Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000304636
Querying Taster for transcript #2: ENST00000317840
MT speed 3.77 s - this script 8.032329 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COL3A1polymorphism_automatic0.562414084081511simple_aaeA698Tsingle base exchangers1800255show file
COL3A1polymorphism_automatic0.562414084081511simple_aaeA698Tsingle base exchangers1800255show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.437585915918489 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM086593)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:189864080G>AN/A show variant in all transcripts   IGV
HGNC symbol COL3A1
Ensembl transcript ID ENST00000304636
Genbank transcript ID NM_000090
UniProt peptide P02461
alteration type single base exchange
alteration region CDS
DNA changes c.2092G>A
cDNA.2262G>A
g.25035G>A
AA changes A698T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
698
frameshift no
known variant Reference ID: rs1800255
databasehomozygous (A/A)heterozygousallele carriers
1000G122850972
ExAC27011672719428

known disease mutation at this position, please check HGMD for details (HGMD ID CM086593)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2340.018
1.2990.833
(flanking)3.2570.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      698GLAGAPGLRGGAGPPGPEGGKGAA
mutated  not conserved    698GLAGAPGLRGGTGPPGPEGGKGA
Ptroglodytes  all identical  ENSPTRG00000012728  698GLAGAPGLRGGAGPPGPEGGKGA
Mmulatta  all identical  ENSMMUG00000021286  698GLAGAPGLRGGAGPPGPEGGKGA
Fcatus  all identical  ENSFCAG00000014740  671GALGPLGPRGGAGLPGPEGGK
Mmusculus  all identical  ENSMUSG00000026043  697GTAGIPGARGGAGPPGPEGGKGP
Ggallus  not conserved  ENSGALG00000002552  733GPPGPTGARGGPGPAGSEGAKGP
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000010783  701GTPGPPGSRGGSGPPGPDGAK
protein features
start (aa)end (aa)featuredetails 
1681196REGIONTriple-helical region.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4401 / 4401
position (AA) of stopcodon in wt / mu AA sequence 1467 / 1467
position of stopcodon in wt / mu cDNA 4571 / 4571
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 171 / 171
chromosome 2
strand 1
last intron/exon boundary 4425
theoretical NMD boundary in CDS 4204
length of CDS 4401
coding sequence (CDS) position 2092
cDNA position
(for ins/del: last normal base / first normal base)
2262
gDNA position
(for ins/del: last normal base / first normal base)
25035
chromosomal position
(for ins/del: last normal base / first normal base)
189864080
original gDNA sequence snippet CCCCAGGACTTAGAGGTGGAGCTGGTCCCCCTGGTCCCGAA
altered gDNA sequence snippet CCCCAGGACTTAGAGGTGGAACTGGTCCCCCTGGTCCCGAA
original cDNA sequence snippet CCCCAGGACTTAGAGGTGGAGCTGGTCCCCCTGGTCCCGAA
altered cDNA sequence snippet CCCCAGGACTTAGAGGTGGAACTGGTCCCCCTGGTCCCGAA
wildtype AA sequence MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV
LCDDIICDDQ ELDCPNPEIP FGECCAVCPQ PPTAPTRPPN GQGPQGPKGD PGPPGIPGRN
GDPGIPGQPG SPGSPGPPGI CESCPTGPQN YSPQYDSYDV KSGVAVGGLA GYPGPAGPPG
PPGPPGTSGH PGSPGSPGYQ GPPGEPGQAG PSGPPGPPGA IGPSGPAGKD GESGRPGRPG
ERGLPGPPGI KGPAGIPGFP GMKGHRGFDG RNGEKGETGA PGLKGENGLP GENGAPGPMG
PRGAPGERGR PGLPGAAGAR GNDGARGSDG QPGPPGPPGT AGFPGSPGAK GEVGPAGSPG
SNGAPGQRGE PGPQGHAGAQ GPPGPPGING SPGGKGEMGP AGIPGAPGLM GARGPPGPAG
ANGAPGLRGG AGEPGKNGAK GEPGPRGERG EAGIPGVPGA KGEDGKDGSP GEPGANGLPG
AAGERGAPGF RGPAGPNGIP GEKGPAGERG APGPAGPRGA AGEPGRDGVP GGPGMRGMPG
SPGGPGSDGK PGPPGSQGES GRPGPPGPSG PRGQPGVMGF PGPKGNDGAP GKNGERGGPG
GPGPQGPPGK NGETGPQGPP GPTGPGGDKG DTGPPGPQGL QGLPGTGGPP GENGKPGEPG
PKGDAGAPGA PGGKGDAGAP GERGPPGLAG APGLRGGAGP PGPEGGKGAA GPPGPPGAAG
TPGLQGMPGE RGGLGSPGPK GDKGEPGGPG ADGVPGKDGP RGPTGPIGPP GPAGQPGDKG
EGGAPGLPGI AGPRGSPGER GETGPPGPAG FPGAPGQNGE PGGKGERGAP GEKGEGGPPG
VAGPPGGSGP AGPPGPQGVK GERGSPGGPG AAGFPGARGL PGPPGSNGNP GPPGPSGSPG
KDGPPGPAGN TGAPGSPGVS GPKGDAGQPG EKGSPGAQGP PGAPGPLGIA GITGARGLAG
PPGMPGPRGS PGPQGVKGES GKPGANGLSG ERGPPGPQGL PGLAGTAGEP GRDGNPGSDG
LPGRDGSPGG KGDRGENGSP GAPGAPGHPG PPGPVGPAGK SGDRGESGPA GPAGAPGPAG
SRGAPGPQGP RGDKGETGER GAAGIKGHRG FPGNPGAPGS PGPAGQQGAI GSPGPAGPRG
PVGPSGPPGK DGTSGHPGPI GPPGPRGNRG ERGSEGSPGH PGQPGPPGPP GAPGPCCGGV
GAAAIAGIGG EKAGGFAPYY GDEPMDFKIN TDEIMTSLKS VNGQIESLIS PDGSRKNPAR
NCRDLKFCHP ELKSGEYWVD PNQGCKLDAI KVFCNMETGE TCISANPLNV PRKHWWTDSS
AEKKHVWFGE SMDGGFQFSY GNPELPEDVL DVHLAFLRLL SSRASQNITY HCKNSIAYMD
QASGNVKKAL KLMGSNEGEF KAEGNSKFTY TVLEDGCTKH TGEWSKTVFE YRTRKAVRLP
IVDIAPYDIG GPDQEFGVDV GPVCFL*
mutated AA sequence MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV
LCDDIICDDQ ELDCPNPEIP FGECCAVCPQ PPTAPTRPPN GQGPQGPKGD PGPPGIPGRN
GDPGIPGQPG SPGSPGPPGI CESCPTGPQN YSPQYDSYDV KSGVAVGGLA GYPGPAGPPG
PPGPPGTSGH PGSPGSPGYQ GPPGEPGQAG PSGPPGPPGA IGPSGPAGKD GESGRPGRPG
ERGLPGPPGI KGPAGIPGFP GMKGHRGFDG RNGEKGETGA PGLKGENGLP GENGAPGPMG
PRGAPGERGR PGLPGAAGAR GNDGARGSDG QPGPPGPPGT AGFPGSPGAK GEVGPAGSPG
SNGAPGQRGE PGPQGHAGAQ GPPGPPGING SPGGKGEMGP AGIPGAPGLM GARGPPGPAG
ANGAPGLRGG AGEPGKNGAK GEPGPRGERG EAGIPGVPGA KGEDGKDGSP GEPGANGLPG
AAGERGAPGF RGPAGPNGIP GEKGPAGERG APGPAGPRGA AGEPGRDGVP GGPGMRGMPG
SPGGPGSDGK PGPPGSQGES GRPGPPGPSG PRGQPGVMGF PGPKGNDGAP GKNGERGGPG
GPGPQGPPGK NGETGPQGPP GPTGPGGDKG DTGPPGPQGL QGLPGTGGPP GENGKPGEPG
PKGDAGAPGA PGGKGDAGAP GERGPPGLAG APGLRGGTGP PGPEGGKGAA GPPGPPGAAG
TPGLQGMPGE RGGLGSPGPK GDKGEPGGPG ADGVPGKDGP RGPTGPIGPP GPAGQPGDKG
EGGAPGLPGI AGPRGSPGER GETGPPGPAG FPGAPGQNGE PGGKGERGAP GEKGEGGPPG
VAGPPGGSGP AGPPGPQGVK GERGSPGGPG AAGFPGARGL PGPPGSNGNP GPPGPSGSPG
KDGPPGPAGN TGAPGSPGVS GPKGDAGQPG EKGSPGAQGP PGAPGPLGIA GITGARGLAG
PPGMPGPRGS PGPQGVKGES GKPGANGLSG ERGPPGPQGL PGLAGTAGEP GRDGNPGSDG
LPGRDGSPGG KGDRGENGSP GAPGAPGHPG PPGPVGPAGK SGDRGESGPA GPAGAPGPAG
SRGAPGPQGP RGDKGETGER GAAGIKGHRG FPGNPGAPGS PGPAGQQGAI GSPGPAGPRG
PVGPSGPPGK DGTSGHPGPI GPPGPRGNRG ERGSEGSPGH PGQPGPPGPP GAPGPCCGGV
GAAAIAGIGG EKAGGFAPYY GDEPMDFKIN TDEIMTSLKS VNGQIESLIS PDGSRKNPAR
NCRDLKFCHP ELKSGEYWVD PNQGCKLDAI KVFCNMETGE TCISANPLNV PRKHWWTDSS
AEKKHVWFGE SMDGGFQFSY GNPELPEDVL DVHLAFLRLL SSRASQNITY HCKNSIAYMD
QASGNVKKAL KLMGSNEGEF KAEGNSKFTY TVLEDGCTKH TGEWSKTVFE YRTRKAVRLP
IVDIAPYDIG GPDQEFGVDV GPVCFL*
speed 2.24 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
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.437585915918489 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM086593)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:189864080G>AN/A show variant in all transcripts   IGV
HGNC symbol COL3A1
Ensembl transcript ID ENST00000317840
Genbank transcript ID N/A
UniProt peptide P02461
alteration type single base exchange
alteration region CDS
DNA changes c.2092G>A
cDNA.2209G>A
g.25035G>A
AA changes A698T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS
698
frameshift no
known variant Reference ID: rs1800255
databasehomozygous (A/A)heterozygousallele carriers
1000G122850972
ExAC27011672719428

known disease mutation at this position, please check HGMD for details (HGMD ID CM086593)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2340.018
1.2990.833
(flanking)3.2570.997
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 30
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      698GLAGAPGLRGGAGPPGPEGGKGAA
mutated  not conserved    698GLAGAPGLRGGTGPPGPEGGKGA
Ptroglodytes  all identical  ENSPTRG00000012728  698GLAGAPGLRGGAGPPGPEGGKGA
Mmulatta  all identical  ENSMMUG00000021286  698GLAGAPGLRGGAGPPGPEGGKGA
Fcatus  all identical  ENSFCAG00000014740  671GALGPLGPRGGAGLPGPEGGK
Mmusculus  all identical  ENSMUSG00000026043  697GTAGIPGARGGAGPPGPEGGKGP
Ggallus  not conserved  ENSGALG00000002552  733GPPGPTGARGGPGPAGSEGAKGP
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000010783  701GTPGPPGSRGGSGPPGPDGAK
protein features
start (aa)end (aa)featuredetails 
1681196REGIONTriple-helical region.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3492 / 3492
position (AA) of stopcodon in wt / mu AA sequence 1164 / 1164
position of stopcodon in wt / mu cDNA 3609 / 3609
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 118 / 118
chromosome 2
strand 1
last intron/exon boundary 3463
theoretical NMD boundary in CDS 3295
length of CDS 3492
coding sequence (CDS) position 2092
cDNA position
(for ins/del: last normal base / first normal base)
2209
gDNA position
(for ins/del: last normal base / first normal base)
25035
chromosomal position
(for ins/del: last normal base / first normal base)
189864080
original gDNA sequence snippet CCCCAGGACTTAGAGGTGGAGCTGGTCCCCCTGGTCCCGAA
altered gDNA sequence snippet CCCCAGGACTTAGAGGTGGAACTGGTCCCCCTGGTCCCGAA
original cDNA sequence snippet CCCCAGGACTTAGAGGTGGAGCTGGTCCCCCTGGTCCCGAA
altered cDNA sequence snippet CCCCAGGACTTAGAGGTGGAACTGGTCCCCCTGGTCCCGAA
wildtype AA sequence MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV
LCDDIICDDQ ELDCPNPEIP FGECCAVCPQ PPTAPTRPPN GQGPQGPKGD PGPPGIPGRN
GDPGIPGQPG SPGSPGPPGI CESCPTGPQN YSPQYDSYDV KSGVAVGGLA GYPGPAGPPG
PPGPPGTSGH PGSPGSPGYQ GPPGEPGQAG PSGPPGPPGA IGPSGPAGKD GESGRPGRPG
ERGLPGPPGI KGPAGIPGFP GMKGHRGFDG RNGEKGETGA PGLKGENGLP GENGAPGPMG
PRGAPGERGR PGLPGAAGAR GNDGARGSDG QPGPPGPPGT AGFPGSPGAK GEVGPAGSPG
SNGAPGQRGE PGPQGHAGAQ GPPGPPGING SPGGKGEMGP AGIPGAPGLM GARGPPGPAG
ANGAPGLRGG AGEPGKNGAK GEPGPRGERG EAGIPGVPGA KGEDGKDGSP GEPGANGLPG
AAGERGAPGF RGPAGPNGIP GEKGPAGERG APGPAGPRGA AGEPGRDGVP GGPGMRGMPG
SPGGPGSDGK PGPPGSQGES GRPGPPGPSG PRGQPGVMGF PGPKGNDGAP GKNGERGGPG
GPGPQGPPGK NGETGPQGPP GPTGPGGDKG DTGPPGPQGL QGLPGTGGPP GENGKPGEPG
PKGDAGAPGA PGGKGDAGAP GERGPPGLAG APGLRGGAGP PGPEGGKGAA GPPGPPGAAG
TPGLQGMPGE RGGLGSPGPK GDKGEPGGPG ADGVPGKDGP RGPTGPIGPP GPAGQPGDKG
EGGAPGLPGI AGPRGSPGER GETGPPGPAG FPGAPGQNGE PGGKGERGAP GEKGEGGPPG
LFGPPGKDGT SGHPGPIGPP GPRGNRGERG SEGSPGHPGQ PGPPGPPGAP GPCCGGVGAA
AIAGIGGEKA GGFAPYYGDE PMDFKINTDE IMTSLKSVNG QIESLISPDG SRKNPARNCR
DLKFCHPELK SGEYWVDPNQ GCKLDAIKVF CNMETGETCI SANPLNVPRK HWWTDSSAEK
KHVWFGESMD GGFQFSYGNP ELPEDVLDVH LAFLRLLSSR ASQNITYHCK NSIAYMDQAS
GNVKKALKLM GSNEGEFKAE GNSKFTYTVL EDGCTKHTGE WSKTVFEYRT RKAVRLPIVD
IAPYDIGGPD QEFGVDVGPV CFL*
mutated AA sequence MMSFVQKGSW LLLALLHPTI ILAQQEAVEG GCSHLGQSYA DRDVWKPEPC QICVCDSGSV
LCDDIICDDQ ELDCPNPEIP FGECCAVCPQ PPTAPTRPPN GQGPQGPKGD PGPPGIPGRN
GDPGIPGQPG SPGSPGPPGI CESCPTGPQN YSPQYDSYDV KSGVAVGGLA GYPGPAGPPG
PPGPPGTSGH PGSPGSPGYQ GPPGEPGQAG PSGPPGPPGA IGPSGPAGKD GESGRPGRPG
ERGLPGPPGI KGPAGIPGFP GMKGHRGFDG RNGEKGETGA PGLKGENGLP GENGAPGPMG
PRGAPGERGR PGLPGAAGAR GNDGARGSDG QPGPPGPPGT AGFPGSPGAK GEVGPAGSPG
SNGAPGQRGE PGPQGHAGAQ GPPGPPGING SPGGKGEMGP AGIPGAPGLM GARGPPGPAG
ANGAPGLRGG AGEPGKNGAK GEPGPRGERG EAGIPGVPGA KGEDGKDGSP GEPGANGLPG
AAGERGAPGF RGPAGPNGIP GEKGPAGERG APGPAGPRGA AGEPGRDGVP GGPGMRGMPG
SPGGPGSDGK PGPPGSQGES GRPGPPGPSG PRGQPGVMGF PGPKGNDGAP GKNGERGGPG
GPGPQGPPGK NGETGPQGPP GPTGPGGDKG DTGPPGPQGL QGLPGTGGPP GENGKPGEPG
PKGDAGAPGA PGGKGDAGAP GERGPPGLAG APGLRGGTGP PGPEGGKGAA GPPGPPGAAG
TPGLQGMPGE RGGLGSPGPK GDKGEPGGPG ADGVPGKDGP RGPTGPIGPP GPAGQPGDKG
EGGAPGLPGI AGPRGSPGER GETGPPGPAG FPGAPGQNGE PGGKGERGAP GEKGEGGPPG
LFGPPGKDGT SGHPGPIGPP GPRGNRGERG SEGSPGHPGQ PGPPGPPGAP GPCCGGVGAA
AIAGIGGEKA GGFAPYYGDE PMDFKINTDE IMTSLKSVNG QIESLISPDG SRKNPARNCR
DLKFCHPELK SGEYWVDPNQ GCKLDAIKVF CNMETGETCI SANPLNVPRK HWWTDSSAEK
KHVWFGESMD GGFQFSYGNP ELPEDVLDVH LAFLRLLSSR ASQNITYHCK NSIAYMDQAS
GNVKKALKLM GSNEGEFKAE GNSKFTYTVL EDGCTKHTGE WSKTVFEYRT RKAVRLPIVD
IAPYDIGGPD QEFGVDVGPV CFL*
speed 1.53 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
back to results table

Problems