Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999998 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:238244963A>GN/A show variant in all transcripts   IGV
HGNC symbol COL6A3
Ensembl transcript ID ENST00000346358
Genbank transcript ID N/A
UniProt peptide P12111
alteration type single base exchange
alteration region CDS
DNA changes c.8180T>C
cDNA.8465T>C
g.78056T>C
AA changes M2727T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 2727
frameshift no
known variant Reference ID: rs6728818
databasehomozygous (G/G)heterozygousallele carriers
1000G107010482118
ExAC25150-175337617
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8770
0.1560
(flanking)-1.4540
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased78048wt: 0.8509 / mu: 0.8900 (marginal change - not scored)wt: GTGGCCACAAAGATG
mu: GTGGCCACAAAGACG		 GGCC|acaa
Donor marginally increased78053wt: 0.2851 / mu: 0.3345 (marginal change - not scored)wt: CACAAAGATGGCCAC
mu: CACAAAGACGGCCAC		 CAAA|gatg
Donor marginally increased78051wt: 0.8907 / mu: 0.9485 (marginal change - not scored)wt: GCCACAAAGATGGCC
mu: GCCACAAAGACGGCC		 CACA|aaga
Donor gained780570.52mu: AAGACGGCCACTGTT GACG|gcca
distance from splice site 186
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      2727KPVAAKPVATKMATVRPPVAVKPA
mutated  not conserved    2727KPVAAKPVATKTATVRPPVAVKP
Ptroglodytes  not conserved  ENSPTRG00000013074  2927AAKPVATKTATVRPPVAVRP
Mmulatta  not conserved  ENSMMUG00000014049  2714KPVAAKPVATKTATVRPPVAVKP
Fcatus  no alignment  ENSFCAG00000012720  n/a
Mmusculus  not conserved  ENSMUSG00000048126  2378QPAAAKPVPAKPAVPAQPAPPQPAAAKPVPAKPAVPAQPAAAQPMPAQPVLTKSAAVKPA
Ggallus  not conserved  ENSGALG00000003923  2906KTTTASTTAQTRATERP------
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000077139  3502VVNTHNVNGHVASTYKGIVPTK
Dmelanogaster  no homologue    
Celegans  no alignment  C18H7.1  n/a
Xtropicalis  no alignment  ENSXETG00000031229  n/a
protein features
start (aa)end (aa)featuredetails 
23763177REGIONNonhelical region.lost
26192815DOMAINVWFA 12.lost
28612861CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
28632898COMPBIASThr-rich.might get lost (downstream of altered splice site)
29082983COMPBIASAla-rich.might get lost (downstream of altered splice site)
29562956CONFLICTMissing (in Ref. 1; CAA36267).might get lost (downstream of altered splice site)
29883076DOMAINFibronectin type-III.might get lost (downstream of altered splice site)
29922992CONFLICTS -> L (in Ref. 1; CAA36267).might get lost (downstream of altered splice site)
30373037CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
31103113HELIXmight get lost (downstream of altered splice site)
31123112DISULFIDBy similarity.might get lost (downstream of altered splice site)
31123162DOMAINBPTI/Kunitz inhibitor.might get lost (downstream of altered splice site)
31203122STRANDmight get lost (downstream of altered splice site)
31213121DISULFIDBy similarity.might get lost (downstream of altered splice site)
31223123SITEReactive bond.might get lost (downstream of altered splice site)
31253131STRANDmight get lost (downstream of altered splice site)
31323135TURNmight get lost (downstream of altered splice site)
31363142STRANDmight get lost (downstream of altered splice site)
31373137DISULFIDBy similarity.might get lost (downstream of altered splice site)
31443146STRANDmight get lost (downstream of altered splice site)
31453145DISULFIDBy similarity.might get lost (downstream of altered splice site)
31523154STRANDmight get lost (downstream of altered splice site)
31553162HELIXmight get lost (downstream of altered splice site)
31583158DISULFIDBy similarity.might get lost (downstream of altered splice site)
31623162DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 8934 / 8934
position (AA) of stopcodon in wt / mu AA sequence 2978 / 2978
position of stopcodon in wt / mu cDNA 9219 / 9219
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 286 / 286
chromosome 2
strand -1
last intron/exon boundary 9179
theoretical NMD boundary in CDS 8843
length of CDS 8934
coding sequence (CDS) position 8180
cDNA position
(for ins/del: last normal base / first normal base)		 8465
gDNA position
(for ins/del: last normal base / first normal base)		 78056
chromosomal position
(for ins/del: last normal base / first normal base)		 238244963
original gDNA sequence snippet CAAGCCTGTGGCCACAAAGATGGCCACTGTTAGACCCCCAG
altered gDNA sequence snippet CAAGCCTGTGGCCACAAAGACGGCCACTGTTAGACCCCCAG
original cDNA sequence snippet CAAGCCTGTGGCCACAAAGATGGCCACTGTTAGACCCCCAG
altered cDNA sequence snippet CAAGCCTGTGGCCACAAAGACGGCCACTGTTAGACCCCCAG
wildtype AA sequence MRKHRHLPLV AVFCLFLSGF PTTHAQQQQA DVKNGAAADI IFLVDSSWTI GEEHFQLVRE
FLYDVVKSLA VGENDFHFAL VQFNGNPHTE FLLNTYRTKQ EVLSHISNMS YIGGTNQTGK
GLEYIMQSHL TKAAGSRAGD GVPQVIVVLT DGHSKDGLAL PSAELKSADV NVFAIGVEDA
DEGALKEIAS EPLNMHMFNL ENFTSLHDIV GNLVSCVHSS VSPERAGDTE TLKDITAQDS
ADIIFLIDGS NNTGSVNFAV ILDFLVNLLE KLPIGTQQIR VGVVQFSDEP RTMFSLDTYS
TKAQVLGAVK ALGFAGGELA NIGLALDFVV ENHFTRAGGS RVEEGVPQVL VLISAGPSSD
EIRYGVVALK QASVFSFGLG AQAASRAELQ HIATDDNLVF TVPEFRSFGD LQEKLLPYIV
GVAQRHIVLK PPTIVTQVIE VNKRDIVFLV DGSSALGLAN FNAIRDFIAK VIQRLEIGQD
LIQVAVAQYA DTVRPEFYFN THPTKREVIT AVRKMKPLDG SALYTGSALD FVRNNLFTSS
AGYRAAEGIP KLLVLITGGK SLDEISQPAQ ELKRSSIMAF AIGNKGADQA ELEEIAFDSS
LVFIPAEFRA APLQGMLPGL LAPLRTLSGT PEESKRDILF LFDGSANLVG QFPVVRDFLY
KIIDELNVKP EGTRIAVAQY SDDVKVESRF DEHQSKPEIL NLVKRMKIKT GKALNLGYAL
DYAQRYIFVK SAGSRIEDGV LQFLVLLVAG RSSDRVDGPA SNLKQSGVVP FIFQAKNADP
AELEQIVLSP AFILAAESLP KIGDLHPQIV NLLKSVHNGA PAPVSGEKDV VFLLDGSEGV
RSGFPLLKEF VQRVVESLDV GQDRVRVAVV QYSDRTRPEF YLNSYMNKQD VVNAVRQLTL
LGGPTPNTGA ALEFVLRNIL VSSAGSRITE GVPQLLIVLT ADRSGDDVRN PSVVVKRGGA
VPIGIGIGNA DITEMQTISF IPDFAVAIPT FRQLGTVQQV ISERVTQLTR EELSRLQPVL
QPLPSPGVGG KRDVVFLIDG SQSAGPEFQY VRTLIERLVD YLDVGFDTTR VAVIQFSDDP
KVEFLLNAHS SKDEVQNAVQ RLRPKGGRQI NVGNALEYVS RNIFKRPLGS RIEEGVPQFL
VLISSGKSDD EVDDPAVELK QFGVAPFTIA RNADQEELVK ISLSPEYVFS VSTFRELPSL
EQKLLTPITT LTSEQIQKLL ASTRYPPPAV ESDAADIVFL IDSSEGVRPD GFAHIRDFVS
RIVRRLNIGP SKVRVGVVQF SNDVFPEFYL KTYRSQAPVL DAIRRLRLRG GSPLNTGKAL
EFVARNLFVK SAGSRIEDGV PQHLVLVLGG KSQDDVSRFA QVIRSSGIVS LGVGDRNIDR
TELQTITNDP RLVFTVREFR ELPNIEERIM NSFGPSAATP APPGVDTPPP SRPEKKKADI
VFLLDGSINF RRDSFQEVLR FVSEIVDTVY EDGDSIQVGL VQYNSDPTDE FFLKDFSTKR
QIIDAINKVV YKGGRHANTK VGLEHLRVNH FVPEAGSRLD QRVPQIAFVI TGGKSVEDAQ
DVSLALTQRG VKVFAVGVRN IDSEEVGKIA SNSATAFRVG NVQELSELSE QVLETLHDAM
HETLCPGVTD AAKACNLDVI LGFDGSRDQN VFVAQKGFES KVDAILNRIS QMHRVSCSGG
RSPTVRVSVV ANTPSGPVEA FDFDEYQPEM LEKFRNMRSQ HPYVLTEDTL KVYLNKFRQS
SPDSVKVVIH FTDGADGDLA DLHRASENLR QEGVRALILV GLERVVNLER LMHLEFGRGF
MYDRPLRLNL LDLDYELAEQ LDNIAEKACC GVPCKCSGQR GDRGPIGSIG PKGIPGEDGY
RGYPGDEGGP GERGPPGVNG TQGFQGCPGQ RGVKGSRGFP GEKGEVGEIG LDGLDGEDGD
KGLPGSSGEK GNPGRRGDKG PRGEKGERGD VGIRGDPGNP GQDSQERGPK GETGDLGPMG
VPGRDGVPGG PGETGKNGGF GRRGPPGAKG NKGGPGQPGF EGEQGTRGAQ GPAGPAGPPG
LIGEQGISGP RGSGGAAGAP GERGRTGPLG RKGEPGEPGP KGGIGNRGPR GETGDDGRDG
VGSEGRRGKK GERGFPGYPG PKGNPGEPGL NGTTGPKGIR GRRGNSGPPG IVGQKGDPGY
PGPAGPKGNR GDSIDQCALI QSIKDKCPCC YGPLECPVFP TELAFALDTS EGVNQDTFGR
MRDVVLSIVN DLTIAESNCP RGARVAVVTY NNEVTTEIRF ADSKRKSVLL DKIKNLQVAL
TSKQQSLETA MSFVARNTFK RVRNGFLMRK VAVFFSNTPT RASPQLREAV LKLSDAGITP
LFLTRQEDRQ LINALQINNT AVGHALVLPA GRDLTDFLEN VLTCHVCLDI CNIDPSCGFG
SWRPSFRDRR AAGSDVDIDM AFILDSAETT TLFQFNEMKK YIAYLVRQLD MSPDPKASQH
FARVAVVQHA PSESVDNASM PPVKVEFSLT DYGSKEKLVD FLSRGMTQLQ GTRALGSAIE
YTIENVFESA PNPRDLKIVV LMLTGEVPEQ QLEEAQRVIL QAKCKGYFFV VLGIGRKVNI
KEVYTFASEP NDVFFKLVDK STELNEEPLM RFGRLLPSFV SSENAFYLSP DIRKQCDWFQ
GDQPTKNLVK FGHKQVNVPN NVTSSPTSNP VTTTKPVTTT KPVTTTTKPV TTTTKPVTII
NQPSVKPAAA KPAPAKPVAA KPVATKMATV RPPVAVKPAT AAKPVAAKPA AVRPPAAAAA
KPVATKPEVP RPQAAKPAAT KPATTKPMVK MSREVQVFEI TENSAKLHWE RAEPPGPYFY
DLTVTSAHDQ SLVLKQNLTV TDRVIGGLLA GQTYHVAVVC YLRSQVRATY HGSFSTKKSQ
PPPPQPARSA SSSTINLMVS TEPLALTETD ICKLPKDEGT CRDFILKWYY DPNTKSCARF
WYGGCGGNEN KFGSQKECEK VCAPVLAKPG VISVMGT*
mutated AA sequence MRKHRHLPLV AVFCLFLSGF PTTHAQQQQA DVKNGAAADI IFLVDSSWTI GEEHFQLVRE
FLYDVVKSLA VGENDFHFAL VQFNGNPHTE FLLNTYRTKQ EVLSHISNMS YIGGTNQTGK
GLEYIMQSHL TKAAGSRAGD GVPQVIVVLT DGHSKDGLAL PSAELKSADV NVFAIGVEDA
DEGALKEIAS EPLNMHMFNL ENFTSLHDIV GNLVSCVHSS VSPERAGDTE TLKDITAQDS
ADIIFLIDGS NNTGSVNFAV ILDFLVNLLE KLPIGTQQIR VGVVQFSDEP RTMFSLDTYS
TKAQVLGAVK ALGFAGGELA NIGLALDFVV ENHFTRAGGS RVEEGVPQVL VLISAGPSSD
EIRYGVVALK QASVFSFGLG AQAASRAELQ HIATDDNLVF TVPEFRSFGD LQEKLLPYIV
GVAQRHIVLK PPTIVTQVIE VNKRDIVFLV DGSSALGLAN FNAIRDFIAK VIQRLEIGQD
LIQVAVAQYA DTVRPEFYFN THPTKREVIT AVRKMKPLDG SALYTGSALD FVRNNLFTSS
AGYRAAEGIP KLLVLITGGK SLDEISQPAQ ELKRSSIMAF AIGNKGADQA ELEEIAFDSS
LVFIPAEFRA APLQGMLPGL LAPLRTLSGT PEESKRDILF LFDGSANLVG QFPVVRDFLY
KIIDELNVKP EGTRIAVAQY SDDVKVESRF DEHQSKPEIL NLVKRMKIKT GKALNLGYAL
DYAQRYIFVK SAGSRIEDGV LQFLVLLVAG RSSDRVDGPA SNLKQSGVVP FIFQAKNADP
AELEQIVLSP AFILAAESLP KIGDLHPQIV NLLKSVHNGA PAPVSGEKDV VFLLDGSEGV
RSGFPLLKEF VQRVVESLDV GQDRVRVAVV QYSDRTRPEF YLNSYMNKQD VVNAVRQLTL
LGGPTPNTGA ALEFVLRNIL VSSAGSRITE GVPQLLIVLT ADRSGDDVRN PSVVVKRGGA
VPIGIGIGNA DITEMQTISF IPDFAVAIPT FRQLGTVQQV ISERVTQLTR EELSRLQPVL
QPLPSPGVGG KRDVVFLIDG SQSAGPEFQY VRTLIERLVD YLDVGFDTTR VAVIQFSDDP
KVEFLLNAHS SKDEVQNAVQ RLRPKGGRQI NVGNALEYVS RNIFKRPLGS RIEEGVPQFL
VLISSGKSDD EVDDPAVELK QFGVAPFTIA RNADQEELVK ISLSPEYVFS VSTFRELPSL
EQKLLTPITT LTSEQIQKLL ASTRYPPPAV ESDAADIVFL IDSSEGVRPD GFAHIRDFVS
RIVRRLNIGP SKVRVGVVQF SNDVFPEFYL KTYRSQAPVL DAIRRLRLRG GSPLNTGKAL
EFVARNLFVK SAGSRIEDGV PQHLVLVLGG KSQDDVSRFA QVIRSSGIVS LGVGDRNIDR
TELQTITNDP RLVFTVREFR ELPNIEERIM NSFGPSAATP APPGVDTPPP SRPEKKKADI
VFLLDGSINF RRDSFQEVLR FVSEIVDTVY EDGDSIQVGL VQYNSDPTDE FFLKDFSTKR
QIIDAINKVV YKGGRHANTK VGLEHLRVNH FVPEAGSRLD QRVPQIAFVI TGGKSVEDAQ
DVSLALTQRG VKVFAVGVRN IDSEEVGKIA SNSATAFRVG NVQELSELSE QVLETLHDAM
HETLCPGVTD AAKACNLDVI LGFDGSRDQN VFVAQKGFES KVDAILNRIS QMHRVSCSGG
RSPTVRVSVV ANTPSGPVEA FDFDEYQPEM LEKFRNMRSQ HPYVLTEDTL KVYLNKFRQS
SPDSVKVVIH FTDGADGDLA DLHRASENLR QEGVRALILV GLERVVNLER LMHLEFGRGF
MYDRPLRLNL LDLDYELAEQ LDNIAEKACC GVPCKCSGQR GDRGPIGSIG PKGIPGEDGY
RGYPGDEGGP GERGPPGVNG TQGFQGCPGQ RGVKGSRGFP GEKGEVGEIG LDGLDGEDGD
KGLPGSSGEK GNPGRRGDKG PRGEKGERGD VGIRGDPGNP GQDSQERGPK GETGDLGPMG
VPGRDGVPGG PGETGKNGGF GRRGPPGAKG NKGGPGQPGF EGEQGTRGAQ GPAGPAGPPG
LIGEQGISGP RGSGGAAGAP GERGRTGPLG RKGEPGEPGP KGGIGNRGPR GETGDDGRDG
VGSEGRRGKK GERGFPGYPG PKGNPGEPGL NGTTGPKGIR GRRGNSGPPG IVGQKGDPGY
PGPAGPKGNR GDSIDQCALI QSIKDKCPCC YGPLECPVFP TELAFALDTS EGVNQDTFGR
MRDVVLSIVN DLTIAESNCP RGARVAVVTY NNEVTTEIRF ADSKRKSVLL DKIKNLQVAL
TSKQQSLETA MSFVARNTFK RVRNGFLMRK VAVFFSNTPT RASPQLREAV LKLSDAGITP
LFLTRQEDRQ LINALQINNT AVGHALVLPA GRDLTDFLEN VLTCHVCLDI CNIDPSCGFG
SWRPSFRDRR AAGSDVDIDM AFILDSAETT TLFQFNEMKK YIAYLVRQLD MSPDPKASQH
FARVAVVQHA PSESVDNASM PPVKVEFSLT DYGSKEKLVD FLSRGMTQLQ GTRALGSAIE
YTIENVFESA PNPRDLKIVV LMLTGEVPEQ QLEEAQRVIL QAKCKGYFFV VLGIGRKVNI
KEVYTFASEP NDVFFKLVDK STELNEEPLM RFGRLLPSFV SSENAFYLSP DIRKQCDWFQ
GDQPTKNLVK FGHKQVNVPN NVTSSPTSNP VTTTKPVTTT KPVTTTTKPV TTTTKPVTII
NQPSVKPAAA KPAPAKPVAA KPVATKTATV RPPVAVKPAT AAKPVAAKPA AVRPPAAAAA
KPVATKPEVP RPQAAKPAAT KPATTKPMVK MSREVQVFEI TENSAKLHWE RAEPPGPYFY
DLTVTSAHDQ SLVLKQNLTV TDRVIGGLLA GQTYHVAVVC YLRSQVRATY HGSFSTKKSQ
PPPPQPARSA SSSTINLMVS TEPLALTETD ICKLPKDEGT CRDFILKWYY DPNTKSCARF
WYGGCGGNEN KFGSQKECEK VCAPVLAKPG VISVMGT*
speed 1.08 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project