ENST00000496607.1,ENST00000486937.1,ENST00000397708.1,ENST00000291688.1
exon_skip_3628922147681193:47681325:47684030:47684131:47685234:4768543747684030:47684131ENSG00000160294.6ENST00000496607.1,ENST00000486937.1,ENST00000397708.1,ENST00000291688.1
exon_skip_3628962147685234:47685437:47685838:47686080:47686895:4768705647685838:47686080ENSG00000160294.6ENST00000486937.1,ENST00000397708.1,ENST00000291688.1
exon_skip_3629002147686895:47687056:47690314:47690477:47692474:4769253747690314:47690477ENSG00000160294.6ENST00000397708.1,ENST00000291688.1
exon_skip_3629032147690314:47690477:47692474:47692743:47693301:4769349947692474:47692743ENSG00000160294.6ENST00000397708.1,ENST00000291688.1
exon_skip_3629042147692474:47692743:47693301:47693499:47695099:4769523947693301:47693499ENSG00000160294.6ENST00000397708.1,ENST00000291688.1
exon_skip_3629072147699906:47700051:47700410:47700489:47703528:4770375247700410:47700489ENSG00000160294.6ENST00000397708.1,ENST00000291688.1

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 MCM3AP

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
ENST000002916884766271547662845Frame-shift
ENST000003977084766271547662845Frame-shift
ENST000002916884766654147666800Frame-shift
ENST000003977084766654147666800Frame-shift
ENST000002916884767144247671596Frame-shift
ENST000003977084767144247671596Frame-shift
ENST000002916884768403047684131Frame-shift
ENST000003977084768403047684131Frame-shift
ENST000002916884768583847686080Frame-shift
ENST000003977084768583847686080Frame-shift
ENST000002916884769031447690477Frame-shift
ENST000003977084769031447690477Frame-shift
ENST000002916884769247447692743Frame-shift
ENST000003977084769247447692743Frame-shift
ENST000002916884770041047700489Frame-shift
ENST000003977084770041047700489Frame-shift
ENST000002916884767430547674440In-frame
ENST000003977084767430547674440In-frame
ENST000002916884767885247679005In-frame
ENST000003977084767885247679005In-frame
ENST000002916884769330147693499In-frame
ENST000003977084769330147693499In-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
ENST000002916884766271547662845Frame-shift
ENST000003977084766271547662845Frame-shift
ENST000002916884766654147666800Frame-shift
ENST000003977084766654147666800Frame-shift
ENST000002916884767144247671596Frame-shift
ENST000003977084767144247671596Frame-shift
ENST000002916884768403047684131Frame-shift
ENST000003977084768403047684131Frame-shift
ENST000002916884768583847686080Frame-shift
ENST000003977084768583847686080Frame-shift
ENST000002916884769031447690477Frame-shift
ENST000003977084769031447690477Frame-shift
ENST000002916884769247447692743Frame-shift
ENST000003977084769247447692743Frame-shift
ENST000002916884770041047700489Frame-shift
ENST000003977084770041047700489Frame-shift
ENST000002916884767430547674440In-frame
ENST000003977084767430547674440In-frame
ENST000002916884767885247679005In-frame
ENST000003977084767885247679005In-frame
ENST000002916884769330147693499In-frame
ENST000003977084769330147693499In-frame

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Infer the effects of exon skipping event on protein functional features for MCM3AP

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
ENST0000029168861301980476933014769349920352232666732
ENST0000039770863501980476933014769349922542451666732
ENST000002916886130198047678852476790053618377011941244
ENST000003977086350198047678852476790053837398911941244
ENST000002916886130198047674305476744404038417213341378
ENST000003977086350198047674305476744404257439113341378

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
ENST0000029168861301980476933014769349920352232666732
ENST0000039770863501980476933014769349922542451666732
ENST000002916886130198047678852476790053618377011941244
ENST000003977086350198047678852476790053837398911941244
ENST000002916886130198047674305476744404038417213341378
ENST000003977086350198047674305476744404257439113341378

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
O6031866673211259Alternative sequenceID=VSP_053438;Note=In isoform MCM3AP. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O6031866673211259Alternative sequenceID=VSP_053438;Note=In isoform MCM3AP. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O6031866673211980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O6031866673211980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O603181194124411259Alternative sequenceID=VSP_053438;Note=In isoform MCM3AP. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O603181194124411259Alternative sequenceID=VSP_053438;Note=In isoform MCM3AP. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O603181194124411980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O603181194124411980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O603181194124411681232HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4DHX
O603181194124411681232HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4DHX
O603181194124411621256RegionNote=CID
O603181194124411621256RegionNote=CID
O603181334137811980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O603181334137811980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein


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
O6031866673211259Alternative sequenceID=VSP_053438;Note=In isoform MCM3AP. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O6031866673211259Alternative sequenceID=VSP_053438;Note=In isoform MCM3AP. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O6031866673211980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O6031866673211980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O603181194124411259Alternative sequenceID=VSP_053438;Note=In isoform MCM3AP. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O603181194124411259Alternative sequenceID=VSP_053438;Note=In isoform MCM3AP. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O603181194124411980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O603181194124411980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O603181194124411681232HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4DHX
O603181194124411681232HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:4DHX
O603181194124411621256RegionNote=CID
O603181194124411621256RegionNote=CID
O603181334137811980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein
O603181334137811980ChainID=PRO_0000096284;Note=Germinal-center associated nuclear protein


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SNVs in the skipped exons for MCM3AP

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
STADTCGA-BR-7851-01exon_skip_362876
47662716476628454766280547662805Frame_Shift_DelA-p.K1780fs
UCSTCGA-N7-A4Y0-01exon_skip_362876
47662716476628454766280547662805Frame_Shift_DelA-p.F1779fs
UCSTCGA-N7-A4Y0-01exon_skip_362876
47662716476628454766280547662805Frame_Shift_DelA-p.K1780fs
LIHCTCGA-DD-A3A0-01exon_skip_362879
47666221476668004766670547666705Frame_Shift_DelG-p.P1462fs
LIHCTCGA-DD-A3A0-01exon_skip_362881
47666542476668004766670547666705Frame_Shift_DelG-p.P1462fs
LIHCTCGA-DD-A1EG-01exon_skip_362892
47684031476841314768405847684058Frame_Shift_DelC-p.G1103fs
LIHCTCGA-DD-A39Y-01exon_skip_362896
47685839476860804768585547685855Frame_Shift_DelG-p.P1005fs
STADTCGA-CD-A4MG-01exon_skip_362896
47685839476860804768595147685951Frame_Shift_DelG-p.V974fs
PRADTCGA-EJ-7314-01exon_skip_362903
47692475476927434769256447692565Frame_Shift_DelGT-p.792_793del
PRADTCGA-EJ-7314-01exon_skip_362903
47692475476927434769256447692565Frame_Shift_DelGT-p.D792fs
READTCGA-BM-6198-01exon_skip_362903
47692475476927434769261047692610Frame_Shift_DelT-p.E777fs
LIHCTCGA-DD-A1EG-01exon_skip_362907
47700411477004894770045247700452Frame_Shift_DelA-p.L494fs
STADTCGA-BR-8368-01exon_skip_362876
47662716476628454766280547662806Frame_Shift_Ins-Ap.F1779fs
COADTCGA-D5-6927-01exon_skip_362907
47700411477004894770045947700460Frame_Shift_Ins-Cp.K492fs
SKCMTCGA-GN-A26C-01exon_skip_362890
47678853476790054767888747678887Nonsense_MutationGAp.Q1234*
SKCMTCGA-GN-A26C-01exon_skip_362890
47678853476790054767888747678887Nonsense_MutationGAp.Q1234X
CESCTCGA-EK-A3GK-01exon_skip_362900
47690315476904774769043747690437Nonsense_MutationCAp.E836*
KIRCTCGA-BP-4993-01exon_skip_362903
47692475476927434769247647692476Nonsense_MutationTAp.R822X
SARCTCGA-QC-A7B5-01exon_skip_362876
47662716476628454766271547662715Splice_SiteCTe25+1
COADTCGA-CM-4746-01exon_skip_362890
47678853476790054767885247678852Splice_SiteCT.

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
IGROV1_OVARY47662716476628454766280547662805Frame_Shift_DelA-p.F1779fs
HEC6_ENDOMETRIUM47685839476860804768589547685896Frame_Shift_Ins-Cp.E992fs
JHUEM2_ENDOMETRIUM47666542476668004766660747666607Missense_MutationGAp.A1495V
JHUEM2_ENDOMETRIUM47666221476668004766660747666607Missense_MutationGAp.A1495V
SUM149PT_BREAST47666542476668004766670647666706Missense_MutationGTp.P1462H
SUM149PT_BREAST47666221476668004766670647666706Missense_MutationGTp.P1462H
HEC6_ENDOMETRIUM47666542476668004766671047666710Missense_MutationGTp.P1461T
HEC6_ENDOMETRIUM47666221476668004766671047666710Missense_MutationGTp.P1461T
CCK81_LARGE_INTESTINE47666542476668004766675147666751Missense_MutationTGp.Q1447P
CCK81_LARGE_INTESTINE47666221476668004766675147666751Missense_MutationTGp.Q1447P
SCMCRM2_SOFT_TISSUE47666542476668004766677547666775Missense_MutationCAp.G1439V
SCMCRM2_SOFT_TISSUE47666221476668004766677547666775Missense_MutationCAp.G1439V
SNU626_CENTRAL_NERVOUS_SYSTEM47666542476668004766677547666775Missense_MutationCAp.G1439V
SNU626_CENTRAL_NERVOUS_SYSTEM47666221476668004766677547666775Missense_MutationCAp.G1439V
MOTN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47666542476668004766677547666775Missense_MutationCAp.G1439V
MOTN1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47666221476668004766677547666775Missense_MutationCAp.G1439V
NCIH1563_LUNG47674306476744404767436447674364Missense_MutationACp.W1360G
SNU1040_LARGE_INTESTINE47674306476744404767436947674369Missense_MutationAGp.V1358A
MDAMB134VI_BREAST47674306476744404767437047674370Missense_MutationCTp.V1358M
HEC108_ENDOMETRIUM47685839476860804768587247685872Missense_MutationCTp.V1000I
SKGIIIA_CERVIX47685839476860804768600447686004Missense_MutationTCp.R956G
HEC251_ENDOMETRIUM47690315476904774769039147690391Missense_MutationTGp.N851T
NUGC3_STOMACH47690315476904774769041947690419Missense_MutationGCp.Q842E
CA922_UPPER_AERODIGESTIVE_TRACT47690315476904774769041947690419Missense_MutationGCp.Q842E
SISO_CERVIX47690315476904774769041947690419Missense_MutationGCp.Q842E
JHUEM7_ENDOMETRIUM47692475476927434769253347692533Missense_MutationCTp.E803K
HEC251_ENDOMETRIUM47692475476927434769262147692621Missense_MutationCAp.K773N
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47692475476927434769265447692654Missense_MutationCTp.M762I
EN_ENDOMETRIUM47692475476927434769267047692670Missense_MutationTCp.H757R
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47693302476934994769333147693331Missense_MutationCTp.V723M
JHUEM7_ENDOMETRIUM47693302476934994769333347693333Missense_MutationAGp.F722S
HCT15_LARGE_INTESTINE47693302476934994769336547693365Missense_MutationCAp.Q711H
HRT18_LARGE_INTESTINE47693302476934994769336547693365Missense_MutationCAp.Q711H
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47693302476934994769340547693405Missense_MutationCTp.S698N
RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47693302476934994769346547693465Missense_MutationCTp.R678Q
MERO48A_LUNG47693302476934994769349647693496Missense_MutationCGp.D668H
RH30_SOFT_TISSUE47700411477004894770043247700432Missense_MutationAGp.F501L
HEL9217_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47700411477004894770045547700455Missense_MutationCTp.S493N
HEL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47700411477004894770045547700455Missense_MutationCTp.S493N
SNU349_KIDNEY47700411477004894770045947700459Missense_MutationTCp.K492E
SNU407_LARGE_INTESTINE47700411477004894770046147700461Missense_MutationCAp.G491V
SARC9371_BONE47690315476904774769036547690365Nonsense_MutationGAp.Q860*
U698M_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE47692475476927434769256947692569Nonsense_MutationGAp.Q791*
NCIH1618_LUNG47662716476628454766271747662717Splice_SiteGAp.R1809C
CHLA258_BONE47700411477004894770041147700411Splice_SiteTCp.S508G

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for MCM3AP

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MCM3AP


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for MCM3AP


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RelatedDrugs for MCM3AP

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 MCM3AP

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