| Transcript | Gene symbol | Prediction | Tree vote | Model | Prediction problem | Splice site change | Known ClinVar disease mutation | Potential ClinVar disease mutation | Amino acid changes | Variant type | dbSNP ID | Protein length | Features at a glance |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENST00000257430(MANE Select) | APC | Deleterious | 59|41 | simple_ | No | Single base exchange | Normal |
| |||||
| APC | Deleterious | 63|37 | simple_ | No | Single base exchange | Normal |
| ||||||
| APC | Deleterious | 65|35 | simple_ | No | Single base exchange | Normal |
| ||||||
| APC | Deleterious | 66|34 | simple_ | No | Single base exchange | Normal |
| ||||||
| APC | Deleterious | 69|31 | simple_ | No | Single base exchange | Normal |
| ||||||
| APC | Deleterious | 71|29 | simple_ | No | Single base exchange | Normal |
| ||||||
| APC | Benign | 27|73 | 3utr | No | Single base exchange | N/A | |||||||
| APC | Benign | 35|65 | simple_ | No | Single base exchange | Normal |
|
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr5:112840487T>A (GRCh38) | |||||||||||||
| Gene symbol | APC | |||||||||||||
| Gene constraints | LOEUF: 0.32, LOF (oe): 0.26, misssense (oe): 0.96, synonymous (oe): 1.02 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000257430.9 | |||||||||||||
| Genbank transcript ID | NM_000038 (exact from MANE), NM_001354903 (by similarity), NM_001354899 (by similarity), NM_001407467 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | APC_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4893T>A g.132970T>A | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features |
| |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 5 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered gDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Original cDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered cDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Wildtype AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KESTLKSVLS ALWNLSAHCT ENKADICAVD GALAFLVGTL TYRSQTNTLA IIESGGGILR NVSSLIATNE DHRQILRENN CLQTLLQHLK SHSLTIVSNA CGTLWNLSAR NPKDQEALWD MGAVSMLKNL IHSKHKMIAM GSAAALRNLM ANRPAKYKDA NIMSPGSSLP SLHVRKQKAL EAELDAQHLS ETFDNIDNLS PKASHRSKQR HKQSLYGDYV FDTNRHDDNR SDNFNTGNMT VLSPYLNTTV LPSSSSSRGS LDSSRSEKDR SLERERGIGL GNYHPATENP GTSSKRGLQI STTAAQIAKV MEEVSAIHTS QEDRSSGSTT ELHCVTDERN ALRRSSAAHT HSNTYNFTKS ENSNRTCSMP YAKLEYKRSS NDSLNSVSSS DGYGKRGQMK PSIESYSEDD ESKFCSYGQY PADLAHKIHS ANHMDDNDGE LDTPINYSLK YSDEQLNSGR QSPSQNERWA RPKHIIEDEI KQSEQRQSRN QSTTYPVYTE STDDKHLKFQ PHFGQQECVS PYRSRGANGS ETNRVGSNHG INQNVSQSLC QEDDYEDDKP TNYSERYSEE EQHEEEERPT NYSIKYNEEK RHVDQPIDYS LKYATDIPSS QKQSFSFSKS SSGQSSKTEH MSSSSENTST PSSNAKRQNQ LHPSSAQSRS GQPQKAATCK VSSINQETIQ TYCVEDTPIC FSRCSSLSSL SSAEDEIGCN QTTQEADSAN TLQIAEIKEK IGTRSAEDPV SEVPAVSQHP RTKSSRLQGS SLSSESARHK AVEFSSGAKS PSKSGAQTPK SPPEHYVQET PLMFSRCTSV SSLDSFESRS IASSVQSEPC SGMVSGIISP SDLPDSPGQT MPPSRSKTPP PPPQTAQTKR EVPKNKAPTA EKRESGPKQA AVNAAVQRVQ VLPDADTLLH FATESTPDGF SCSSSLSALS LDEPFIQKDV ELRIMPPVQE NDNGNETESE QPKESNENQE KEAEKTIDSE KDLLDDSDDD DIEILEECII SAMPTKSSRK AKKPAQTASK LPPPVARKPS QLPVYKLLPS QNRLQPQKHV SFTPGDDMPR VYCVEGTPIN FSTATSLSDL TIESPPNELA AGEGVRGGAQ SGEFEKRDTI PTEGRSTDEA QGGKTSSVTI PELDDNKAEE GDILAECINS AMPKGKSHKP FRVKKIMDQV QQASASSSAP NKNQLDGKKK KPTSPVKPIP QNTEYRTRVR KNADSKNNLN AERVFSDNKD SKKQNLKNNS KVFNDKLPNN EDRVRGSFAF DSPHHYTPIE GTPYCFSRND SLSSLDFDDD DVDLSREKAE LRKAKENKES EAKVTSHTEL TSNQQSANKT QAIAKQPINR GQPKPILQKQ STFPQSSKDI PDRGAATDEK LQNFAIENTP VCFSHNSSLS SLSDIDQENN NKENEPIKET EPPDSQGEPS KPQASGYAPK SFHVEDTPVC FSRNSSLSSL SIDSEDDLLQ ECISSAMPKK KKPSRLKGDN EKHSPRNMGG ILGEDLTLDL KDIQRPDSEH GLSPDSENFD WKAIQEGANS IVSSLHQAAA AACLSRQASS DSDSILSLKS GISLGSPFHL TPDQEEKPFT SNKGPRILKP GEKSTLETKK IESESKGIKG GKKVYKSLIT GKVRSNSEIS GQMKQPLQAN MPSISRGRTM IHIPGVRNSS SSTSPVSKKG PPLKTPASKS PSEGQTATTS PRGAKPSVKS ELSPVARQTS QIGGSSKAPS RSGSRDSTPS RPAQQPLSRP IQSPGRNSIS PGRNGISPPN KLSQLPRTSS PSTASTKSSG SGKMSYTSPG RQMSQQNLTK QTGLSKNASS IPRSESASKG LNQMNNGNGA NKKVELSRMS STKSSGSESD RSERPVLVRQ STFIKEAPSP TLRRKLEESA SFESLSPSSR PASPTRSQAQ TPVLSPSLPD MSLSTHSSVQ AGGWRKLPPN LSPTIEYNDG RPAKRHDIAR SHSESPSRLP INRSGTWKRE HSKHSSSLPR VSTWRRTGSS SSILSASSES SEKAKSEDEK HVNSISGTKQ SKENQVSAKG TWRKIKENEF SPTNSTSQTV SSGATNGAES KTLIYQMAPA VSKTEDVWVR IEDCPINNPR SGRSPTGNTP PVIDSVSEKA NPNIKDSKDN QAKQNVGNGS VPMRTVGLEN RLNSFIQVDA PDQKGTEIKP GQNNPVPVSE TNESSIVERT PFSSSSSSKH SSPSGTVAAR VTPFNYNPSP RKSSADSTSA RPSQIPTPVN NNTKKRDSKT DSTESSGTQS PKRHSGSYLV TSV* | |||||||||||||
| Mutated AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KESTLKSVLS ALWNLSAHCT ENKADICAVD GALAFLVGTL TYRSQTNTLA IIESGGGILR NVSSLIATNE DHRQILRENN CLQTLLQHLK SHSLTIVSNA CGTLWNLSAR NPKDQEALWD MGAVSMLKNL IHSKHKMIAM GSAAALRNLM ANRPAKYKDA NIMSPGSSLP SLHVRKQKAL EAELDAQHLS ETFDNIDNLS PKASHRSKQR HKQSLYGDYV FDTNRHDDNR SDNFNTGNMT VLSPYLNTTV LPSSSSSRGS LDSSRSEKDR SLERERGIGL GNYHPATENP GTSSKRGLQI STTAAQIAKV MEEVSAIHTS QEDRSSGSTT ELHCVTDERN ALRRSSAAHT HSNTYNFTKS ENSNRTCSMP YAKLEYKRSS NDSLNSVSSS DGYGKRGQMK PSIESYSEDD ESKFCSYGQY PADLAHKIHS ANHMDDNDGE LDTPINYSLK YSDEQLNSGR QSPSQNERWA RPKHIIEDEI KQSEQRQSRN QSTTYPVYTE STDDKHLKFQ PHFGQQECVS PYRSRGANGS ETNRVGSNHG INQNVSQSLC QEDDYEDDKP TNYSERYSEE EQHEEEERPT NYSIKYNEEK RHVDQPIDYS LKYATDIPSS QKQSFSFSKS SSGQSSKTEH MSSSSENTST PSSNAKRQNQ LHPSSAQSRS GQPQKAATCK VSSINQETIQ TYCVEDTPIC FSRCSSLSSL SSAEDEIGCN QTTQEADSAN TLQIAEIKEK IGTRSAEDPV SEVPAVSQHP RTKSSRLQGS SLSSESARHK AVEFSSGAKS PSKSGAQTPK SPPEHYVQET PLMFSRCTSV SSLDSFESRS IASSVQSEPC SGMVSGIISP SDLPDSPGQT MPPSRSKTPP PPPQTAQTKR EVPKNKAPTA EKRESGPKQA AVNAAVQRVQ VLPDADTLLH FATESTPDGF SCSSSLSALS LDEPFIQKDV ELRIMPPVQE NDNGNETESE QPKESNENQE KEAEKTIDSE KDLLDDSDDD DIEILEECII SAMPTKSSRK AKKPAQTASK LPPPVARKPS QLPVYKLLPS QNRLQPQKHV RFTPGDDMPR VYCVEGTPIN FSTATSLSDL TIESPPNELA AGEGVRGGAQ SGEFEKRDTI PTEGRSTDEA QGGKTSSVTI PELDDNKAEE GDILAECINS AMPKGKSHKP FRVKKIMDQV QQASASSSAP NKNQLDGKKK KPTSPVKPIP QNTEYRTRVR KNADSKNNLN AERVFSDNKD SKKQNLKNNS KVFNDKLPNN EDRVRGSFAF DSPHHYTPIE GTPYCFSRND SLSSLDFDDD DVDLSREKAE LRKAKENKES EAKVTSHTEL TSNQQSANKT QAIAKQPINR GQPKPILQKQ STFPQSSKDI PDRGAATDEK LQNFAIENTP VCFSHNSSLS SLSDIDQENN NKENEPIKET EPPDSQGEPS KPQASGYAPK SFHVEDTPVC FSRNSSLSSL SIDSEDDLLQ ECISSAMPKK KKPSRLKGDN EKHSPRNMGG ILGEDLTLDL KDIQRPDSEH GLSPDSENFD WKAIQEGANS IVSSLHQAAA AACLSRQASS DSDSILSLKS GISLGSPFHL TPDQEEKPFT SNKGPRILKP GEKSTLETKK IESESKGIKG GKKVYKSLIT GKVRSNSEIS GQMKQPLQAN MPSISRGRTM IHIPGVRNSS SSTSPVSKKG PPLKTPASKS PSEGQTATTS PRGAKPSVKS ELSPVARQTS QIGGSSKAPS RSGSRDSTPS RPAQQPLSRP IQSPGRNSIS PGRNGISPPN KLSQLPRTSS PSTASTKSSG SGKMSYTSPG RQMSQQNLTK QTGLSKNASS IPRSESASKG LNQMNNGNGA NKKVELSRMS STKSSGSESD RSERPVLVRQ STFIKEAPSP TLRRKLEESA SFESLSPSSR PASPTRSQAQ TPVLSPSLPD MSLSTHSSVQ AGGWRKLPPN LSPTIEYNDG RPAKRHDIAR SHSESPSRLP INRSGTWKRE HSKHSSSLPR VSTWRRTGSS SSILSASSES SEKAKSEDEK HVNSISGTKQ SKENQVSAKG TWRKIKENEF SPTNSTSQTV SSGATNGAES KTLIYQMAPA VSKTEDVWVR IEDCPINNPR SGRSPTGNTP PVIDSVSEKA NPNIKDSKDN QAKQNVGNGS VPMRTVGLEN RLNSFIQVDA PDQKGTEIKP GQNNPVPVSE TNESSIVERT PFSSSSSSKH SSPSGTVAAR VTPFNYNPSP RKSSADSTSA RPSQIPTPVN NNTKKRDSKT DSTESSGTQS PKRHSGSYLV TSV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 8532 / 8532 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2844 / 2844 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 8591 / 8591 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 60 / 60 | |||||||||||||
| Last intron/exon boundary | 2017 | |||||||||||||
| Theoretical NMD boundary in CDS | 1907 | |||||||||||||
| Length of CDS | 8532 | |||||||||||||
| Coding sequence (CDS) position | 4893 | |||||||||||||
| cDNA position | 4952 | |||||||||||||
| gDNA position | 132970 | |||||||||||||
| Chromosomal position | 112840487 | |||||||||||||
| Speed | 0.12 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr5:112840487T>A (GRCh38) | |||||||||||||
| Gene symbol | APC | |||||||||||||
| Gene constraints | LOEUF: 0.32, LOF (oe): 0.26, misssense (oe): 0.96, synonymous (oe): 1.02 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000508376.6 | |||||||||||||
| Genbank transcript ID | NM_001127510 (by similarity), NM_001407459 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | APC_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4893T>A g.132970T>A | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features |
| |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 5 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered gDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Original cDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered cDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Wildtype AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KESTLKSVLS ALWNLSAHCT ENKADICAVD GALAFLVGTL TYRSQTNTLA IIESGGGILR NVSSLIATNE DHRQILRENN CLQTLLQHLK SHSLTIVSNA CGTLWNLSAR NPKDQEALWD MGAVSMLKNL IHSKHKMIAM GSAAALRNLM ANRPAKYKDA NIMSPGSSLP SLHVRKQKAL EAELDAQHLS ETFDNIDNLS PKASHRSKQR HKQSLYGDYV FDTNRHDDNR SDNFNTGNMT VLSPYLNTTV LPSSSSSRGS LDSSRSEKDR SLERERGIGL GNYHPATENP GTSSKRGLQI STTAAQIAKV MEEVSAIHTS QEDRSSGSTT ELHCVTDERN ALRRSSAAHT HSNTYNFTKS ENSNRTCSMP YAKLEYKRSS NDSLNSVSSS DGYGKRGQMK PSIESYSEDD ESKFCSYGQY PADLAHKIHS ANHMDDNDGE LDTPINYSLK YSDEQLNSGR QSPSQNERWA RPKHIIEDEI KQSEQRQSRN QSTTYPVYTE STDDKHLKFQ PHFGQQECVS PYRSRGANGS ETNRVGSNHG INQNVSQSLC QEDDYEDDKP TNYSERYSEE EQHEEEERPT NYSIKYNEEK RHVDQPIDYS LKYATDIPSS QKQSFSFSKS SSGQSSKTEH MSSSSENTST PSSNAKRQNQ LHPSSAQSRS GQPQKAATCK VSSINQETIQ TYCVEDTPIC FSRCSSLSSL SSAEDEIGCN QTTQEADSAN TLQIAEIKEK IGTRSAEDPV SEVPAVSQHP RTKSSRLQGS SLSSESARHK AVEFSSGAKS PSKSGAQTPK SPPEHYVQET PLMFSRCTSV SSLDSFESRS IASSVQSEPC SGMVSGIISP SDLPDSPGQT MPPSRSKTPP PPPQTAQTKR EVPKNKAPTA EKRESGPKQA AVNAAVQRVQ VLPDADTLLH FATESTPDGF SCSSSLSALS LDEPFIQKDV ELRIMPPVQE NDNGNETESE QPKESNENQE KEAEKTIDSE KDLLDDSDDD DIEILEECII SAMPTKSSRK AKKPAQTASK LPPPVARKPS QLPVYKLLPS QNRLQPQKHV SFTPGDDMPR VYCVEGTPIN FSTATSLSDL TIESPPNELA AGEGVRGGAQ SGEFEKRDTI PTEGRSTDEA QGGKTSSVTI PELDDNKAEE GDILAECINS AMPKGKSHKP FRVKKIMDQV QQASASSSAP NKNQLDGKKK KPTSPVKPIP QNTEYRTRVR KNADSKNNLN AERVFSDNKD SKKQNLKNNS KVFNDKLPNN EDRVRGSFAF DSPHHYTPIE GTPYCFSRND SLSSLDFDDD DVDLSREKAE LRKAKENKES EAKVTSHTEL TSNQQSANKT QAIAKQPINR GQPKPILQKQ STFPQSSKDI PDRGAATDEK LQNFAIENTP VCFSHNSSLS SLSDIDQENN NKENEPIKET EPPDSQGEPS KPQASGYAPK SFHVEDTPVC FSRNSSLSSL SIDSEDDLLQ ECISSAMPKK KKPSRLKGDN EKHSPRNMGG ILGEDLTLDL KDIQRPDSEH GLSPDSENFD WKAIQEGANS IVSSLHQAAA AACLSRQASS DSDSILSLKS GISLGSPFHL TPDQEEKPFT SNKGPRILKP GEKSTLETKK IESESKGIKG GKKVYKSLIT GKVRSNSEIS GQMKQPLQAN MPSISRGRTM IHIPGVRNSS SSTSPVSKKG PPLKTPASKS PSEGQTATTS PRGAKPSVKS ELSPVARQTS QIGGSSKAPS RSGSRDSTPS RPAQQPLSRP IQSPGRNSIS PGRNGISPPN KLSQLPRTSS PSTASTKSSG SGKMSYTSPG RQMSQQNLTK QTGLSKNASS IPRSESASKG LNQMNNGNGA NKKVELSRMS STKSSGSESD RSERPVLVRQ STFIKEAPSP TLRRKLEESA SFESLSPSSR PASPTRSQAQ TPVLSPSLPD MSLSTHSSVQ AGGWRKLPPN LSPTIEYNDG RPAKRHDIAR SHSESPSRLP INRSGTWKRE HSKHSSSLPR VSTWRRTGSS SSILSASSES SEKAKSEDEK HVNSISGTKQ SKENQVSAKG TWRKIKENEF SPTNSTSQTV SSGATNGAES KTLIYQMAPA VSKTEDVWVR IEDCPINNPR SGRSPTGNTP PVIDSVSEKA NPNIKDSKDN QAKQNVGNGS VPMRTVGLEN RLNSFIQVDA PDQKGTEIKP GQNNPVPVSE TNESSIVERT PFSSSSSSKH SSPSGTVAAR VTPFNYNPSP RKSSADSTSA RPSQIPTPVN NNTKKRDSKT DSTESSGTQS PKRHSGSYLV TSV* | |||||||||||||
| Mutated AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KESTLKSVLS ALWNLSAHCT ENKADICAVD GALAFLVGTL TYRSQTNTLA IIESGGGILR NVSSLIATNE DHRQILRENN CLQTLLQHLK SHSLTIVSNA CGTLWNLSAR NPKDQEALWD MGAVSMLKNL IHSKHKMIAM GSAAALRNLM ANRPAKYKDA NIMSPGSSLP SLHVRKQKAL EAELDAQHLS ETFDNIDNLS PKASHRSKQR HKQSLYGDYV FDTNRHDDNR SDNFNTGNMT VLSPYLNTTV LPSSSSSRGS LDSSRSEKDR SLERERGIGL GNYHPATENP GTSSKRGLQI STTAAQIAKV MEEVSAIHTS QEDRSSGSTT ELHCVTDERN ALRRSSAAHT HSNTYNFTKS ENSNRTCSMP YAKLEYKRSS NDSLNSVSSS DGYGKRGQMK PSIESYSEDD ESKFCSYGQY PADLAHKIHS ANHMDDNDGE LDTPINYSLK YSDEQLNSGR QSPSQNERWA RPKHIIEDEI KQSEQRQSRN QSTTYPVYTE STDDKHLKFQ PHFGQQECVS PYRSRGANGS ETNRVGSNHG INQNVSQSLC QEDDYEDDKP TNYSERYSEE EQHEEEERPT NYSIKYNEEK RHVDQPIDYS LKYATDIPSS QKQSFSFSKS SSGQSSKTEH MSSSSENTST PSSNAKRQNQ LHPSSAQSRS GQPQKAATCK VSSINQETIQ TYCVEDTPIC FSRCSSLSSL SSAEDEIGCN QTTQEADSAN TLQIAEIKEK IGTRSAEDPV SEVPAVSQHP RTKSSRLQGS SLSSESARHK AVEFSSGAKS PSKSGAQTPK SPPEHYVQET PLMFSRCTSV SSLDSFESRS IASSVQSEPC SGMVSGIISP SDLPDSPGQT MPPSRSKTPP PPPQTAQTKR EVPKNKAPTA EKRESGPKQA AVNAAVQRVQ VLPDADTLLH FATESTPDGF SCSSSLSALS LDEPFIQKDV ELRIMPPVQE NDNGNETESE QPKESNENQE KEAEKTIDSE KDLLDDSDDD DIEILEECII SAMPTKSSRK AKKPAQTASK LPPPVARKPS QLPVYKLLPS QNRLQPQKHV RFTPGDDMPR VYCVEGTPIN FSTATSLSDL TIESPPNELA AGEGVRGGAQ SGEFEKRDTI PTEGRSTDEA QGGKTSSVTI PELDDNKAEE GDILAECINS AMPKGKSHKP FRVKKIMDQV QQASASSSAP NKNQLDGKKK KPTSPVKPIP QNTEYRTRVR KNADSKNNLN AERVFSDNKD SKKQNLKNNS KVFNDKLPNN EDRVRGSFAF DSPHHYTPIE GTPYCFSRND SLSSLDFDDD DVDLSREKAE LRKAKENKES EAKVTSHTEL TSNQQSANKT QAIAKQPINR GQPKPILQKQ STFPQSSKDI PDRGAATDEK LQNFAIENTP VCFSHNSSLS SLSDIDQENN NKENEPIKET EPPDSQGEPS KPQASGYAPK SFHVEDTPVC FSRNSSLSSL SIDSEDDLLQ ECISSAMPKK KKPSRLKGDN EKHSPRNMGG ILGEDLTLDL KDIQRPDSEH GLSPDSENFD WKAIQEGANS IVSSLHQAAA AACLSRQASS DSDSILSLKS GISLGSPFHL TPDQEEKPFT SNKGPRILKP GEKSTLETKK IESESKGIKG GKKVYKSLIT GKVRSNSEIS GQMKQPLQAN MPSISRGRTM IHIPGVRNSS SSTSPVSKKG PPLKTPASKS PSEGQTATTS PRGAKPSVKS ELSPVARQTS QIGGSSKAPS RSGSRDSTPS RPAQQPLSRP IQSPGRNSIS PGRNGISPPN KLSQLPRTSS PSTASTKSSG SGKMSYTSPG RQMSQQNLTK QTGLSKNASS IPRSESASKG LNQMNNGNGA NKKVELSRMS STKSSGSESD RSERPVLVRQ STFIKEAPSP TLRRKLEESA SFESLSPSSR PASPTRSQAQ TPVLSPSLPD MSLSTHSSVQ AGGWRKLPPN LSPTIEYNDG RPAKRHDIAR SHSESPSRLP INRSGTWKRE HSKHSSSLPR VSTWRRTGSS SSILSASSES SEKAKSEDEK HVNSISGTKQ SKENQVSAKG TWRKIKENEF SPTNSTSQTV SSGATNGAES KTLIYQMAPA VSKTEDVWVR IEDCPINNPR SGRSPTGNTP PVIDSVSEKA NPNIKDSKDN QAKQNVGNGS VPMRTVGLEN RLNSFIQVDA PDQKGTEIKP GQNNPVPVSE TNESSIVERT PFSSSSSSKH SSPSGTVAAR VTPFNYNPSP RKSSADSTSA RPSQIPTPVN NNTKKRDSKT DSTESSGTQS PKRHSGSYLV TSV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 8532 / 8532 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2844 / 2844 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 8689 / 8689 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 158 / 158 | |||||||||||||
| Last intron/exon boundary | 2115 | |||||||||||||
| Theoretical NMD boundary in CDS | 1907 | |||||||||||||
| Length of CDS | 8532 | |||||||||||||
| Coding sequence (CDS) position | 4893 | |||||||||||||
| cDNA position | 5050 | |||||||||||||
| gDNA position | 132970 | |||||||||||||
| Chromosomal position | 112840487 | |||||||||||||
| Speed | 0.10 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr5:112840487T>A (GRCh38) | |||||||||||||
| Gene symbol | APC | |||||||||||||
| Gene constraints | LOEUF: 0.42, LOF (oe): 0.32, misssense (oe): 0.90, synonymous (oe): 0.98 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000512211.7 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | APC_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4893T>A g.132970T>A | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features |
| |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 5 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered gDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Original cDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered cDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Wildtype AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KESTLKSVLS ALWNLSAHCT ENKADICAVD GALAFLVGTL TYRSQTNTLA IIESGGGILR NVSSLIATNE DHRQILRENN CLQTLLQHLK SHSLTIVSNA CGTLWNLSAR NPKDQEALWD MGAVSMLKNL IHSKHKMIAM GSAAALRNLM ANRPAKYKDA NIMSPGSSLP SLHVRKQKAL EAELDAQHLS ETFDNIDNLS PKASHRSKQR HKQSLYGDYV FDTNRHDDNR SDNFNTGNMT VLSPYLNTTV LPSSSSSRGS LDSSRSEKDR SLERERGIGL GNYHPATENP GTSSKRGLQI STTAAQIAKV MEEVSAIHTS QEDRSSGSTT ELHCVTDERN ALRRSSAAHT HSNTYNFTKS ENSNRTCSMP YAKLEYKRSS NDSLNSVSSS DGYGKRGQMK PSIESYSEDD ESKFCSYGQY PADLAHKIHS ANHMDDNDGE LDTPINYSLK YSDEQLNSGR QSPSQNERWA RPKHIIEDEI KQSEQRQSRN QSTTYPVYTE STDDKHLKFQ PHFGQQECVS PYRSRGANGS ETNRVGSNHG INQNVSQSLC QEDDYEDDKP TNYSERYSEE EQHEEEERPT NYSIKYNEEK RHVDQPIDYS LKYATDIPSS QKQSFSFSKS SSGQSSKTEH MSSSSENTST PSSNAKRQNQ LHPSSAQSRS GQPQKAATCK VSSINQETIQ TYCVEDTPIC FSRCSSLSSL SSAEDEIGCN QTTQEADSAN TLQIAEIKEK IGTRSAEDPV SEVPAVSQHP RTKSSRLQGS SLSSESARHK AVEFSSGAKS PSKSGAQTPK SPPEHYVQET PLMFSRCTSV SSLDSFESRS IASSVQSEPC SGMVSGIISP SDLPDSPGQT MPPSRSKTPP PPPQTAQTKR EVPKNKAPTA EKRESGPKQA AVNAAVQRVQ VLPDADTLLH FATESTPDGF SCSSSLSALS LDEPFIQKDV ELRIMPPVQE NDNGNETESE QPKESNENQE KEAEKTIDSE KDLLDDSDDD DIEILEECII SAMPTKSSRK AKKPAQTASK LPPPVARKPS QLPVYKLLPS QNRLQPQKHV SFTPGDDMPR VYCVEGTPIN FSTATSLSDL TIESPPNELA AGEGVRGGAQ SGEFEKRDTI PTEGRSTDEA QGGKTSSVTI PELDDNKAEE GDILAECINS AMPKGKSHKP FRVKKIMDQV QQASASSSAP NKNQLDGKKK KPTSPVKPIP QNTEYRTRVR KNADSKNNLN AERVFSDNKD SKKQNLKNNS KVFNDKLPNN EDRVRGSFAF DSPHHYTPIE GTPYCFSRND SLSSLDFDDD DVDLSREKAE LRKAKENKES EAKVTSHTEL TSNQQSANKT QAIAKQPINR GQPKPILQKQ STFPQSSKDI PDRGAATDEK LQNFAIENTP VCFSHNSSLS SLSDIDQENN NKENEPIKET EPPDSQGEPS KPQASGYAPK SFHVEDTPVC FSRNSSLSSL SIDSEDDLLQ ECISSAMPKK KKPSRLKGDN EKHSPRNMGG ILGEDLTLDL KDIQRPDSEH GLSPDSENFD WKAIQEGANS IVSSLHQAAA AACLSRQASS DSDSILSLKS GISLGSPFHL TPDQEEKPFT SNKGPRILKP GEKSTLETKK IESESKGIKG GKKVYKSLIT GKVRSNSEIS GQMKQPLQAN MPSISRGRTM IHIPGVRNSS SSTSPVSKKG PPLKTPASKS PSEGQTATTS PRGAKPSVKS ELSPVARQTS QIGGSSKAPS RSGSRDSTPS RPAQQPLSRP IQSPGRNSIS PGRNGISPPN KLSQLPRTSS PSTASTKSSG SGKMSYTSPG RQMSQQNLTK QTGLSKNASS IPRSESASKG LNQMNNGNGA NKKVELSRMS STKSSGSESD RSERPVLVRQ STFIKEAPSP TLRRKLEESA SFESLSPSSR PASPTRSQAQ TPVLSPSLPD MSLSTHSSVQ AGGWRKLPPN LSPTIEYNDG RPAKRHDIAR SHSESPSRLP INRSGTWKRE HSKHSSSLPR VSTWRRTGSS SSILSASSES SEKAKSEDEK HVNSISGTKQ SKENQVSAKG TWRKIKENEF SPTNSTSQTV SSGATNGAES KTLIYQMAPA VSKTEDVWVR IEDCPINNPR SGRSPTGNTP PVIDSVSEKA NPNIKDSKDN QAKQNVGNGS VPMRTVGLEN RLNSFIQVDA PDQKGTEIKP GQNNPVPVSE TNESSIVERT PFSSSSSSKH SSPSGTVAAR VTPFNYNPSP RKSSADSTSA RPSQIPTPVN NNTKKRDSKT DSTESSGTQS PKRHSGSYLV TSV* | |||||||||||||
| Mutated AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KESTLKSVLS ALWNLSAHCT ENKADICAVD GALAFLVGTL TYRSQTNTLA IIESGGGILR NVSSLIATNE DHRQILRENN CLQTLLQHLK SHSLTIVSNA CGTLWNLSAR NPKDQEALWD MGAVSMLKNL IHSKHKMIAM GSAAALRNLM ANRPAKYKDA NIMSPGSSLP SLHVRKQKAL EAELDAQHLS ETFDNIDNLS PKASHRSKQR HKQSLYGDYV FDTNRHDDNR SDNFNTGNMT VLSPYLNTTV LPSSSSSRGS LDSSRSEKDR SLERERGIGL GNYHPATENP GTSSKRGLQI STTAAQIAKV MEEVSAIHTS QEDRSSGSTT ELHCVTDERN ALRRSSAAHT HSNTYNFTKS ENSNRTCSMP YAKLEYKRSS NDSLNSVSSS DGYGKRGQMK PSIESYSEDD ESKFCSYGQY PADLAHKIHS ANHMDDNDGE LDTPINYSLK YSDEQLNSGR QSPSQNERWA RPKHIIEDEI KQSEQRQSRN QSTTYPVYTE STDDKHLKFQ PHFGQQECVS PYRSRGANGS ETNRVGSNHG INQNVSQSLC QEDDYEDDKP TNYSERYSEE EQHEEEERPT NYSIKYNEEK RHVDQPIDYS LKYATDIPSS QKQSFSFSKS SSGQSSKTEH MSSSSENTST PSSNAKRQNQ LHPSSAQSRS GQPQKAATCK VSSINQETIQ TYCVEDTPIC FSRCSSLSSL SSAEDEIGCN QTTQEADSAN TLQIAEIKEK IGTRSAEDPV SEVPAVSQHP RTKSSRLQGS SLSSESARHK AVEFSSGAKS PSKSGAQTPK SPPEHYVQET PLMFSRCTSV SSLDSFESRS IASSVQSEPC SGMVSGIISP SDLPDSPGQT MPPSRSKTPP PPPQTAQTKR EVPKNKAPTA EKRESGPKQA AVNAAVQRVQ VLPDADTLLH FATESTPDGF SCSSSLSALS LDEPFIQKDV ELRIMPPVQE NDNGNETESE QPKESNENQE KEAEKTIDSE KDLLDDSDDD DIEILEECII SAMPTKSSRK AKKPAQTASK LPPPVARKPS QLPVYKLLPS QNRLQPQKHV RFTPGDDMPR VYCVEGTPIN FSTATSLSDL TIESPPNELA AGEGVRGGAQ SGEFEKRDTI PTEGRSTDEA QGGKTSSVTI PELDDNKAEE GDILAECINS AMPKGKSHKP FRVKKIMDQV QQASASSSAP NKNQLDGKKK KPTSPVKPIP QNTEYRTRVR KNADSKNNLN AERVFSDNKD SKKQNLKNNS KVFNDKLPNN EDRVRGSFAF DSPHHYTPIE GTPYCFSRND SLSSLDFDDD DVDLSREKAE LRKAKENKES EAKVTSHTEL TSNQQSANKT QAIAKQPINR GQPKPILQKQ STFPQSSKDI PDRGAATDEK LQNFAIENTP VCFSHNSSLS SLSDIDQENN NKENEPIKET EPPDSQGEPS KPQASGYAPK SFHVEDTPVC FSRNSSLSSL SIDSEDDLLQ ECISSAMPKK KKPSRLKGDN EKHSPRNMGG ILGEDLTLDL KDIQRPDSEH GLSPDSENFD WKAIQEGANS IVSSLHQAAA AACLSRQASS DSDSILSLKS GISLGSPFHL TPDQEEKPFT SNKGPRILKP GEKSTLETKK IESESKGIKG GKKVYKSLIT GKVRSNSEIS GQMKQPLQAN MPSISRGRTM IHIPGVRNSS SSTSPVSKKG PPLKTPASKS PSEGQTATTS PRGAKPSVKS ELSPVARQTS QIGGSSKAPS RSGSRDSTPS RPAQQPLSRP IQSPGRNSIS PGRNGISPPN KLSQLPRTSS PSTASTKSSG SGKMSYTSPG RQMSQQNLTK QTGLSKNASS IPRSESASKG LNQMNNGNGA NKKVELSRMS STKSSGSESD RSERPVLVRQ STFIKEAPSP TLRRKLEESA SFESLSPSSR PASPTRSQAQ TPVLSPSLPD MSLSTHSSVQ AGGWRKLPPN LSPTIEYNDG RPAKRHDIAR SHSESPSRLP INRSGTWKRE HSKHSSSLPR VSTWRRTGSS SSILSASSES SEKAKSEDEK HVNSISGTKQ SKENQVSAKG TWRKIKENEF SPTNSTSQTV SSGATNGAES KTLIYQMAPA VSKTEDVWVR IEDCPINNPR SGRSPTGNTP PVIDSVSEKA NPNIKDSKDN QAKQNVGNGS VPMRTVGLEN RLNSFIQVDA PDQKGTEIKP GQNNPVPVSE TNESSIVERT PFSSSSSSKH SSPSGTVAAR VTPFNYNPSP RKSSADSTSA RPSQIPTPVN NNTKKRDSKT DSTESSGTQS PKRHSGSYLV TSV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 8532 / 8532 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2844 / 2844 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 8883 / 8883 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 352 / 352 | |||||||||||||
| Last intron/exon boundary | 2309 | |||||||||||||
| Theoretical NMD boundary in CDS | 1907 | |||||||||||||
| Length of CDS | 8532 | |||||||||||||
| Coding sequence (CDS) position | 4893 | |||||||||||||
| cDNA position | 5244 | |||||||||||||
| gDNA position | 132970 | |||||||||||||
| Chromosomal position | 112840487 | |||||||||||||
| Speed | 0.12 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr5:112840487T>A (GRCh38) | |||||||||||||
| Gene symbol | APC | |||||||||||||
| Gene constraints | LOEUF: 0.45, LOF (oe): 0.34, misssense (oe): 0.91, synonymous (oe): 0.99 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000507379.6 | |||||||||||||
| Genbank transcript ID | NM_001407470 (by similarity), NM_001354897 (by similarity), NM_001354902 (by similarity), NM_001127511 (by similarity), NM_001354906 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | APC_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4839T>A g.132970T>A | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features |
| |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 5 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered gDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Original cDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered cDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Wildtype AA sequence | MYASLGSGPV APLPASVPPS VLGSWSTGGS RSCVRQETKS PGGARTSGHW ASVWQEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRSSQN KHETGSHDAE RQNEGQGVGE INMATSGNGQ GSTTRMDHET ASVLSSSSTH SAPRRLTSHL GTKVEMVYSL LSMLGTHDKD DMSRTLLAMS SSQDSCISMR QSGCLPLLIQ LLHGNDKDSV LLGNSRGSKE ARARASAALH NIIHSQPDDK RGRREIRVLH LLEQIRAYCE TCWEWQEAHE PGMDQDKNPM PAPVEHQICP AVCVLMKLSF DEEHRHAMNE LGGLQAIAEL LQVDCEMYGL TNDHYSITLR RYAGMALTNL TFGDVANKAT LCSMKGCMRA LVAQLKSESE DLQQVIASVL RNLSWRADVN SKKTLREVGS VKALMECALE VKKESTLKSV LSALWNLSAH CTENKADICA VDGALAFLVG TLTYRSQTNT LAIIESGGGI LRNVSSLIAT NEDHRQILRE NNCLQTLLQH LKSHSLTIVS NACGTLWNLS ARNPKDQEAL WDMGAVSMLK NLIHSKHKMI AMGSAAALRN LMANRPAKYK DANIMSPGSS LPSLHVRKQK ALEAELDAQH LSETFDNIDN LSPKASHRSK QRHKQSLYGD YVFDTNRHDD NRSDNFNTGN MTVLSPYLNT TVLPSSSSSR GSLDSSRSEK DRSLERERGI GLGNYHPATE NPGTSSKRGL QISTTAAQIA KVMEEVSAIH TSQEDRSSGS TTELHCVTDE RNALRRSSAA HTHSNTYNFT KSENSNRTCS MPYAKLEYKR SSNDSLNSVS SSDGYGKRGQ MKPSIESYSE DDESKFCSYG QYPADLAHKI HSANHMDDND GELDTPINYS LKYSDEQLNS GRQSPSQNER WARPKHIIED EIKQSEQRQS RNQSTTYPVY TESTDDKHLK FQPHFGQQEC VSPYRSRGAN GSETNRVGSN HGINQNVSQS LCQEDDYEDD KPTNYSERYS EEEQHEEEER PTNYSIKYNE EKRHVDQPID YSLKYATDIP SSQKQSFSFS KSSSGQSSKT EHMSSSSENT STPSSNAKRQ NQLHPSSAQS RSGQPQKAAT CKVSSINQET IQTYCVEDTP ICFSRCSSLS SLSSAEDEIG CNQTTQEADS ANTLQIAEIK EKIGTRSAED PVSEVPAVSQ HPRTKSSRLQ GSSLSSESAR HKAVEFSSGA KSPSKSGAQT PKSPPEHYVQ ETPLMFSRCT SVSSLDSFES RSIASSVQSE PCSGMVSGII SPSDLPDSPG QTMPPSRSKT PPPPPQTAQT KREVPKNKAP TAEKRESGPK QAAVNAAVQR VQVLPDADTL LHFATESTPD GFSCSSSLSA LSLDEPFIQK DVELRIMPPV QENDNGNETE SEQPKESNEN QEKEAEKTID SEKDLLDDSD DDDIEILEEC IISAMPTKSS RKAKKPAQTA SKLPPPVARK PSQLPVYKLL PSQNRLQPQK HVSFTPGDDM PRVYCVEGTP INFSTATSLS DLTIESPPNE LAAGEGVRGG AQSGEFEKRD TIPTEGRSTD EAQGGKTSSV TIPELDDNKA EEGDILAECI NSAMPKGKSH KPFRVKKIMD QVQQASASSS APNKNQLDGK KKKPTSPVKP IPQNTEYRTR VRKNADSKNN LNAERVFSDN KDSKKQNLKN NSKVFNDKLP NNEDRVRGSF AFDSPHHYTP IEGTPYCFSR NDSLSSLDFD DDDVDLSREK AELRKAKENK ESEAKVTSHT ELTSNQQSAN KTQAIAKQPI NRGQPKPILQ KQSTFPQSSK DIPDRGAATD EKLQNFAIEN TPVCFSHNSS LSSLSDIDQE NNNKENEPIK ETEPPDSQGE PSKPQASGYA PKSFHVEDTP VCFSRNSSLS SLSIDSEDDL LQECISSAMP KKKKPSRLKG DNEKHSPRNM GGILGEDLTL DLKDIQRPDS EHGLSPDSEN FDWKAIQEGA NSIVSSLHQA AAAACLSRQA SSDSDSILSL KSGISLGSPF HLTPDQEEKP FTSNKGPRIL KPGEKSTLET KKIESESKGI KGGKKVYKSL ITGKVRSNSE ISGQMKQPLQ ANMPSISRGR TMIHIPGVRN SSSSTSPVSK KGPPLKTPAS KSPSEGQTAT TSPRGAKPSV KSELSPVARQ TSQIGGSSKA PSRSGSRDST PSRPAQQPLS RPIQSPGRNS ISPGRNGISP PNKLSQLPRT SSPSTASTKS SGSGKMSYTS PGRQMSQQNL TKQTGLSKNA SSIPRSESAS KGLNQMNNGN GANKKVELSR MSSTKSSGSE SDRSERPVLV RQSTFIKEAP SPTLRRKLEE SASFESLSPS SRPASPTRSQ AQTPVLSPSL PDMSLSTHSS VQAGGWRKLP PNLSPTIEYN DGRPAKRHDI ARSHSESPSR LPINRSGTWK REHSKHSSSL PRVSTWRRTG SSSSILSASS ESSEKAKSED EKHVNSISGT KQSKENQVSA KGTWRKIKEN EFSPTNSTSQ TVSSGATNGA ESKTLIYQMA PAVSKTEDVW VRIEDCPINN PRSGRSPTGN TPPVIDSVSE KANPNIKDSK DNQAKQNVGN GSVPMRTVGL ENRLNSFIQV DAPDQKGTEI KPGQNNPVPV SETNESSIVE RTPFSSSSSS KHSSPSGTVA ARVTPFNYNP SPRKSSADST SARPSQIPTP VNNNTKKRDS KTDSTESSGT QSPKRHSGSY LVTSV* | |||||||||||||
| Mutated AA sequence | MYASLGSGPV APLPASVPPS VLGSWSTGGS RSCVRQETKS PGGARTSGHW ASVWQEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRSSQN KHETGSHDAE RQNEGQGVGE INMATSGNGQ GSTTRMDHET ASVLSSSSTH SAPRRLTSHL GTKVEMVYSL LSMLGTHDKD DMSRTLLAMS SSQDSCISMR QSGCLPLLIQ LLHGNDKDSV LLGNSRGSKE ARARASAALH NIIHSQPDDK RGRREIRVLH LLEQIRAYCE TCWEWQEAHE PGMDQDKNPM PAPVEHQICP AVCVLMKLSF DEEHRHAMNE LGGLQAIAEL LQVDCEMYGL TNDHYSITLR RYAGMALTNL TFGDVANKAT LCSMKGCMRA LVAQLKSESE DLQQVIASVL RNLSWRADVN SKKTLREVGS VKALMECALE VKKESTLKSV LSALWNLSAH CTENKADICA VDGALAFLVG TLTYRSQTNT LAIIESGGGI LRNVSSLIAT NEDHRQILRE NNCLQTLLQH LKSHSLTIVS NACGTLWNLS ARNPKDQEAL WDMGAVSMLK NLIHSKHKMI AMGSAAALRN LMANRPAKYK DANIMSPGSS LPSLHVRKQK ALEAELDAQH LSETFDNIDN LSPKASHRSK QRHKQSLYGD YVFDTNRHDD NRSDNFNTGN MTVLSPYLNT TVLPSSSSSR GSLDSSRSEK DRSLERERGI GLGNYHPATE NPGTSSKRGL QISTTAAQIA KVMEEVSAIH TSQEDRSSGS TTELHCVTDE RNALRRSSAA HTHSNTYNFT KSENSNRTCS MPYAKLEYKR SSNDSLNSVS SSDGYGKRGQ MKPSIESYSE DDESKFCSYG QYPADLAHKI HSANHMDDND GELDTPINYS LKYSDEQLNS GRQSPSQNER WARPKHIIED EIKQSEQRQS RNQSTTYPVY TESTDDKHLK FQPHFGQQEC VSPYRSRGAN GSETNRVGSN HGINQNVSQS LCQEDDYEDD KPTNYSERYS EEEQHEEEER PTNYSIKYNE EKRHVDQPID YSLKYATDIP SSQKQSFSFS KSSSGQSSKT EHMSSSSENT STPSSNAKRQ NQLHPSSAQS RSGQPQKAAT CKVSSINQET IQTYCVEDTP ICFSRCSSLS SLSSAEDEIG CNQTTQEADS ANTLQIAEIK EKIGTRSAED PVSEVPAVSQ HPRTKSSRLQ GSSLSSESAR HKAVEFSSGA KSPSKSGAQT PKSPPEHYVQ ETPLMFSRCT SVSSLDSFES RSIASSVQSE PCSGMVSGII SPSDLPDSPG QTMPPSRSKT PPPPPQTAQT KREVPKNKAP TAEKRESGPK QAAVNAAVQR VQVLPDADTL LHFATESTPD GFSCSSSLSA LSLDEPFIQK DVELRIMPPV QENDNGNETE SEQPKESNEN QEKEAEKTID SEKDLLDDSD DDDIEILEEC IISAMPTKSS RKAKKPAQTA SKLPPPVARK PSQLPVYKLL PSQNRLQPQK HVRFTPGDDM PRVYCVEGTP INFSTATSLS DLTIESPPNE LAAGEGVRGG AQSGEFEKRD TIPTEGRSTD EAQGGKTSSV TIPELDDNKA EEGDILAECI NSAMPKGKSH KPFRVKKIMD QVQQASASSS APNKNQLDGK KKKPTSPVKP IPQNTEYRTR VRKNADSKNN LNAERVFSDN KDSKKQNLKN NSKVFNDKLP NNEDRVRGSF AFDSPHHYTP IEGTPYCFSR NDSLSSLDFD DDDVDLSREK AELRKAKENK ESEAKVTSHT ELTSNQQSAN KTQAIAKQPI NRGQPKPILQ KQSTFPQSSK DIPDRGAATD EKLQNFAIEN TPVCFSHNSS LSSLSDIDQE NNNKENEPIK ETEPPDSQGE PSKPQASGYA PKSFHVEDTP VCFSRNSSLS SLSIDSEDDL LQECISSAMP KKKKPSRLKG DNEKHSPRNM GGILGEDLTL DLKDIQRPDS EHGLSPDSEN FDWKAIQEGA NSIVSSLHQA AAAACLSRQA SSDSDSILSL KSGISLGSPF HLTPDQEEKP FTSNKGPRIL KPGEKSTLET KKIESESKGI KGGKKVYKSL ITGKVRSNSE ISGQMKQPLQ ANMPSISRGR TMIHIPGVRN SSSSTSPVSK KGPPLKTPAS KSPSEGQTAT TSPRGAKPSV KSELSPVARQ TSQIGGSSKA PSRSGSRDST PSRPAQQPLS RPIQSPGRNS ISPGRNGISP PNKLSQLPRT SSPSTASTKS SGSGKMSYTS PGRQMSQQNL TKQTGLSKNA SSIPRSESAS KGLNQMNNGN GANKKVELSR MSSTKSSGSE SDRSERPVLV RQSTFIKEAP SPTLRRKLEE SASFESLSPS SRPASPTRSQ AQTPVLSPSL PDMSLSTHSS VQAGGWRKLP PNLSPTIEYN DGRPAKRHDI ARSHSESPSR LPINRSGTWK REHSKHSSSL PRVSTWRRTG SSSSILSASS ESSEKAKSED EKHVNSISGT KQSKENQVSA KGTWRKIKEN EFSPTNSTSQ TVSSGATNGA ESKTLIYQMA PAVSKTEDVW VRIEDCPINN PRSGRSPTGN TPPVIDSVSE KANPNIKDSK DNQAKQNVGN GSVPMRTVGL ENRLNSFIQV DAPDQKGTEI KPGQNNPVPV SETNESSIVE RTPFSSSSSS KHSSPSGTVA ARVTPFNYNP SPRKSSADST SARPSQIPTP VNNNTKKRDS KTDSTESSGT QSPKRHSGSY LVTSV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 8478 / 8478 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2826 / 2826 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 8674 / 8674 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 197 / 197 | |||||||||||||
| Last intron/exon boundary | 2100 | |||||||||||||
| Theoretical NMD boundary in CDS | 1853 | |||||||||||||
| Length of CDS | 8478 | |||||||||||||
| Coding sequence (CDS) position | 4839 | |||||||||||||
| cDNA position | 5035 | |||||||||||||
| gDNA position | 132970 | |||||||||||||
| Chromosomal position | 112840487 | |||||||||||||
| Speed | 0.13 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr5:112840487T>A (GRCh38) | |||||||||||||
| Gene symbol | APC | |||||||||||||
| Gene constraints | LOEUF: 0.56, LOF (oe): 0.32, misssense (oe): 0.73, synonymous (oe): 0.98 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000504915.3 | |||||||||||||
| Genbank transcript ID | NM_001407447 (by similarity), NM_001407456 (by similarity), NM_001407452 (by similarity), NM_001407446 (by similarity), NM_001407448 (by similarity), NM_001407457 (by similarity), NM_001407449 (by similarity), NM_001407455 (by similarity), NM_001407451 (by similarity), NM_001354896 (by similarity), NM_001407454 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4947T>A g.132970T>A | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 5 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered gDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Original cDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered cDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Wildtype AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG RKATRGISSQ ELGQGLSGGL QAIAELLQVD CEMYGLTNDH YSITLRRYAG MALTNLTFGD VANKATLCSM KGCMRALVAQ LKSESEDLQQ VIASVLRNLS WRADVNSKKT LREVGSVKAL MECALEVKKE STLKSVLSAL WNLSAHCTEN KADICAVDGA LAFLVGTLTY RSQTNTLAII ESGGGILRNV SSLIATNEDH RQILRENNCL QTLLQHLKSH SLTIVSNACG TLWNLSARNP KDQEALWDMG AVSMLKNLIH SKHKMIAMGS AAALRNLMAN RPAKYKDANI MSPGSSLPSL HVRKQKALEA ELDAQHLSET FDNIDNLSPK ASHRSKQRHK QSLYGDYVFD TNRHDDNRSD NFNTGNMTVL SPYLNTTVLP SSSSSRGSLD SSRSEKDRSL ERERGIGLGN YHPATENPGT SSKRGLQIST TAAQIAKVME EVSAIHTSQE DRSSGSTTEL HCVTDERNAL RRSSAAHTHS NTYNFTKSEN SNRTCSMPYA KLEYKRSSND SLNSVSSSDG YGKRGQMKPS IESYSEDDES KFCSYGQYPA DLAHKIHSAN HMDDNDGELD TPINYSLKYS DEQLNSGRQS PSQNERWARP KHIIEDEIKQ SEQRQSRNQS TTYPVYTEST DDKHLKFQPH FGQQECVSPY RSRGANGSET NRVGSNHGIN QNVSQSLCQE DDYEDDKPTN YSERYSEEEQ HEEEERPTNY SIKYNEEKRH VDQPIDYSLK YATDIPSSQK QSFSFSKSSS GQSSKTEHMS SSSENTSTPS SNAKRQNQLH PSSAQSRSGQ PQKAATCKVS SINQETIQTY CVEDTPICFS RCSSLSSLSS AEDEIGCNQT TQEADSANTL QIAEIKEKIG TRSAEDPVSE VPAVSQHPRT KSSRLQGSSL SSESARHKAV EFSSGAKSPS KSGAQTPKSP PEHYVQETPL MFSRCTSVSS LDSFESRSIA SSVQSEPCSG MVSGIISPSD LPDSPGQTMP PSRSKTPPPP PQTAQTKREV PKNKAPTAEK RESGPKQAAV NAAVQRVQVL PDADTLLHFA TESTPDGFSC SSSLSALSLD EPFIQKDVEL RIMPPVQEND NGNETESEQP KESNENQEKE AEKTIDSEKD LLDDSDDDDI EILEECIISA MPTKSSRKAK KPAQTASKLP PPVARKPSQL PVYKLLPSQN RLQPQKHVSF TPGDDMPRVY CVEGTPINFS TATSLSDLTI ESPPNELAAG EGVRGGAQSG EFEKRDTIPT EGRSTDEAQG GKTSSVTIPE LDDNKAEEGD ILAECINSAM PKGKSHKPFR VKKIMDQVQQ ASASSSAPNK NQLDGKKKKP TSPVKPIPQN TEYRTRVRKN ADSKNNLNAE RVFSDNKDSK KQNLKNNSKV FNDKLPNNED RVRGSFAFDS PHHYTPIEGT PYCFSRNDSL SSLDFDDDDV DLSREKAELR KAKENKESEA KVTSHTELTS NQQSANKTQA IAKQPINRGQ PKPILQKQST FPQSSKDIPD RGAATDEKLQ NFAIENTPVC FSHNSSLSSL SDIDQENNNK ENEPIKETEP PDSQGEPSKP QASGYAPKSF HVEDTPVCFS RNSSLSSLSI DSEDDLLQEC ISSAMPKKKK PSRLKGDNEK HSPRNMGGIL GEDLTLDLKD IQRPDSEHGL SPDSENFDWK AIQEGANSIV SSLHQAAAAA CLSRQASSDS DSILSLKSGI SLGSPFHLTP DQEEKPFTSN KGPRILKPGE KSTLETKKIE SESKGIKGGK KVYKSLITGK VRSNSEISGQ MKQPLQANMP SISRGRTMIH IPGVRNSSSS TSPVSKKGPP LKTPASKSPS EGQTATTSPR GAKPSVKSEL SPVARQTSQI GGSSKAPSRS GSRDSTPSRP AQQPLSRPIQ SPGRNSISPG RNGISPPNKL SQLPRTSSPS TASTKSSGSG KMSYTSPGRQ MSQQNLTKQT GLSKNASSIP RSESASKGLN QMNNGNGANK KVELSRMSST KSSGSESDRS ERPVLVRQST FIKEAPSPTL RRKLEESASF ESLSPSSRPA SPTRSQAQTP VLSPSLPDMS LSTHSSVQAG GWRKLPPNLS PTIEYNDGRP AKRHDIARSH SESPSRLPIN RSGTWKREHS KHSSSLPRVS TWRRTGSSSS ILSASSESSE KAKSEDEKHV NSISGTKQSK ENQVSAKGTW RKIKENEFSP TNSTSQTVSS GATNGAESKT LIYQMAPAVS KTEDVWVRIE DCPINNPRSG RSPTGNTPPV IDSVSEKANP NIKDSKDNQA KQNVGNGSVP MRTVGLENRL NSFIQVDAPD QKGTEIKPGQ NNPVPVSETN ESSIVERTPF SSSSSSKHSS PSGTVAARVT PFNYNPSPRK SSADSTSARP SQIPTPVNNN TKKRDSKTDS TESSGTQSPK RHSGSYLVTS V* | |||||||||||||
| Mutated AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG RKATRGISSQ ELGQGLSGGL QAIAELLQVD CEMYGLTNDH YSITLRRYAG MALTNLTFGD VANKATLCSM KGCMRALVAQ LKSESEDLQQ VIASVLRNLS WRADVNSKKT LREVGSVKAL MECALEVKKE STLKSVLSAL WNLSAHCTEN KADICAVDGA LAFLVGTLTY RSQTNTLAII ESGGGILRNV SSLIATNEDH RQILRENNCL QTLLQHLKSH SLTIVSNACG TLWNLSARNP KDQEALWDMG AVSMLKNLIH SKHKMIAMGS AAALRNLMAN RPAKYKDANI MSPGSSLPSL HVRKQKALEA ELDAQHLSET FDNIDNLSPK ASHRSKQRHK QSLYGDYVFD TNRHDDNRSD NFNTGNMTVL SPYLNTTVLP SSSSSRGSLD SSRSEKDRSL ERERGIGLGN YHPATENPGT SSKRGLQIST TAAQIAKVME EVSAIHTSQE DRSSGSTTEL HCVTDERNAL RRSSAAHTHS NTYNFTKSEN SNRTCSMPYA KLEYKRSSND SLNSVSSSDG YGKRGQMKPS IESYSEDDES KFCSYGQYPA DLAHKIHSAN HMDDNDGELD TPINYSLKYS DEQLNSGRQS PSQNERWARP KHIIEDEIKQ SEQRQSRNQS TTYPVYTEST DDKHLKFQPH FGQQECVSPY RSRGANGSET NRVGSNHGIN QNVSQSLCQE DDYEDDKPTN YSERYSEEEQ HEEEERPTNY SIKYNEEKRH VDQPIDYSLK YATDIPSSQK QSFSFSKSSS GQSSKTEHMS SSSENTSTPS SNAKRQNQLH PSSAQSRSGQ PQKAATCKVS SINQETIQTY CVEDTPICFS RCSSLSSLSS AEDEIGCNQT TQEADSANTL QIAEIKEKIG TRSAEDPVSE VPAVSQHPRT KSSRLQGSSL SSESARHKAV EFSSGAKSPS KSGAQTPKSP PEHYVQETPL MFSRCTSVSS LDSFESRSIA SSVQSEPCSG MVSGIISPSD LPDSPGQTMP PSRSKTPPPP PQTAQTKREV PKNKAPTAEK RESGPKQAAV NAAVQRVQVL PDADTLLHFA TESTPDGFSC SSSLSALSLD EPFIQKDVEL RIMPPVQEND NGNETESEQP KESNENQEKE AEKTIDSEKD LLDDSDDDDI EILEECIISA MPTKSSRKAK KPAQTASKLP PPVARKPSQL PVYKLLPSQN RLQPQKHVRF TPGDDMPRVY CVEGTPINFS TATSLSDLTI ESPPNELAAG EGVRGGAQSG EFEKRDTIPT EGRSTDEAQG GKTSSVTIPE LDDNKAEEGD ILAECINSAM PKGKSHKPFR VKKIMDQVQQ ASASSSAPNK NQLDGKKKKP TSPVKPIPQN TEYRTRVRKN ADSKNNLNAE RVFSDNKDSK KQNLKNNSKV FNDKLPNNED RVRGSFAFDS PHHYTPIEGT PYCFSRNDSL SSLDFDDDDV DLSREKAELR KAKENKESEA KVTSHTELTS NQQSANKTQA IAKQPINRGQ PKPILQKQST FPQSSKDIPD RGAATDEKLQ NFAIENTPVC FSHNSSLSSL SDIDQENNNK ENEPIKETEP PDSQGEPSKP QASGYAPKSF HVEDTPVCFS RNSSLSSLSI DSEDDLLQEC ISSAMPKKKK PSRLKGDNEK HSPRNMGGIL GEDLTLDLKD IQRPDSEHGL SPDSENFDWK AIQEGANSIV SSLHQAAAAA CLSRQASSDS DSILSLKSGI SLGSPFHLTP DQEEKPFTSN KGPRILKPGE KSTLETKKIE SESKGIKGGK KVYKSLITGK VRSNSEISGQ MKQPLQANMP SISRGRTMIH IPGVRNSSSS TSPVSKKGPP LKTPASKSPS EGQTATTSPR GAKPSVKSEL SPVARQTSQI GGSSKAPSRS GSRDSTPSRP AQQPLSRPIQ SPGRNSISPG RNGISPPNKL SQLPRTSSPS TASTKSSGSG KMSYTSPGRQ MSQQNLTKQT GLSKNASSIP RSESASKGLN QMNNGNGANK KVELSRMSST KSSGSESDRS ERPVLVRQST FIKEAPSPTL RRKLEESASF ESLSPSSRPA SPTRSQAQTP VLSPSLPDMS LSTHSSVQAG GWRKLPPNLS PTIEYNDGRP AKRHDIARSH SESPSRLPIN RSGTWKREHS KHSSSLPRVS TWRRTGSSSS ILSASSESSE KAKSEDEKHV NSISGTKQSK ENQVSAKGTW RKIKENEFSP TNSTSQTVSS GATNGAESKT LIYQMAPAVS KTEDVWVRIE DCPINNPRSG RSPTGNTPPV IDSVSEKANP NIKDSKDNQA KQNVGNGSVP MRTVGLENRL NSFIQVDAPD QKGTEIKPGQ NNPVPVSETN ESSIVERTPF SSSSSSKHSS PSGTVAARVT PFNYNPSPRK SSADSTSARP SQIPTPVNNN TKKRDSKTDS TESSGTQSPK RHSGSYLVTS V* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 8586 / 8586 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2862 / 2862 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 8642 / 8642 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 57 / 57 | |||||||||||||
| Last intron/exon boundary | 2068 | |||||||||||||
| Theoretical NMD boundary in CDS | 1961 | |||||||||||||
| Length of CDS | 8586 | |||||||||||||
| Coding sequence (CDS) position | 4947 | |||||||||||||
| cDNA position | 5003 | |||||||||||||
| gDNA position | 132970 | |||||||||||||
| Chromosomal position | 112840487 | |||||||||||||
| Speed | 0.11 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr5:112840487T>A (GRCh38) | |||||||||||||
| Gene symbol | APC | |||||||||||||
| Gene constraints | LOEUF: 1.74, LOF (oe): 1.07, misssense (oe): 0.95, synonymous (oe): 0.73 (gnomAD) | |||||||||||||
| Ensembl transcript ID | ENST00000509732.6 | |||||||||||||
| Genbank transcript ID | NM_001354895 (by similarity), NM_001407460 (by similarity), NM_001407469 (by similarity), NM_001407450 (by similarity), NM_001407458 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | APC_HUMAN | AlphaMissense: transcript, gene | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4893T>A g.132970T>A | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features |
| |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 5 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered gDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Original cDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered cDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Wildtype AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KESTLKSVLS ALWNLSAHCT ENKADICAVD GALAFLVGTL TYRSQTNTLA IIESGGGILR NVSSLIATNE DHRQILRENN CLQTLLQHLK SHSLTIVSNA CGTLWNLSAR NPKDQEALWD MGAVSMLKNL IHSKHKMIAM GSAAALRNLM ANRPAKYKDA NIMSPGSSLP SLHVRKQKAL EAELDAQHLS ETFDNIDNLS PKASHRSKQR HKQSLYGDYV FDTNRHDDNR SDNFNTGNMT VLSPYLNTTV LPSSSSSRGS LDSSRSEKDR SLERERGIGL GNYHPATENP GTSSKRGLQI STTAAQIAKV MEEVSAIHTS QEDRSSGSTT ELHCVTDERN ALRRSSAAHT HSNTYNFTKS ENSNRTCSMP YAKLEYKRSS NDSLNSVSSS DGYGKRGQMK PSIESYSEDD ESKFCSYGQY PADLAHKIHS ANHMDDNDGE LDTPINYSLK YSDEQLNSGR QSPSQNERWA RPKHIIEDEI KQSEQRQSRN QSTTYPVYTE STDDKHLKFQ PHFGQQECVS PYRSRGANGS ETNRVGSNHG INQNVSQSLC QEDDYEDDKP TNYSERYSEE EQHEEEERPT NYSIKYNEEK RHVDQPIDYS LKYATDIPSS QKQSFSFSKS SSGQSSKTEH MSSSSENTST PSSNAKRQNQ LHPSSAQSRS GQPQKAATCK VSSINQETIQ TYCVEDTPIC FSRCSSLSSL SSAEDEIGCN QTTQEADSAN TLQIAEIKEK IGTRSAEDPV SEVPAVSQHP RTKSSRLQGS SLSSESARHK AVEFSSGAKS PSKSGAQTPK SPPEHYVQET PLMFSRCTSV SSLDSFESRS IASSVQSEPC SGMVSGIISP SDLPDSPGQT MPPSRSKTPP PPPQTAQTKR EVPKNKAPTA EKRESGPKQA AVNAAVQRVQ VLPDADTLLH FATESTPDGF SCSSSLSALS LDEPFIQKDV ELRIMPPVQE NDNGNETESE QPKESNENQE KEAEKTIDSE KDLLDDSDDD DIEILEECII SAMPTKSSRK AKKPAQTASK LPPPVARKPS QLPVYKLLPS QNRLQPQKHV SFTPGDDMPR VYCVEGTPIN FSTATSLSDL TIESPPNELA AGEGVRGGAQ SGEFEKRDTI PTEGRSTDEA QGGKTSSVTI PELDDNKAEE GDILAECINS AMPKGKSHKP FRVKKIMDQV QQASASSSAP NKNQLDGKKK KPTSPVKPIP QNTEYRTRVR KNADSKNNLN AERVFSDNKD SKKQNLKNNS KVFNDKLPNN EDRVRGSFAF DSPHHYTPIE GTPYCFSRND SLSSLDFDDD DVDLSREKAE LRKAKENKES EAKVTSHTEL TSNQQSANKT QAIAKQPINR GQPKPILQKQ STFPQSSKDI PDRGAATDEK LQNFAIENTP VCFSHNSSLS SLSDIDQENN NKENEPIKET EPPDSQGEPS KPQASGYAPK SFHVEDTPVC FSRNSSLSSL SIDSEDDLLQ ECISSAMPKK KKPSRLKGDN EKHSPRNMGG ILGEDLTLDL KDIQRPDSEH GLSPDSENFD WKAIQEGANS IVSSLHQAAA AACLSRQASS DSDSILSLKS GISLGSPFHL TPDQEEKPFT SNKGPRILKP GEKSTLETKK IESESKGIKG GKKVYKSLIT GKVRSNSEIS GQMKQPLQAN MPSISRGRTM IHIPGVRNSS SSTSPVSKKG PPLKTPASKS PSEGQTATTS PRGAKPSVKS ELSPVARQTS QIGGSSKAPS RSGSRDSTPS RPAQQPLSRP IQSPGRNSIS PGRNGISPPN KLSQLPRTSS PSTASTKSSG SGKMSYTSPG RQMSQQNLTK QTGLSKNASS IPRSESASKG LNQMNNGNGA NKKVELSRMS STKSSGSESD RSERPVLVRQ STFIKEAPSP TLRRKLEESA SFESLSPSSR PASPTRSQAQ TPVLSPSLPD MSLSTHSSVQ AGGWRKLPPN LSPTIEYNDG RPAKRHDIAR SHSESPSRLP INRSGTWKRE HSKHSSSLPR VSTWRRTGSS SSILSASSES SEKAKSEDEK HVNSISGTKQ SKENQVSAKG TWRKIKENEF SPTNSTSQTV SSGATNGAES KTLIYQMAPA VSKTEDVWVR IEDCPINNPR SGRSPTGNTP PVIDSVSEKA NPNIKDSKDN QAKQNVGNGS VPMRTVGLEN RLNSFIQVDA PDQKGTEIKP GQNNPVPVSE TNESSIVERT PFSSSSSSKH SSPSGTVAAR VTPFNYNPSP RKSSADSTSA RPSQIPTPVN NNTKKRDSKT DSTESSGTQS PKRHSGSYLV TSV* | |||||||||||||
| Mutated AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KESTLKSVLS ALWNLSAHCT ENKADICAVD GALAFLVGTL TYRSQTNTLA IIESGGGILR NVSSLIATNE DHRQILRENN CLQTLLQHLK SHSLTIVSNA CGTLWNLSAR NPKDQEALWD MGAVSMLKNL IHSKHKMIAM GSAAALRNLM ANRPAKYKDA NIMSPGSSLP SLHVRKQKAL EAELDAQHLS ETFDNIDNLS PKASHRSKQR HKQSLYGDYV FDTNRHDDNR SDNFNTGNMT VLSPYLNTTV LPSSSSSRGS LDSSRSEKDR SLERERGIGL GNYHPATENP GTSSKRGLQI STTAAQIAKV MEEVSAIHTS QEDRSSGSTT ELHCVTDERN ALRRSSAAHT HSNTYNFTKS ENSNRTCSMP YAKLEYKRSS NDSLNSVSSS DGYGKRGQMK PSIESYSEDD ESKFCSYGQY PADLAHKIHS ANHMDDNDGE LDTPINYSLK YSDEQLNSGR QSPSQNERWA RPKHIIEDEI KQSEQRQSRN QSTTYPVYTE STDDKHLKFQ PHFGQQECVS PYRSRGANGS ETNRVGSNHG INQNVSQSLC QEDDYEDDKP TNYSERYSEE EQHEEEERPT NYSIKYNEEK RHVDQPIDYS LKYATDIPSS QKQSFSFSKS SSGQSSKTEH MSSSSENTST PSSNAKRQNQ LHPSSAQSRS GQPQKAATCK VSSINQETIQ TYCVEDTPIC FSRCSSLSSL SSAEDEIGCN QTTQEADSAN TLQIAEIKEK IGTRSAEDPV SEVPAVSQHP RTKSSRLQGS SLSSESARHK AVEFSSGAKS PSKSGAQTPK SPPEHYVQET PLMFSRCTSV SSLDSFESRS IASSVQSEPC SGMVSGIISP SDLPDSPGQT MPPSRSKTPP PPPQTAQTKR EVPKNKAPTA EKRESGPKQA AVNAAVQRVQ VLPDADTLLH FATESTPDGF SCSSSLSALS LDEPFIQKDV ELRIMPPVQE NDNGNETESE QPKESNENQE KEAEKTIDSE KDLLDDSDDD DIEILEECII SAMPTKSSRK AKKPAQTASK LPPPVARKPS QLPVYKLLPS QNRLQPQKHV RFTPGDDMPR VYCVEGTPIN FSTATSLSDL TIESPPNELA AGEGVRGGAQ SGEFEKRDTI PTEGRSTDEA QGGKTSSVTI PELDDNKAEE GDILAECINS AMPKGKSHKP FRVKKIMDQV QQASASSSAP NKNQLDGKKK KPTSPVKPIP QNTEYRTRVR KNADSKNNLN AERVFSDNKD SKKQNLKNNS KVFNDKLPNN EDRVRGSFAF DSPHHYTPIE GTPYCFSRND SLSSLDFDDD DVDLSREKAE LRKAKENKES EAKVTSHTEL TSNQQSANKT QAIAKQPINR GQPKPILQKQ STFPQSSKDI PDRGAATDEK LQNFAIENTP VCFSHNSSLS SLSDIDQENN NKENEPIKET EPPDSQGEPS KPQASGYAPK SFHVEDTPVC FSRNSSLSSL SIDSEDDLLQ ECISSAMPKK KKPSRLKGDN EKHSPRNMGG ILGEDLTLDL KDIQRPDSEH GLSPDSENFD WKAIQEGANS IVSSLHQAAA AACLSRQASS DSDSILSLKS GISLGSPFHL TPDQEEKPFT SNKGPRILKP GEKSTLETKK IESESKGIKG GKKVYKSLIT GKVRSNSEIS GQMKQPLQAN MPSISRGRTM IHIPGVRNSS SSTSPVSKKG PPLKTPASKS PSEGQTATTS PRGAKPSVKS ELSPVARQTS QIGGSSKAPS RSGSRDSTPS RPAQQPLSRP IQSPGRNSIS PGRNGISPPN KLSQLPRTSS PSTASTKSSG SGKMSYTSPG RQMSQQNLTK QTGLSKNASS IPRSESASKG LNQMNNGNGA NKKVELSRMS STKSSGSESD RSERPVLVRQ STFIKEAPSP TLRRKLEESA SFESLSPSSR PASPTRSQAQ TPVLSPSLPD MSLSTHSSVQ AGGWRKLPPN LSPTIEYNDG RPAKRHDIAR SHSESPSRLP INRSGTWKRE HSKHSSSLPR VSTWRRTGSS SSILSASSES SEKAKSEDEK HVNSISGTKQ SKENQVSAKG TWRKIKENEF SPTNSTSQTV SSGATNGAES KTLIYQMAPA VSKTEDVWVR IEDCPINNPR SGRSPTGNTP PVIDSVSEKA NPNIKDSKDN QAKQNVGNGS VPMRTVGLEN RLNSFIQVDA PDQKGTEIKP GQNNPVPVSE TNESSIVERT PFSSSSSSKH SSPSGTVAAR VTPFNYNPSP RKSSADSTSA RPSQIPTPVN NNTKKRDSKT DSTESSGTQS PKRHSGSYLV TSV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 8532 / 8532 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2844 / 2844 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 8682 / 8682 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 151 / 151 | |||||||||||||
| Last intron/exon boundary | 2108 | |||||||||||||
| Theoretical NMD boundary in CDS | 1907 | |||||||||||||
| Length of CDS | 8532 | |||||||||||||
| Coding sequence (CDS) position | 4893 | |||||||||||||
| cDNA position | 5043 | |||||||||||||
| gDNA position | 132970 | |||||||||||||
| Chromosomal position | 112840487 | |||||||||||||
| Speed | 0.10 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr5:112840487T>A (GRCh38) | |||||||||||||
| Gene symbol | APC | |||||||||||||
| Gene constraints | no data | |||||||||||||
| Ensembl transcript ID | ENST00000713638.1 | |||||||||||||
| Genbank transcript ID | ||||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | 3'UTR | |||||||||||||
| DNA changes | cDNA.4734T>A g.132970T>A | |||||||||||||
| AA changes | N/A | |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | N/A | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | N/A | |||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | N/A | |||||||||||||
| poly(A) signal | polyA signal ok | |||||||||||||
| AA sequence altered | N/A | |||||||||||||
| Chromosome | 5 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered gDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Original cDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered cDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Wildtype AA sequence | MAAASYDQLL KQVEALKMEN SNLRQELEDN SNHLTKLETE ASNMKEVLKQ LQGSIEDEAM ASSGQIDLLE RLKELNLDSS NFPGVKLRSK MSLRSYGSRE GSVSSRSGEC SPVPMGSFPR RGFVNGSRES TGYLEELEKE RSLLLADLDK EEKEKDWYYA QLQNLTKRID SLPLTENFSL QTDMTRRQLE YEARQIRVAM EEQLGTCQDM EKRAQRRIAR IQQIEKDILR IRQLLQSQAT EAERSSQNKH ETGSHDAERQ NEGQGVGEIN MATSGNGQGS TTRMDHETAS VLSSSSTHSA PRRLTSHLGT KVEMVYSLLS MLGTHDKDDM SRTLLAMSSS QDSCISMRQS GCLPLLIQLL HGNDKDSVLL GNSRGSKEAR ARASAALHNI IHSQPDDKRG RREIRVLHLL EQIRAYCETC WEWQEAHEPG MDQDKNPMPA PVEHQICPAV CVLMKLSFDE EHRHAMNELG GLQAIAELLQ VDCEMYGLTN DHYSITLRRY AGMALTNLTF GDVANKATLC SMKGCMRALV AQLKSESEDL QQVIASVLRN LSWRADVNSK KTLREVGSVK ALMECALEVK KANPKREQLS TNFITTLKIS * | |||||||||||||
| Mutated AA sequence | ||||||||||||||
| Position of stopcodon in wt / mu CDS | N/A | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | N/A | |||||||||||||
| Position of stopcodon in wt / mu cDNA | N/A | |||||||||||||
| Position of start ATG in wt / mu cDNA | 57 / 57 | |||||||||||||
| Last intron/exon boundary | 1799 | |||||||||||||
| Theoretical NMD boundary in CDS | 1692 | |||||||||||||
| Length of CDS | 1803 | |||||||||||||
| Coding sequence (CDS) position | N/A | |||||||||||||
| cDNA position | 4734 | |||||||||||||
| gDNA position | 132970 | |||||||||||||
| Chromosomal position | 112840487 | |||||||||||||
| Speed | 0.11 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
| Analysed issue | Analysis result | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Variant | Chr5:112840487T>A (GRCh38) | |||||||||||||
| Gene symbol | APC | |||||||||||||
| Gene constraints | no data | |||||||||||||
| Ensembl transcript ID | ENST00000713639.1 | |||||||||||||
| Genbank transcript ID | NM_001407472 (by similarity), NM_001407453 (by similarity), NM_001354898 (by similarity), NM_001354904 (by similarity), NM_001407471 (by similarity), NM_001354900 (by similarity), NM_001354901 (by similarity), NM_001354905 (by similarity) | |||||||||||||
| UniProt / AlphaMissense peptide | N/A | |||||||||||||
| Variant type | Single base exchange | |||||||||||||
| Gene region | CDS | |||||||||||||
| DNA changes | c.4575T>A g.132970T>A | |||||||||||||
| AA changes |
| |||||||||||||
| Frameshift | No | |||||||||||||
| Length of protein | Normal | |||||||||||||
| Pathogenic variant (ClinVar) | Variant not listed in ClinVar as (likely) pathogenic. | |||||||||||||
| Variant DBs |
| |||||||||||||
| Protein conservation | ||||||||||||||
| Protein features | N/A | |||||||||||||
| Phylogenetic conservation |
| |||||||||||||
| Splice sites | No abrogation of potential splice sites predicted by MaxEntScan. | |||||||||||||
| Distance from splice site | N/A | |||||||||||||
| Kozak consensus sequence altered? | No | |||||||||||||
| poly(A) signal | N/A | |||||||||||||
| AA sequence altered | Yes | |||||||||||||
| Chromosome | 5 | |||||||||||||
| Strand | 1 | |||||||||||||
| Original gDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered gDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Original cDNA sequence snippet | CAACCCCAAAAGCATGTTAGTTTTACACCGGGGGATGATAT | |||||||||||||
| Altered cDNA sequence snippet | CAACCCCAAAAGCATGTTAGATTTACACCGGGGGATGATAT | |||||||||||||
| Wildtype AA sequence | MASSGQIDLL ERLKELNLDS SNFPGVKLRS KMSLRSYGSR EGSVSSRSGE CSPVPMGSFP RRGFVNGSRE STGYLEELEK ERSLLLADLD KEEKEKDWYY AQLQNLTKRI DSLPLTENFS LQTDMTRRQL EYEARQIRVA MEEQLGTCQD MEKRAQRRIA RIQQIEKDIL RIRQLLQSQA TEAERSSQNK HETGSHDAER QNEGQGVGEI NMATSGNGQG STTRMDHETA SVLSSSSTHS APRRLTSHLG TKLLHGNDKD SVLLGNSRGS KEARARASAA LHNIIHSQPD DKRGRREIRV LHLLEQIRAY CETCWEWQEA HEPGMDQDKN PMPAPVEHQI CPAVCVLMKL SFDEEHRHAM NELGGLQAIA ELLQVDCEMY GLTNDHYSIT LRRYAGMALT NLTFGDVANK ATLCSMKGCM RALVAQLKSE SEDLQQVIAS VLRNLSWRAD VNSKKTLREV GSVKALMECA LEVKKESTLK SVLSALWNLS AHCTENKADI CAVDGALAFL VGTLTYRSQT NTLAIIESGG GILRNVSSLI ATNEDHRQIL RENNCLQTLL QHLKSHSLTI VSNACGTLWN LSARNPKDQE ALWDMGAVSM LKNLIHSKHK MIAMGSAAAL RNLMANRPAK YKDANIMSPG SSLPSLHVRK QKALEAELDA QHLSETFDNI DNLSPKASHR SKQRHKQSLY GDYVFDTNRH DDNRSDNFNT GNMTVLSPYL NTTVLPSSSS SRGSLDSSRS EKDRSLERER GIGLGNYHPA TENPGTSSKR GLQISTTAAQ IAKVMEEVSA IHTSQEDRSS GSTTELHCVT DERNALRRSS AAHTHSNTYN FTKSENSNRT CSMPYAKLEY KRSSNDSLNS VSSSDGYGKR GQMKPSIESY SEDDESKFCS YGQYPADLAH KIHSANHMDD NDGELDTPIN YSLKYSDEQL NSGRQSPSQN ERWARPKHII EDEIKQSEQR QSRNQSTTYP VYTESTDDKH LKFQPHFGQQ ECVSPYRSRG ANGSETNRVG SNHGINQNVS QSLCQEDDYE DDKPTNYSER YSEEEQHEEE ERPTNYSIKY NEEKRHVDQP IDYSLKYATD IPSSQKQSFS FSKSSSGQSS KTEHMSSSSE NTSTPSSNAK RQNQLHPSSA QSRSGQPQKA ATCKVSSINQ ETIQTYCVED TPICFSRCSS LSSLSSAEDE IGCNQTTQEA DSANTLQIAE IKEKIGTRSA EDPVSEVPAV SQHPRTKSSR LQGSSLSSES ARHKAVEFSS GAKSPSKSGA QTPKSPPEHY VQETPLMFSR CTSVSSLDSF ESRSIASSVQ SEPCSGMVSG IISPSDLPDS PGQTMPPSRS KTPPPPPQTA QTKREVPKNK APTAEKRESG PKQAAVNAAV QRVQVLPDAD TLLHFATEST PDGFSCSSSL SALSLDEPFI QKDVELRIMP PVQENDNGNE TESEQPKESN ENQEKEAEKT IDSEKDLLDD SDDDDIEILE ECIISAMPTK SSRKAKKPAQ TASKLPPPVA RKPSQLPVYK LLPSQNRLQP QKHVSFTPGD DMPRVYCVEG TPINFSTATS LSDLTIESPP NELAAGEGVR GGAQSGEFEK RDTIPTEGRS TDEAQGGKTS SVTIPELDDN KAEEGDILAE CINSAMPKGK SHKPFRVKKI MDQVQQASAS SSAPNKNQLD GKKKKPTSPV KPIPQNTEYR TRVRKNADSK NNLNAERVFS DNKDSKKQNL KNNSKVFNDK LPNNEDRVRG SFAFDSPHHY TPIEGTPYCF SRNDSLSSLD FDDDDVDLSR EKAELRKAKE NKESEAKVTS HTELTSNQQS ANKTQAIAKQ PINRGQPKPI LQKQSTFPQS SKDIPDRGAA TDEKLQNFAI ENTPVCFSHN SSLSSLSDID QENNNKENEP IKETEPPDSQ GEPSKPQASG YAPKSFHVED TPVCFSRNSS LSSLSIDSED DLLQECISSA MPKKKKPSRL KGDNEKHSPR NMGGILGEDL TLDLKDIQRP DSEHGLSPDS ENFDWKAIQE GANSIVSSLH QAAAAACLSR QASSDSDSIL SLKSGISLGS PFHLTPDQEE KPFTSNKGPR ILKPGEKSTL ETKKIESESK GIKGGKKVYK SLITGKVRSN SEISGQMKQP LQANMPSISR GRTMIHIPGV RNSSSSTSPV SKKGPPLKTP ASKSPSEGQT ATTSPRGAKP SVKSELSPVA RQTSQIGGSS KAPSRSGSRD STPSRPAQQP LSRPIQSPGR NSISPGRNGI SPPNKLSQLP RTSSPSTAST KSSGSGKMSY TSPGRQMSQQ NLTKQTGLSK NASSIPRSES ASKGLNQMNN GNGANKKVEL SRMSSTKSSG SESDRSERPV LVRQSTFIKE APSPTLRRKL EESASFESLS PSSRPASPTR SQAQTPVLSP SLPDMSLSTH SSVQAGGWRK LPPNLSPTIE YNDGRPAKRH DIARSHSESP SRLPINRSGT WKREHSKHSS SLPRVSTWRR TGSSSSILSA SSESSEKAKS EDEKHVNSIS GTKQSKENQV SAKGTWRKIK ENEFSPTNST SQTVSSGATN GAESKTLIYQ MAPAVSKTED VWVRIEDCPI NNPRSGRSPT GNTPPVIDSV SEKANPNIKD SKDNQAKQNV GNGSVPMRTV GLENRLNSFI QVDAPDQKGT EIKPGQNNPV PVSETNESSI VERTPFSSSS SSKHSSPSGT VAARVTPFNY NPSPRKSSAD STSARPSQIP TPVNNNTKKR DSKTDSTESS GTQSPKRHSG SYLVTSV* | |||||||||||||
| Mutated AA sequence | MASSGQIDLL ERLKELNLDS SNFPGVKLRS KMSLRSYGSR EGSVSSRSGE CSPVPMGSFP RRGFVNGSRE STGYLEELEK ERSLLLADLD KEEKEKDWYY AQLQNLTKRI DSLPLTENFS LQTDMTRRQL EYEARQIRVA MEEQLGTCQD MEKRAQRRIA RIQQIEKDIL RIRQLLQSQA TEAERSSQNK HETGSHDAER QNEGQGVGEI NMATSGNGQG STTRMDHETA SVLSSSSTHS APRRLTSHLG TKLLHGNDKD SVLLGNSRGS KEARARASAA LHNIIHSQPD DKRGRREIRV LHLLEQIRAY CETCWEWQEA HEPGMDQDKN PMPAPVEHQI CPAVCVLMKL SFDEEHRHAM NELGGLQAIA ELLQVDCEMY GLTNDHYSIT LRRYAGMALT NLTFGDVANK ATLCSMKGCM RALVAQLKSE SEDLQQVIAS VLRNLSWRAD VNSKKTLREV GSVKALMECA LEVKKESTLK SVLSALWNLS AHCTENKADI CAVDGALAFL VGTLTYRSQT NTLAIIESGG GILRNVSSLI ATNEDHRQIL RENNCLQTLL QHLKSHSLTI VSNACGTLWN LSARNPKDQE ALWDMGAVSM LKNLIHSKHK MIAMGSAAAL RNLMANRPAK YKDANIMSPG SSLPSLHVRK QKALEAELDA QHLSETFDNI DNLSPKASHR SKQRHKQSLY GDYVFDTNRH DDNRSDNFNT GNMTVLSPYL NTTVLPSSSS SRGSLDSSRS EKDRSLERER GIGLGNYHPA TENPGTSSKR GLQISTTAAQ IAKVMEEVSA IHTSQEDRSS GSTTELHCVT DERNALRRSS AAHTHSNTYN FTKSENSNRT CSMPYAKLEY KRSSNDSLNS VSSSDGYGKR GQMKPSIESY SEDDESKFCS YGQYPADLAH KIHSANHMDD NDGELDTPIN YSLKYSDEQL NSGRQSPSQN ERWARPKHII EDEIKQSEQR QSRNQSTTYP VYTESTDDKH LKFQPHFGQQ ECVSPYRSRG ANGSETNRVG SNHGINQNVS QSLCQEDDYE DDKPTNYSER YSEEEQHEEE ERPTNYSIKY NEEKRHVDQP IDYSLKYATD IPSSQKQSFS FSKSSSGQSS KTEHMSSSSE NTSTPSSNAK RQNQLHPSSA QSRSGQPQKA ATCKVSSINQ ETIQTYCVED TPICFSRCSS LSSLSSAEDE IGCNQTTQEA DSANTLQIAE IKEKIGTRSA EDPVSEVPAV SQHPRTKSSR LQGSSLSSES ARHKAVEFSS GAKSPSKSGA QTPKSPPEHY VQETPLMFSR CTSVSSLDSF ESRSIASSVQ SEPCSGMVSG IISPSDLPDS PGQTMPPSRS KTPPPPPQTA QTKREVPKNK APTAEKRESG PKQAAVNAAV QRVQVLPDAD TLLHFATEST PDGFSCSSSL SALSLDEPFI QKDVELRIMP PVQENDNGNE TESEQPKESN ENQEKEAEKT IDSEKDLLDD SDDDDIEILE ECIISAMPTK SSRKAKKPAQ TASKLPPPVA RKPSQLPVYK LLPSQNRLQP QKHVRFTPGD DMPRVYCVEG TPINFSTATS LSDLTIESPP NELAAGEGVR GGAQSGEFEK RDTIPTEGRS TDEAQGGKTS SVTIPELDDN KAEEGDILAE CINSAMPKGK SHKPFRVKKI MDQVQQASAS SSAPNKNQLD GKKKKPTSPV KPIPQNTEYR TRVRKNADSK NNLNAERVFS DNKDSKKQNL KNNSKVFNDK LPNNEDRVRG SFAFDSPHHY TPIEGTPYCF SRNDSLSSLD FDDDDVDLSR EKAELRKAKE NKESEAKVTS HTELTSNQQS ANKTQAIAKQ PINRGQPKPI LQKQSTFPQS SKDIPDRGAA TDEKLQNFAI ENTPVCFSHN SSLSSLSDID QENNNKENEP IKETEPPDSQ GEPSKPQASG YAPKSFHVED TPVCFSRNSS LSSLSIDSED DLLQECISSA MPKKKKPSRL KGDNEKHSPR NMGGILGEDL TLDLKDIQRP DSEHGLSPDS ENFDWKAIQE GANSIVSSLH QAAAAACLSR QASSDSDSIL SLKSGISLGS PFHLTPDQEE KPFTSNKGPR ILKPGEKSTL ETKKIESESK GIKGGKKVYK SLITGKVRSN SEISGQMKQP LQANMPSISR GRTMIHIPGV RNSSSSTSPV SKKGPPLKTP ASKSPSEGQT ATTSPRGAKP SVKSELSPVA RQTSQIGGSS KAPSRSGSRD STPSRPAQQP LSRPIQSPGR NSISPGRNGI SPPNKLSQLP RTSSPSTAST KSSGSGKMSY TSPGRQMSQQ NLTKQTGLSK NASSIPRSES ASKGLNQMNN GNGANKKVEL SRMSSTKSSG SESDRSERPV LVRQSTFIKE APSPTLRRKL EESASFESLS PSSRPASPTR SQAQTPVLSP SLPDMSLSTH SSVQAGGWRK LPPNLSPTIE YNDGRPAKRH DIARSHSESP SRLPINRSGT WKREHSKHSS SLPRVSTWRR TGSSSSILSA SSESSEKAKS EDEKHVNSIS GTKQSKENQV SAKGTWRKIK ENEFSPTNST SQTVSSGATN GAESKTLIYQ MAPAVSKTED VWVRIEDCPI NNPRSGRSPT GNTPPVIDSV SEKANPNIKD SKDNQAKQNV GNGSVPMRTV GLENRLNSFI QVDAPDQKGT EIKPGQNNPV PVSETNESSI VERTPFSSSS SSKHSSPSGT VAARVTPFNY NPSPRKSSAD STSARPSQIP TPVNNNTKKR DSKTDSTESS GTQSPKRHSG SYLVTSV* | |||||||||||||
| Position of stopcodon in wt / mu CDS | 8214 / 8214 | |||||||||||||
| Position (AA) of stopcodon in wt / mu AA sequence | 2738 / 2738 | |||||||||||||
| Position of stopcodon in wt / mu cDNA | 8294 / 8294 | |||||||||||||
| Position of start ATG in wt / mu cDNA | 81 / 81 | |||||||||||||
| Last intron/exon boundary | 1720 | |||||||||||||
| Theoretical NMD boundary in CDS | 1589 | |||||||||||||
| Length of CDS | 8214 | |||||||||||||
| Coding sequence (CDS) position | 4575 | |||||||||||||
| cDNA position | 4655 | |||||||||||||
| gDNA position | 132970 | |||||||||||||
| Chromosomal position | 112840487 | |||||||||||||
| Speed | 0.10 s | |||||||||||||
All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project