Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1 (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 ENST00000295550
Genbank transcript ID NM_004369
UniProt peptide P12111
alteration type single base exchange
alteration region CDS
DNA changes c.8780T>C
cDNA.9233T>C
g.78056T>C
AA changes M2927T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 2927
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      2927KPVAAKPVATKMATVRPPVAVKPA
mutated  not conserved    2927KPVAAKPVATKTATVRPPVAVKP
Ptroglodytes  not conserved  ENSPTRG00000013074  2927KPVAAKPVATKTATVRPPVAVRP
Mmulatta  not conserved  ENSMMUG00000014049  2719ATKTATVRPPVAVKP
Fcatus  no alignment  ENSFCAG00000012720  n/a
Mmusculus  not conserved  ENSMUSG00000048126  2413PAQPAAAQPMPAQPVLTKSAAVKPASANKPVAAKPVATNTATATARP
Ggallus  not conserved  ENSGALG00000003923  2926KTTTASTTAQTRATERP------
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000077139  3502NTHNVNGHVASTYKGIVPTK
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
29082983COMPBIASAla-rich.lost
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 9534 / 9534
position (AA) of stopcodon in wt / mu AA sequence 3178 / 3178
position of stopcodon in wt / mu cDNA 9987 / 9987
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 454 / 454
chromosome 2
strand -1
last intron/exon boundary 9947
theoretical NMD boundary in CDS 9443
length of CDS 9534
coding sequence (CDS) position 8780
cDNA position
(for ins/del: last normal base / first normal base)		 9233
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 PEVHSNKRDI IFLLDGSANV GKTNFPYVRD
FVMNLVNSLD IGNDNIRVGL VQFSDTPVTE FSLNTYQTKS DILGHLRQLQ LQGGSGLNTG
SALSYVYANH FTEAGGSRIR EHVPQLLLLL TAGQSEDSYL QAANALTRAG ILTFCVGASQ
ANKAELEQIA FNPSLVYLMD DFSSLPALPQ QLIQPLTTYV SGGVEEVPLA QPESKRDILF
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 PEVHSNKRDI IFLLDGSANV GKTNFPYVRD
FVMNLVNSLD IGNDNIRVGL VQFSDTPVTE FSLNTYQTKS DILGHLRQLQ LQGGSGLNTG
SALSYVYANH FTEAGGSRIR EHVPQLLLLL TAGQSEDSYL QAANALTRAG ILTFCVGASQ
ANKAELEQIA FNPSLVYLMD DFSSLPALPQ QLIQPLTTYV SGGVEEVPLA QPESKRDILF
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 1.11 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