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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000370096
Querying Taster for transcript #2: ENST00000512756
Querying Taster for transcript #3: ENST00000358392
Querying Taster for transcript #4: ENST00000353414
MT speed 0 s - this script 3.82603 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COL11A1disease_causing_automatic0.999999999999935simple_aaeaffected0G509Vsingle base exchangers121912943show file
COL11A1disease_causing_automatic0.999999999999978simple_aaeaffected0G625Vsingle base exchangers121912943show file
COL11A1disease_causing_automatic0.999999999999978simple_aaeaffected0G637Vsingle base exchangers121912943show file
COL11A1disease_causing_automatic0.999999999999978simple_aaeaffected0G586Vsingle base exchangers121912943show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999935 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960317)
  • known disease mutation: rs17131 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:103470189C>AN/A show variant in all transcripts   IGV
HGNC symbol COL11A1
Ensembl transcript ID ENST00000512756
Genbank transcript ID NM_080630
UniProt peptide P12107
alteration type single base exchange
alteration region CDS
DNA changes c.1526G>T
cDNA.1827G>T
g.103864G>T
AA changes G509V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 509
frameshift no
known variant Reference ID: rs121912943
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17131 (pathogenic for Stickler syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9460.008
5.4050.999
(flanking)3.8221
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased103873wt: 0.54 / mu: 0.80wt: AGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTAT
mu: AGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTAT		 ctgg|TGAT
Acc increased103872wt: 0.51 / mu: 0.85wt: AAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTA
mu: AAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTA		 cctg|GTGA
Acc increased103871wt: 0.81 / mu: 0.94wt: CAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGT
mu: CAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGT		 tcct|GGTG
Acc gained1038620.32mu: CGAGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGG tcca|GTTC
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      509HRGERGPQGPPGPPGDDGMRGEDG
mutated  not conserved    509HRGERGPQGPPVPPGDDGMRGED
Ptroglodytes  all identical  ENSPTRG00000001017  625HRGERGPQGPPGPPGDDGMRGED
Mmulatta  all identical  ENSMMUG00000004103  625HRGERGPQGPPGPPGDDGMRGED
Fcatus  all identical  ENSFCAG00000018396  64GPPGPPGEDGMRXXX
Mmusculus  all identical  ENSMUSG00000027966  623HRGERGPQGPPGLPGDDGMRGED
Ggallus  all identical  ENSGALG00000005180  598GDRGFDGLPGLPGDKGNRGDRGPQGPPGLPGEDGSRKQGED
Trubripes  all identical  ENSTRUG00000001411  637PGPIGPTGAVGEDGQRGED
Drerio  all identical  ENSDARG00000026165  556HRGETGPAGPPGPTGEDGPRGED
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000010839  628HRGDKGPHGPPGPPGEDGERGED
protein features
start (aa)end (aa)featuredetails 
36511PROPEPN-terminal propeptide (Potential). /FTId=PRO_0000005774.lost
509511REGIONShort nonhelical segment.lost
512528REGIONTelopeptide.might get lost (downstream of altered splice site)
5291542REGIONTriple-helical region.might get lost (downstream of altered splice site)
532586DOMAINCollagen-like 2.might get lost (downstream of altered splice site)
583641DOMAINCollagen-like 3.might get lost (downstream of altered splice site)
612612MOD_RESAllysine.might get lost (downstream of altered splice site)
616674DOMAINCollagen-like 4.might get lost (downstream of altered splice site)
643699DOMAINCollagen-like 5.might get lost (downstream of altered splice site)
941944CONFLICTKDGL -> RMGC (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
986986CONFLICTH -> Y (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
10741074CONFLICTP -> R (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
11421142CONFLICTD -> G (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
12181218CONFLICTM -> W (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
13931450DOMAINCollagen-like 6.might get lost (downstream of altered splice site)
14291487DOMAINCollagen-like 7.might get lost (downstream of altered splice site)
14521452MOD_RESAllysine.might get lost (downstream of altered splice site)
14831541DOMAINCollagen-like 8.might get lost (downstream of altered splice site)
15431563REGIONNonhelical region (C-terminal).might get lost (downstream of altered splice site)
15641806PROPEPC-terminal propeptide. /FTId=PRO_0000005776.might get lost (downstream of altered splice site)
15771805DOMAINFibrillar collagen NC1.might get lost (downstream of altered splice site)
16071607DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16071607DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16301630DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16301630DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16391639DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16391639DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16401640CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
16481648DISULFIDBy similarity.might get lost (downstream of altered splice site)
17141714DISULFIDBy similarity.might get lost (downstream of altered splice site)
17571757DISULFIDBy similarity.might get lost (downstream of altered splice site)
17581758CONFLICTA -> T (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
17861786CONFLICTN -> S (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
18031803DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5073 / 5073
position (AA) of stopcodon in wt / mu AA sequence 1691 / 1691
position of stopcodon in wt / mu cDNA 5374 / 5374
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 302 / 302
chromosome 1
strand -1
last intron/exon boundary 5228
theoretical NMD boundary in CDS 4876
length of CDS 5073
coding sequence (CDS) position 1526
cDNA position
(for ins/del: last normal base / first normal base)		 1827
gDNA position
(for ins/del: last normal base / first normal base)		 103864
chromosomal position
(for ins/del: last normal base / first normal base)		 103470189
original gDNA sequence snippet AGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAA
altered gDNA sequence snippet AGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAA
original cDNA sequence snippet AGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAA
altered cDNA sequence snippet AGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAA
wildtype AA sequence MEPWSSRWKT KRWLWDFTVT TLALTFLFQA REVRGAAPVD VLKALDFHNS PEGISKTTGF
CTNRKNSKGS DTAYRVSKQA QLSAPTKQLF PGGTFPEDFS ILFTVKPKKG IQSFLLSIYN
EHGIQQIGVE VGRSPVFLFE DHTGKPAPED YPLFRTVNIA DGKWHRVAIS VEKKTVTMIV
DCKKKTTKPL DRSERAIVDT NGITVFGTRI LDEEVFEGDI QQFLITGDPK AAYDYCEHYS
PDCDSSAPKA AQAQEPQIDE YAPEDIIEYD YEYGEAEYKE AESVTEGPTV TEETIAQTEI
NGHGAYGEKG QKGEPAVVEP GMLVEGPPGP AGPAGIMGPP GLQGPTGPPG DPGDRGPPGR
PGLPGADGLP GPPGTMLMLP FRYGGDGSKG PTISAQEAQA QAILQQARIA LRGPPGPMGL
TGRPGPVGGP GSSGAKGESG DPGPQGPRGV QGPPGPTGKP GKRGRPGADG GRGMPGEPGA
KGDRGFDGLP GLPGDKGHRG ERGPQGPPGP PGDDGMRGED GEIGPRGLPG EAGPRGLLGP
RGTPGAPGQP GMAGVDGPPG PKGNMGPQGE PGPPGQQGNP GPQGLPGPQG PIGPPGEKGP
QGKPGLAGLP GADGPPGHPG KEGQSGEKGA LGPPGPQGPI GYPGPRGVKG ADGVRGLKGS
KGEKGEDGFP GFKGDMGLKG DRGEVGQIGP RGEDGPEGPK GRAGPTGDPG PSGQAGEKGK
LGVPGLPGYP GRQGPKGSTG FPGFPGANGE KGARGVAGKP GPRGQRGPTG PRGSRGARGP
TGKPGPKGTS GGDGPPGPPG ERGPQGPQGP VGFPGPKGPP GPPGKDGLPG HPGQRGETGF
QGKTGPPGPG GVVGPQGPTG ETGPIGERGH PGPPGPPGEQ GLPGAAGKEG AKGDPGPQGI
SGKDGPAGLR GFPGERGLPG AQGAPGLKGG EGPQGPPGPV GSPGERGSAG TAGPIGLPGR
PGPQGPPGPA GEKGAPGEKG PQGPAGRDGV QGPVGLPGPA GPAGSPGEDG DKGEIGEPGQ
KGSKGDKGEN GPPGPPGLQG PVGAPGIAGG DGEPGPRGQQ GMFGQKGDEG ARGFPGPPGP
IGLQGLPGPP GEKGENGDVG PMGPPGPPGP RGPQGPNGAD GPQGPPGSVG SVGGVGEKGE
PGEAGNPGPP GEAGVGGPKG ERGEKGEAGP PGAAGPPGAK GPPGDDGPKG NPGPVGFPGD
PGPPGEPGPA GQDGVGGDKG EDGDPGQPGP PGPSGEAGPP GPPGKRGPPG AAGAEGRQGE
KGAKGEAGAE GPPGKTGPVG PQGPAGKPGP EGLRGIPGPV GEQGLPGAAG QDGPPGPMGP
PGLPGLKGDP GSKGEKGHPG LIGLIGPPGE QGEKGDRGLP GTQGSPGAKG DGGIPGPAGP
LGPPGPPGLP GPQGPKGNKG STGPAGQKGD SGLPGPPGSP GPPGEVIQPL PILSSKKTRR
HTEGMQADAD DNILDYSDGM EEIFGSLNSL KQDIEHMKFP MGTQTNPART CKDLQLSHPD
FPDGEYWIDP NQGCSGDSFK VYCNFTSGGE TCIYPDKKSE GVRISSWPKE KPGSWFSEFK
RGKLLSYLDV EGNSINMVQM TFLKLLTASA RQNFTYHCHQ SAAWYDVSSG SYDKALRFLG
SNDEEMSYDN NPFIKTLYDG CASRKGYEKT VIEINTPKID QVPIVDVMIN DFGDQNQKFG
FEVGPVCFLG *
mutated AA sequence MEPWSSRWKT KRWLWDFTVT TLALTFLFQA REVRGAAPVD VLKALDFHNS PEGISKTTGF
CTNRKNSKGS DTAYRVSKQA QLSAPTKQLF PGGTFPEDFS ILFTVKPKKG IQSFLLSIYN
EHGIQQIGVE VGRSPVFLFE DHTGKPAPED YPLFRTVNIA DGKWHRVAIS VEKKTVTMIV
DCKKKTTKPL DRSERAIVDT NGITVFGTRI LDEEVFEGDI QQFLITGDPK AAYDYCEHYS
PDCDSSAPKA AQAQEPQIDE YAPEDIIEYD YEYGEAEYKE AESVTEGPTV TEETIAQTEI
NGHGAYGEKG QKGEPAVVEP GMLVEGPPGP AGPAGIMGPP GLQGPTGPPG DPGDRGPPGR
PGLPGADGLP GPPGTMLMLP FRYGGDGSKG PTISAQEAQA QAILQQARIA LRGPPGPMGL
TGRPGPVGGP GSSGAKGESG DPGPQGPRGV QGPPGPTGKP GKRGRPGADG GRGMPGEPGA
KGDRGFDGLP GLPGDKGHRG ERGPQGPPVP PGDDGMRGED GEIGPRGLPG EAGPRGLLGP
RGTPGAPGQP GMAGVDGPPG PKGNMGPQGE PGPPGQQGNP GPQGLPGPQG PIGPPGEKGP
QGKPGLAGLP GADGPPGHPG KEGQSGEKGA LGPPGPQGPI GYPGPRGVKG ADGVRGLKGS
KGEKGEDGFP GFKGDMGLKG DRGEVGQIGP RGEDGPEGPK GRAGPTGDPG PSGQAGEKGK
LGVPGLPGYP GRQGPKGSTG FPGFPGANGE KGARGVAGKP GPRGQRGPTG PRGSRGARGP
TGKPGPKGTS GGDGPPGPPG ERGPQGPQGP VGFPGPKGPP GPPGKDGLPG HPGQRGETGF
QGKTGPPGPG GVVGPQGPTG ETGPIGERGH PGPPGPPGEQ GLPGAAGKEG AKGDPGPQGI
SGKDGPAGLR GFPGERGLPG AQGAPGLKGG EGPQGPPGPV GSPGERGSAG TAGPIGLPGR
PGPQGPPGPA GEKGAPGEKG PQGPAGRDGV QGPVGLPGPA GPAGSPGEDG DKGEIGEPGQ
KGSKGDKGEN GPPGPPGLQG PVGAPGIAGG DGEPGPRGQQ GMFGQKGDEG ARGFPGPPGP
IGLQGLPGPP GEKGENGDVG PMGPPGPPGP RGPQGPNGAD GPQGPPGSVG SVGGVGEKGE
PGEAGNPGPP GEAGVGGPKG ERGEKGEAGP PGAAGPPGAK GPPGDDGPKG NPGPVGFPGD
PGPPGEPGPA GQDGVGGDKG EDGDPGQPGP PGPSGEAGPP GPPGKRGPPG AAGAEGRQGE
KGAKGEAGAE GPPGKTGPVG PQGPAGKPGP EGLRGIPGPV GEQGLPGAAG QDGPPGPMGP
PGLPGLKGDP GSKGEKGHPG LIGLIGPPGE QGEKGDRGLP GTQGSPGAKG DGGIPGPAGP
LGPPGPPGLP GPQGPKGNKG STGPAGQKGD SGLPGPPGSP GPPGEVIQPL PILSSKKTRR
HTEGMQADAD DNILDYSDGM EEIFGSLNSL KQDIEHMKFP MGTQTNPART CKDLQLSHPD
FPDGEYWIDP NQGCSGDSFK VYCNFTSGGE TCIYPDKKSE GVRISSWPKE KPGSWFSEFK
RGKLLSYLDV EGNSINMVQM TFLKLLTASA RQNFTYHCHQ SAAWYDVSSG SYDKALRFLG
SNDEEMSYDN NPFIKTLYDG CASRKGYEKT VIEINTPKID QVPIVDVMIN DFGDQNQKFG
FEVGPVCFLG *
speed 0.42 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

disease causing

 Model: simple_aae, prob: 0.999999999999978 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960317)
  • known disease mutation: rs17131 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:103470189C>AN/A show variant in all transcripts   IGV
HGNC symbol COL11A1
Ensembl transcript ID ENST00000370096
Genbank transcript ID NM_001854
UniProt peptide P12107
alteration type single base exchange
alteration region CDS
DNA changes c.1874G>T
cDNA.2187G>T
g.103864G>T
AA changes G625V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 625
frameshift no
known variant Reference ID: rs121912943
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17131 (pathogenic for Stickler syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9460.008
5.4050.999
(flanking)3.8221
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased103873wt: 0.54 / mu: 0.80wt: AGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTAT
mu: AGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTAT		 ctgg|TGAT
Acc increased103872wt: 0.51 / mu: 0.85wt: AAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTA
mu: AAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTA		 cctg|GTGA
Acc increased103871wt: 0.81 / mu: 0.94wt: CAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGT
mu: CAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGT		 tcct|GGTG
Acc gained1038620.32mu: CGAGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGG tcca|GTTC
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      625HRGERGPQGPPGPPGDDGMRGEDG
mutated  not conserved    625HRGERGPQGPPVPPGDDGMRGED
Ptroglodytes  all identical  ENSPTRG00000001017  625HRGERGPQGPPGPPGDDGMRGED
Mmulatta  all identical  ENSMMUG00000004103  625HRGERGPQGPPGPPGDDGMRGED
Fcatus  all identical  ENSFCAG00000018396  64GPPGPPGEDGMRXXX
Mmusculus  all identical  ENSMUSG00000027966  623HRGERGPQGPPGLPGDDGMRGED
Ggallus  all identical  ENSGALG00000005180  624NRGDRGPQGPPGLPGEDGSRKQGED
Trubripes  all identical  ENSTRUG00000001411  637HRGEPGPIGPTGAVGEDGQRGED
Drerio  all identical  ENSDARG00000026165  556HRGETGPAGPPGPTGEDGPRGED
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000010839  628HRGDKGPHGPPGPPGEDGERGED
protein features
start (aa)end (aa)featuredetails 
5291542REGIONTriple-helical region.lost
583641DOMAINCollagen-like 3.lost
616674DOMAINCollagen-like 4.lost
643699DOMAINCollagen-like 5.might get lost (downstream of altered splice site)
941944CONFLICTKDGL -> RMGC (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
986986CONFLICTH -> Y (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
10741074CONFLICTP -> R (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
11421142CONFLICTD -> G (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
12181218CONFLICTM -> W (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
13931450DOMAINCollagen-like 6.might get lost (downstream of altered splice site)
14291487DOMAINCollagen-like 7.might get lost (downstream of altered splice site)
14521452MOD_RESAllysine.might get lost (downstream of altered splice site)
14831541DOMAINCollagen-like 8.might get lost (downstream of altered splice site)
15431563REGIONNonhelical region (C-terminal).might get lost (downstream of altered splice site)
15641806PROPEPC-terminal propeptide. /FTId=PRO_0000005776.might get lost (downstream of altered splice site)
15771805DOMAINFibrillar collagen NC1.might get lost (downstream of altered splice site)
16071607DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16071607DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16301630DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16301630DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16391639DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16391639DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16401640CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
16481648DISULFIDBy similarity.might get lost (downstream of altered splice site)
17141714DISULFIDBy similarity.might get lost (downstream of altered splice site)
17571757DISULFIDBy similarity.might get lost (downstream of altered splice site)
17581758CONFLICTA -> T (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
17861786CONFLICTN -> S (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
18031803DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5421 / 5421
position (AA) of stopcodon in wt / mu AA sequence 1807 / 1807
position of stopcodon in wt / mu cDNA 5734 / 5734
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 314 / 314
chromosome 1
strand -1
last intron/exon boundary 5588
theoretical NMD boundary in CDS 5224
length of CDS 5421
coding sequence (CDS) position 1874
cDNA position
(for ins/del: last normal base / first normal base)		 2187
gDNA position
(for ins/del: last normal base / first normal base)		 103864
chromosomal position
(for ins/del: last normal base / first normal base)		 103470189
original gDNA sequence snippet AGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAA
altered gDNA sequence snippet AGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAA
original cDNA sequence snippet AGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAA
altered cDNA sequence snippet AGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAA
wildtype AA sequence MEPWSSRWKT KRWLWDFTVT TLALTFLFQA REVRGAAPVD VLKALDFHNS PEGISKTTGF
CTNRKNSKGS DTAYRVSKQA QLSAPTKQLF PGGTFPEDFS ILFTVKPKKG IQSFLLSIYN
EHGIQQIGVE VGRSPVFLFE DHTGKPAPED YPLFRTVNIA DGKWHRVAIS VEKKTVTMIV
DCKKKTTKPL DRSERAIVDT NGITVFGTRI LDEEVFEGDI QQFLITGDPK AAYDYCEHYS
PDCDSSAPKA AQAQEPQIDE YAPEDIIEYD YEYGEAEYKE AESVTEGPTV TEETIAQTEA
NIVDDFQEYN YGTMESYQTE APRHVSGTNE PNPVEEIFTE EYLTGEDYDS QRKNSEDTLY
ENKEIDGRDS DLLVDGDLGE YDFYEYKEYE DKPTSPPNEE FGPGVPAETD ITETSINGHG
AYGEKGQKGE PAVVEPGMLV EGPPGPAGPA GIMGPPGLQG PTGPPGDPGD RGPPGRPGLP
GADGLPGPPG TMLMLPFRYG GDGSKGPTIS AQEAQAQAIL QQARIALRGP PGPMGLTGRP
GPVGGPGSSG AKGESGDPGP QGPRGVQGPP GPTGKPGKRG RPGADGGRGM PGEPGAKGDR
GFDGLPGLPG DKGHRGERGP QGPPGPPGDD GMRGEDGEIG PRGLPGEAGP RGLLGPRGTP
GAPGQPGMAG VDGPPGPKGN MGPQGEPGPP GQQGNPGPQG LPGPQGPIGP PGEKGPQGKP
GLAGLPGADG PPGHPGKEGQ SGEKGALGPP GPQGPIGYPG PRGVKGADGV RGLKGSKGEK
GEDGFPGFKG DMGLKGDRGE VGQIGPRGED GPEGPKGRAG PTGDPGPSGQ AGEKGKLGVP
GLPGYPGRQG PKGSTGFPGF PGANGEKGAR GVAGKPGPRG QRGPTGPRGS RGARGPTGKP
GPKGTSGGDG PPGPPGERGP QGPQGPVGFP GPKGPPGPPG KDGLPGHPGQ RGETGFQGKT
GPPGPGGVVG PQGPTGETGP IGERGHPGPP GPPGEQGLPG AAGKEGAKGD PGPQGISGKD
GPAGLRGFPG ERGLPGAQGA PGLKGGEGPQ GPPGPVGSPG ERGSAGTAGP IGLPGRPGPQ
GPPGPAGEKG APGEKGPQGP AGRDGVQGPV GLPGPAGPAG SPGEDGDKGE IGEPGQKGSK
GDKGENGPPG PPGLQGPVGA PGIAGGDGEP GPRGQQGMFG QKGDEGARGF PGPPGPIGLQ
GLPGPPGEKG ENGDVGPMGP PGPPGPRGPQ GPNGADGPQG PPGSVGSVGG VGEKGEPGEA
GNPGPPGEAG VGGPKGERGE KGEAGPPGAA GPPGAKGPPG DDGPKGNPGP VGFPGDPGPP
GEPGPAGQDG VGGDKGEDGD PGQPGPPGPS GEAGPPGPPG KRGPPGAAGA EGRQGEKGAK
GEAGAEGPPG KTGPVGPQGP AGKPGPEGLR GIPGPVGEQG LPGAAGQDGP PGPMGPPGLP
GLKGDPGSKG EKGHPGLIGL IGPPGEQGEK GDRGLPGTQG SPGAKGDGGI PGPAGPLGPP
GPPGLPGPQG PKGNKGSTGP AGQKGDSGLP GPPGSPGPPG EVIQPLPILS SKKTRRHTEG
MQADADDNIL DYSDGMEEIF GSLNSLKQDI EHMKFPMGTQ TNPARTCKDL QLSHPDFPDG
EYWIDPNQGC SGDSFKVYCN FTSGGETCIY PDKKSEGVRI SSWPKEKPGS WFSEFKRGKL
LSYLDVEGNS INMVQMTFLK LLTASARQNF TYHCHQSAAW YDVSSGSYDK ALRFLGSNDE
EMSYDNNPFI KTLYDGCASR KGYEKTVIEI NTPKIDQVPI VDVMINDFGD QNQKFGFEVG
PVCFLG*
mutated AA sequence MEPWSSRWKT KRWLWDFTVT TLALTFLFQA REVRGAAPVD VLKALDFHNS PEGISKTTGF
CTNRKNSKGS DTAYRVSKQA QLSAPTKQLF PGGTFPEDFS ILFTVKPKKG IQSFLLSIYN
EHGIQQIGVE VGRSPVFLFE DHTGKPAPED YPLFRTVNIA DGKWHRVAIS VEKKTVTMIV
DCKKKTTKPL DRSERAIVDT NGITVFGTRI LDEEVFEGDI QQFLITGDPK AAYDYCEHYS
PDCDSSAPKA AQAQEPQIDE YAPEDIIEYD YEYGEAEYKE AESVTEGPTV TEETIAQTEA
NIVDDFQEYN YGTMESYQTE APRHVSGTNE PNPVEEIFTE EYLTGEDYDS QRKNSEDTLY
ENKEIDGRDS DLLVDGDLGE YDFYEYKEYE DKPTSPPNEE FGPGVPAETD ITETSINGHG
AYGEKGQKGE PAVVEPGMLV EGPPGPAGPA GIMGPPGLQG PTGPPGDPGD RGPPGRPGLP
GADGLPGPPG TMLMLPFRYG GDGSKGPTIS AQEAQAQAIL QQARIALRGP PGPMGLTGRP
GPVGGPGSSG AKGESGDPGP QGPRGVQGPP GPTGKPGKRG RPGADGGRGM PGEPGAKGDR
GFDGLPGLPG DKGHRGERGP QGPPVPPGDD GMRGEDGEIG PRGLPGEAGP RGLLGPRGTP
GAPGQPGMAG VDGPPGPKGN MGPQGEPGPP GQQGNPGPQG LPGPQGPIGP PGEKGPQGKP
GLAGLPGADG PPGHPGKEGQ SGEKGALGPP GPQGPIGYPG PRGVKGADGV RGLKGSKGEK
GEDGFPGFKG DMGLKGDRGE VGQIGPRGED GPEGPKGRAG PTGDPGPSGQ AGEKGKLGVP
GLPGYPGRQG PKGSTGFPGF PGANGEKGAR GVAGKPGPRG QRGPTGPRGS RGARGPTGKP
GPKGTSGGDG PPGPPGERGP QGPQGPVGFP GPKGPPGPPG KDGLPGHPGQ RGETGFQGKT
GPPGPGGVVG PQGPTGETGP IGERGHPGPP GPPGEQGLPG AAGKEGAKGD PGPQGISGKD
GPAGLRGFPG ERGLPGAQGA PGLKGGEGPQ GPPGPVGSPG ERGSAGTAGP IGLPGRPGPQ
GPPGPAGEKG APGEKGPQGP AGRDGVQGPV GLPGPAGPAG SPGEDGDKGE IGEPGQKGSK
GDKGENGPPG PPGLQGPVGA PGIAGGDGEP GPRGQQGMFG QKGDEGARGF PGPPGPIGLQ
GLPGPPGEKG ENGDVGPMGP PGPPGPRGPQ GPNGADGPQG PPGSVGSVGG VGEKGEPGEA
GNPGPPGEAG VGGPKGERGE KGEAGPPGAA GPPGAKGPPG DDGPKGNPGP VGFPGDPGPP
GEPGPAGQDG VGGDKGEDGD PGQPGPPGPS GEAGPPGPPG KRGPPGAAGA EGRQGEKGAK
GEAGAEGPPG KTGPVGPQGP AGKPGPEGLR GIPGPVGEQG LPGAAGQDGP PGPMGPPGLP
GLKGDPGSKG EKGHPGLIGL IGPPGEQGEK GDRGLPGTQG SPGAKGDGGI PGPAGPLGPP
GPPGLPGPQG PKGNKGSTGP AGQKGDSGLP GPPGSPGPPG EVIQPLPILS SKKTRRHTEG
MQADADDNIL DYSDGMEEIF GSLNSLKQDI EHMKFPMGTQ TNPARTCKDL QLSHPDFPDG
EYWIDPNQGC SGDSFKVYCN FTSGGETCIY PDKKSEGVRI SSWPKEKPGS WFSEFKRGKL
LSYLDVEGNS INMVQMTFLK LLTASARQNF TYHCHQSAAW YDVSSGSYDK ALRFLGSNDE
EMSYDNNPFI KTLYDGCASR KGYEKTVIEI NTPKIDQVPI VDVMINDFGD QNQKFGFEVG
PVCFLG*
speed 0.41 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

disease causing

 Model: simple_aae, prob: 0.999999999999978 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960317)
  • known disease mutation: rs17131 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:103470189C>AN/A show variant in all transcripts   IGV
HGNC symbol COL11A1
Ensembl transcript ID ENST00000358392
Genbank transcript ID NM_080629
UniProt peptide P12107
alteration type single base exchange
alteration region CDS
DNA changes c.1910G>T
cDNA.2228G>T
g.103864G>T
AA changes G637V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 637
frameshift no
known variant Reference ID: rs121912943
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17131 (pathogenic for Stickler syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9460.008
5.4050.999
(flanking)3.8221
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased103873wt: 0.54 / mu: 0.80wt: AGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTAT
mu: AGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTAT		 ctgg|TGAT
Acc increased103872wt: 0.51 / mu: 0.85wt: AAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTA
mu: AAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTA		 cctg|GTGA
Acc increased103871wt: 0.81 / mu: 0.94wt: CAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGT
mu: CAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGT		 tcct|GGTG
Acc gained1038620.32mu: CGAGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGG tcca|GTTC
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      637HRGERGPQGPPGPPGDDGMRGEDG
mutated  not conserved    637HRGERGPQGPPVPPGDDGMRGED
Ptroglodytes  all identical  ENSPTRG00000001017  625HRGERGPQGPPGPPGDDGMRGED
Mmulatta  all identical  ENSMMUG00000004103  625HRGERGPQGPPGPPGDDGMRGED
Fcatus  all identical  ENSFCAG00000018396  64GPPGPPGEDGMRXXX
Mmusculus  all identical  ENSMUSG00000027966  623HRGERGPQGPPGLPGDDGMRGED
Ggallus  all identical  ENSGALG00000005180  624NRGDRGPQGPPGLPGEDGSRKQGED
Trubripes  all identical  ENSTRUG00000001411  637HRGEPGPIGPTGAVGEDGQRGED
Drerio  all identical  ENSDARG00000026165  556HRGETGPAGPPGPTGEDGPRGED
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000010839  628HRGDKGPHGPPGPPGEDGERGED
protein features
start (aa)end (aa)featuredetails 
5291542REGIONTriple-helical region.lost
583641DOMAINCollagen-like 3.lost
616674DOMAINCollagen-like 4.lost
643699DOMAINCollagen-like 5.might get lost (downstream of altered splice site)
941944CONFLICTKDGL -> RMGC (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
986986CONFLICTH -> Y (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
10741074CONFLICTP -> R (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
11421142CONFLICTD -> G (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
12181218CONFLICTM -> W (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
13931450DOMAINCollagen-like 6.might get lost (downstream of altered splice site)
14291487DOMAINCollagen-like 7.might get lost (downstream of altered splice site)
14521452MOD_RESAllysine.might get lost (downstream of altered splice site)
14831541DOMAINCollagen-like 8.might get lost (downstream of altered splice site)
15431563REGIONNonhelical region (C-terminal).might get lost (downstream of altered splice site)
15641806PROPEPC-terminal propeptide. /FTId=PRO_0000005776.might get lost (downstream of altered splice site)
15771805DOMAINFibrillar collagen NC1.might get lost (downstream of altered splice site)
16071607DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16071607DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16301630DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16301630DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16391639DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16391639DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16401640CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
16481648DISULFIDBy similarity.might get lost (downstream of altered splice site)
17141714DISULFIDBy similarity.might get lost (downstream of altered splice site)
17571757DISULFIDBy similarity.might get lost (downstream of altered splice site)
17581758CONFLICTA -> T (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
17861786CONFLICTN -> S (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
18031803DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5457 / 5457
position (AA) of stopcodon in wt / mu AA sequence 1819 / 1819
position of stopcodon in wt / mu cDNA 5775 / 5775
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 319 / 319
chromosome 1
strand -1
last intron/exon boundary 5629
theoretical NMD boundary in CDS 5260
length of CDS 5457
coding sequence (CDS) position 1910
cDNA position
(for ins/del: last normal base / first normal base)		 2228
gDNA position
(for ins/del: last normal base / first normal base)		 103864
chromosomal position
(for ins/del: last normal base / first normal base)		 103470189
original gDNA sequence snippet AGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAA
altered gDNA sequence snippet AGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAA
original cDNA sequence snippet AGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAA
altered cDNA sequence snippet AGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAA
wildtype AA sequence MEPWSSRWKT KRWLWDFTVT TLALTFLFQA REVRGAAPVD VLKALDFHNS PEGISKTTGF
CTNRKNSKGS DTAYRVSKQA QLSAPTKQLF PGGTFPEDFS ILFTVKPKKG IQSFLLSIYN
EHGIQQIGVE VGRSPVFLFE DHTGKPAPED YPLFRTVNIA DGKWHRVAIS VEKKTVTMIV
DCKKKTTKPL DRSERAIVDT NGITVFGTRI LDEEVFEGDI QQFLITGDPK AAYDYCEHYS
PDCDSSAPKA AQAQEPQIDE KKKSNFKKKM RTVATKSKEK SKKFTPPKSE KFSSKKKKSY
QASAKAKLGV KANIVDDFQE YNYGTMESYQ TEAPRHVSGT NEPNPVEEIF TEEYLTGEDY
DSQRKNSEDT LYENKEIDGR DSDLLVDGDL GEYDFYEYKE YEDKPTSPPN EEFGPGVPAE
TDITETSING HGAYGEKGQK GEPAVVEPGM LVEGPPGPAG PAGIMGPPGL QGPTGPPGDP
GDRGPPGRPG LPGADGLPGP PGTMLMLPFR YGGDGSKGPT ISAQEAQAQA ILQQARIALR
GPPGPMGLTG RPGPVGGPGS SGAKGESGDP GPQGPRGVQG PPGPTGKPGK RGRPGADGGR
GMPGEPGAKG DRGFDGLPGL PGDKGHRGER GPQGPPGPPG DDGMRGEDGE IGPRGLPGEA
GPRGLLGPRG TPGAPGQPGM AGVDGPPGPK GNMGPQGEPG PPGQQGNPGP QGLPGPQGPI
GPPGEKGPQG KPGLAGLPGA DGPPGHPGKE GQSGEKGALG PPGPQGPIGY PGPRGVKGAD
GVRGLKGSKG EKGEDGFPGF KGDMGLKGDR GEVGQIGPRG EDGPEGPKGR AGPTGDPGPS
GQAGEKGKLG VPGLPGYPGR QGPKGSTGFP GFPGANGEKG ARGVAGKPGP RGQRGPTGPR
GSRGARGPTG KPGPKGTSGG DGPPGPPGER GPQGPQGPVG FPGPKGPPGP PGKDGLPGHP
GQRGETGFQG KTGPPGPGGV VGPQGPTGET GPIGERGHPG PPGPPGEQGL PGAAGKEGAK
GDPGPQGISG KDGPAGLRGF PGERGLPGAQ GAPGLKGGEG PQGPPGPVGS PGERGSAGTA
GPIGLPGRPG PQGPPGPAGE KGAPGEKGPQ GPAGRDGVQG PVGLPGPAGP AGSPGEDGDK
GEIGEPGQKG SKGDKGENGP PGPPGLQGPV GAPGIAGGDG EPGPRGQQGM FGQKGDEGAR
GFPGPPGPIG LQGLPGPPGE KGENGDVGPM GPPGPPGPRG PQGPNGADGP QGPPGSVGSV
GGVGEKGEPG EAGNPGPPGE AGVGGPKGER GEKGEAGPPG AAGPPGAKGP PGDDGPKGNP
GPVGFPGDPG PPGEPGPAGQ DGVGGDKGED GDPGQPGPPG PSGEAGPPGP PGKRGPPGAA
GAEGRQGEKG AKGEAGAEGP PGKTGPVGPQ GPAGKPGPEG LRGIPGPVGE QGLPGAAGQD
GPPGPMGPPG LPGLKGDPGS KGEKGHPGLI GLIGPPGEQG EKGDRGLPGT QGSPGAKGDG
GIPGPAGPLG PPGPPGLPGP QGPKGNKGST GPAGQKGDSG LPGPPGSPGP PGEVIQPLPI
LSSKKTRRHT EGMQADADDN ILDYSDGMEE IFGSLNSLKQ DIEHMKFPMG TQTNPARTCK
DLQLSHPDFP DGEYWIDPNQ GCSGDSFKVY CNFTSGGETC IYPDKKSEGV RISSWPKEKP
GSWFSEFKRG KLLSYLDVEG NSINMVQMTF LKLLTASARQ NFTYHCHQSA AWYDVSSGSY
DKALRFLGSN DEEMSYDNNP FIKTLYDGCA SRKGYEKTVI EINTPKIDQV PIVDVMINDF
GDQNQKFGFE VGPVCFLG*
mutated AA sequence MEPWSSRWKT KRWLWDFTVT TLALTFLFQA REVRGAAPVD VLKALDFHNS PEGISKTTGF
CTNRKNSKGS DTAYRVSKQA QLSAPTKQLF PGGTFPEDFS ILFTVKPKKG IQSFLLSIYN
EHGIQQIGVE VGRSPVFLFE DHTGKPAPED YPLFRTVNIA DGKWHRVAIS VEKKTVTMIV
DCKKKTTKPL DRSERAIVDT NGITVFGTRI LDEEVFEGDI QQFLITGDPK AAYDYCEHYS
PDCDSSAPKA AQAQEPQIDE KKKSNFKKKM RTVATKSKEK SKKFTPPKSE KFSSKKKKSY
QASAKAKLGV KANIVDDFQE YNYGTMESYQ TEAPRHVSGT NEPNPVEEIF TEEYLTGEDY
DSQRKNSEDT LYENKEIDGR DSDLLVDGDL GEYDFYEYKE YEDKPTSPPN EEFGPGVPAE
TDITETSING HGAYGEKGQK GEPAVVEPGM LVEGPPGPAG PAGIMGPPGL QGPTGPPGDP
GDRGPPGRPG LPGADGLPGP PGTMLMLPFR YGGDGSKGPT ISAQEAQAQA ILQQARIALR
GPPGPMGLTG RPGPVGGPGS SGAKGESGDP GPQGPRGVQG PPGPTGKPGK RGRPGADGGR
GMPGEPGAKG DRGFDGLPGL PGDKGHRGER GPQGPPVPPG DDGMRGEDGE IGPRGLPGEA
GPRGLLGPRG TPGAPGQPGM AGVDGPPGPK GNMGPQGEPG PPGQQGNPGP QGLPGPQGPI
GPPGEKGPQG KPGLAGLPGA DGPPGHPGKE GQSGEKGALG PPGPQGPIGY PGPRGVKGAD
GVRGLKGSKG EKGEDGFPGF KGDMGLKGDR GEVGQIGPRG EDGPEGPKGR AGPTGDPGPS
GQAGEKGKLG VPGLPGYPGR QGPKGSTGFP GFPGANGEKG ARGVAGKPGP RGQRGPTGPR
GSRGARGPTG KPGPKGTSGG DGPPGPPGER GPQGPQGPVG FPGPKGPPGP PGKDGLPGHP
GQRGETGFQG KTGPPGPGGV VGPQGPTGET GPIGERGHPG PPGPPGEQGL PGAAGKEGAK
GDPGPQGISG KDGPAGLRGF PGERGLPGAQ GAPGLKGGEG PQGPPGPVGS PGERGSAGTA
GPIGLPGRPG PQGPPGPAGE KGAPGEKGPQ GPAGRDGVQG PVGLPGPAGP AGSPGEDGDK
GEIGEPGQKG SKGDKGENGP PGPPGLQGPV GAPGIAGGDG EPGPRGQQGM FGQKGDEGAR
GFPGPPGPIG LQGLPGPPGE KGENGDVGPM GPPGPPGPRG PQGPNGADGP QGPPGSVGSV
GGVGEKGEPG EAGNPGPPGE AGVGGPKGER GEKGEAGPPG AAGPPGAKGP PGDDGPKGNP
GPVGFPGDPG PPGEPGPAGQ DGVGGDKGED GDPGQPGPPG PSGEAGPPGP PGKRGPPGAA
GAEGRQGEKG AKGEAGAEGP PGKTGPVGPQ GPAGKPGPEG LRGIPGPVGE QGLPGAAGQD
GPPGPMGPPG LPGLKGDPGS KGEKGHPGLI GLIGPPGEQG EKGDRGLPGT QGSPGAKGDG
GIPGPAGPLG PPGPPGLPGP QGPKGNKGST GPAGQKGDSG LPGPPGSPGP PGEVIQPLPI
LSSKKTRRHT EGMQADADDN ILDYSDGMEE IFGSLNSLKQ DIEHMKFPMG TQTNPARTCK
DLQLSHPDFP DGEYWIDPNQ GCSGDSFKVY CNFTSGGETC IYPDKKSEGV RISSWPKEKP
GSWFSEFKRG KLLSYLDVEG NSINMVQMTF LKLLTASARQ NFTYHCHQSA AWYDVSSGSY
DKALRFLGSN DEEMSYDNNP FIKTLYDGCA SRKGYEKTVI EINTPKIDQV PIVDVMINDF
GDQNQKFGFE VGPVCFLG*
speed 0.77 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

disease causing

 Model: simple_aae, prob: 0.999999999999978 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960317)
  • known disease mutation: rs17131 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:103470189C>AN/A show variant in all transcripts   IGV
HGNC symbol COL11A1
Ensembl transcript ID ENST00000353414
Genbank transcript ID NM_001190709
UniProt peptide P12107
alteration type single base exchange
alteration region CDS
DNA changes c.1757G>T
cDNA.2075G>T
g.103864G>T
AA changes G586V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 586
frameshift no
known variant Reference ID: rs121912943
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17131 (pathogenic for Stickler syndrome type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960317)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9460.008
5.4050.999
(flanking)3.8221
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased103873wt: 0.54 / mu: 0.80wt: AGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTAT
mu: AGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTAT		 ctgg|TGAT
Acc increased103872wt: 0.51 / mu: 0.85wt: AAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTA
mu: AAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTA		 cctg|GTGA
Acc increased103871wt: 0.81 / mu: 0.94wt: CAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGT
mu: CAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGT		 tcct|GGTG
Acc gained1038620.32mu: CGAGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGG tcca|GTTC
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      586HRGERGPQGPPGPPGDDGMRGEDG
mutated  not conserved    586HRGERGPQGPPVPPGDDGMRGED
Ptroglodytes  all identical  ENSPTRG00000001017  625HRGERGPQGPPGPPGDDGMRGED
Mmulatta  all identical  ENSMMUG00000004103  625HRGERGPQGPPGPPGDDGMRGED
Fcatus  all identical  ENSFCAG00000018396  64GPPGPPGEDGMRXXX
Mmusculus  all identical  ENSMUSG00000027966  623HRGERGPQGPPGLPGDDGMRGED
Ggallus  all identical  ENSGALG00000005180  624NRGDRGPQGPPGLPGEDGSRKQGED
Trubripes  all identical  ENSTRUG00000001411  637HRGEPGPIGPTGAVGEDGQRGED
Drerio  all identical  ENSDARG00000026165  556HRGETGPAGPPGPTGEDGPRGED
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000010839  628HRGDKGPHGPPGPPGEDGERGED
protein features
start (aa)end (aa)featuredetails 
5291542REGIONTriple-helical region.lost
532586DOMAINCollagen-like 2.lost
583641DOMAINCollagen-like 3.lost
612612MOD_RESAllysine.might get lost (downstream of altered splice site)
616674DOMAINCollagen-like 4.might get lost (downstream of altered splice site)
643699DOMAINCollagen-like 5.might get lost (downstream of altered splice site)
941944CONFLICTKDGL -> RMGC (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
986986CONFLICTH -> Y (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
10741074CONFLICTP -> R (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
11421142CONFLICTD -> G (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
12181218CONFLICTM -> W (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
13931450DOMAINCollagen-like 6.might get lost (downstream of altered splice site)
14291487DOMAINCollagen-like 7.might get lost (downstream of altered splice site)
14521452MOD_RESAllysine.might get lost (downstream of altered splice site)
14831541DOMAINCollagen-like 8.might get lost (downstream of altered splice site)
15431563REGIONNonhelical region (C-terminal).might get lost (downstream of altered splice site)
15641806PROPEPC-terminal propeptide. /FTId=PRO_0000005776.might get lost (downstream of altered splice site)
15771805DOMAINFibrillar collagen NC1.might get lost (downstream of altered splice site)
16071607DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16071607DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16301630DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16301630DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16391639DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16391639DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16401640CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
16481648DISULFIDBy similarity.might get lost (downstream of altered splice site)
17141714DISULFIDBy similarity.might get lost (downstream of altered splice site)
17571757DISULFIDBy similarity.might get lost (downstream of altered splice site)
17581758CONFLICTA -> T (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
17861786CONFLICTN -> S (in Ref. 1; AAA51891).might get lost (downstream of altered splice site)
18031803DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5304 / 5304
position (AA) of stopcodon in wt / mu AA sequence 1768 / 1768
position of stopcodon in wt / mu cDNA 5622 / 5622
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 319 / 319
chromosome 1
strand -1
last intron/exon boundary 5476
theoretical NMD boundary in CDS 5107
length of CDS 5304
coding sequence (CDS) position 1757
cDNA position
(for ins/del: last normal base / first normal base)		 2075
gDNA position
(for ins/del: last normal base / first normal base)		 103864
chromosomal position
(for ins/del: last normal base / first normal base)		 103470189
original gDNA sequence snippet AGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAA
altered gDNA sequence snippet AGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAA
original cDNA sequence snippet AGGTCCTCAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAA
altered cDNA sequence snippet AGGTCCTCAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAA
wildtype AA sequence MEPWSSRWKT KRWLWDFTVT TLALTFLFQA REVRGAAPVD VLKALDFHNS PEGISKTTGF
CTNRKNSKGS DTAYRVSKQA QLSAPTKQLF PGGTFPEDFS ILFTVKPKKG IQSFLLSIYN
EHGIQQIGVE VGRSPVFLFE DHTGKPAPED YPLFRTVNIA DGKWHRVAIS VEKKTVTMIV
DCKKKTTKPL DRSERAIVDT NGITVFGTRI LDEEVFEGDI QQFLITGDPK AAYDYCEHYS
PDCDSSAPKA AQAQEPQIDE ANIVDDFQEY NYGTMESYQT EAPRHVSGTN EPNPVEEIFT
EEYLTGEDYD SQRKNSEDTL YENKEIDGRD SDLLVDGDLG EYDFYEYKEY EDKPTSPPNE
EFGPGVPAET DITETSINGH GAYGEKGQKG EPAVVEPGML VEGPPGPAGP AGIMGPPGLQ
GPTGPPGDPG DRGPPGRPGL PGADGLPGPP GTMLMLPFRY GGDGSKGPTI SAQEAQAQAI
LQQARIALRG PPGPMGLTGR PGPVGGPGSS GAKGESGDPG PQGPRGVQGP PGPTGKPGKR
GRPGADGGRG MPGEPGAKGD RGFDGLPGLP GDKGHRGERG PQGPPGPPGD DGMRGEDGEI
GPRGLPGEAG PRGLLGPRGT PGAPGQPGMA GVDGPPGPKG NMGPQGEPGP PGQQGNPGPQ
GLPGPQGPIG PPGEKGPQGK PGLAGLPGAD GPPGHPGKEG QSGEKGALGP PGPQGPIGYP
GPRGVKGADG VRGLKGSKGE KGEDGFPGFK GDMGLKGDRG EVGQIGPRGE DGPEGPKGRA
GPTGDPGPSG QAGEKGKLGV PGLPGYPGRQ GPKGSTGFPG FPGANGEKGA RGVAGKPGPR
GQRGPTGPRG SRGARGPTGK PGPKGTSGGD GPPGPPGERG PQGPQGPVGF PGPKGPPGPP
GKDGLPGHPG QRGETGFQGK TGPPGPGGVV GPQGPTGETG PIGERGHPGP PGPPGEQGLP
GAAGKEGAKG DPGPQGISGK DGPAGLRGFP GERGLPGAQG APGLKGGEGP QGPPGPVGSP
GERGSAGTAG PIGLPGRPGP QGPPGPAGEK GAPGEKGPQG PAGRDGVQGP VGLPGPAGPA
GSPGEDGDKG EIGEPGQKGS KGDKGENGPP GPPGLQGPVG APGIAGGDGE PGPRGQQGMF
GQKGDEGARG FPGPPGPIGL QGLPGPPGEK GENGDVGPMG PPGPPGPRGP QGPNGADGPQ
GPPGSVGSVG GVGEKGEPGE AGNPGPPGEA GVGGPKGERG EKGEAGPPGA AGPPGAKGPP
GDDGPKGNPG PVGFPGDPGP PGEPGPAGQD GVGGDKGEDG DPGQPGPPGP SGEAGPPGPP
GKRGPPGAAG AEGRQGEKGA KGEAGAEGPP GKTGPVGPQG PAGKPGPEGL RGIPGPVGEQ
GLPGAAGQDG PPGPMGPPGL PGLKGDPGSK GEKGHPGLIG LIGPPGEQGE KGDRGLPGTQ
GSPGAKGDGG IPGPAGPLGP PGPPGLPGPQ GPKGNKGSTG PAGQKGDSGL PGPPGSPGPP
GEVIQPLPIL SSKKTRRHTE GMQADADDNI LDYSDGMEEI FGSLNSLKQD IEHMKFPMGT
QTNPARTCKD LQLSHPDFPD GEYWIDPNQG CSGDSFKVYC NFTSGGETCI YPDKKSEGVR
ISSWPKEKPG SWFSEFKRGK LLSYLDVEGN SINMVQMTFL KLLTASARQN FTYHCHQSAA
WYDVSSGSYD KALRFLGSND EEMSYDNNPF IKTLYDGCAS RKGYEKTVIE INTPKIDQVP
IVDVMINDFG DQNQKFGFEV GPVCFLG*
mutated AA sequence MEPWSSRWKT KRWLWDFTVT TLALTFLFQA REVRGAAPVD VLKALDFHNS PEGISKTTGF
CTNRKNSKGS DTAYRVSKQA QLSAPTKQLF PGGTFPEDFS ILFTVKPKKG IQSFLLSIYN
EHGIQQIGVE VGRSPVFLFE DHTGKPAPED YPLFRTVNIA DGKWHRVAIS VEKKTVTMIV
DCKKKTTKPL DRSERAIVDT NGITVFGTRI LDEEVFEGDI QQFLITGDPK AAYDYCEHYS
PDCDSSAPKA AQAQEPQIDE ANIVDDFQEY NYGTMESYQT EAPRHVSGTN EPNPVEEIFT
EEYLTGEDYD SQRKNSEDTL YENKEIDGRD SDLLVDGDLG EYDFYEYKEY EDKPTSPPNE
EFGPGVPAET DITETSINGH GAYGEKGQKG EPAVVEPGML VEGPPGPAGP AGIMGPPGLQ
GPTGPPGDPG DRGPPGRPGL PGADGLPGPP GTMLMLPFRY GGDGSKGPTI SAQEAQAQAI
LQQARIALRG PPGPMGLTGR PGPVGGPGSS GAKGESGDPG PQGPRGVQGP PGPTGKPGKR
GRPGADGGRG MPGEPGAKGD RGFDGLPGLP GDKGHRGERG PQGPPVPPGD DGMRGEDGEI
GPRGLPGEAG PRGLLGPRGT PGAPGQPGMA GVDGPPGPKG NMGPQGEPGP PGQQGNPGPQ
GLPGPQGPIG PPGEKGPQGK PGLAGLPGAD GPPGHPGKEG QSGEKGALGP PGPQGPIGYP
GPRGVKGADG VRGLKGSKGE KGEDGFPGFK GDMGLKGDRG EVGQIGPRGE DGPEGPKGRA
GPTGDPGPSG QAGEKGKLGV PGLPGYPGRQ GPKGSTGFPG FPGANGEKGA RGVAGKPGPR
GQRGPTGPRG SRGARGPTGK PGPKGTSGGD GPPGPPGERG PQGPQGPVGF PGPKGPPGPP
GKDGLPGHPG QRGETGFQGK TGPPGPGGVV GPQGPTGETG PIGERGHPGP PGPPGEQGLP
GAAGKEGAKG DPGPQGISGK DGPAGLRGFP GERGLPGAQG APGLKGGEGP QGPPGPVGSP
GERGSAGTAG PIGLPGRPGP QGPPGPAGEK GAPGEKGPQG PAGRDGVQGP VGLPGPAGPA
GSPGEDGDKG EIGEPGQKGS KGDKGENGPP GPPGLQGPVG APGIAGGDGE PGPRGQQGMF
GQKGDEGARG FPGPPGPIGL QGLPGPPGEK GENGDVGPMG PPGPPGPRGP QGPNGADGPQ
GPPGSVGSVG GVGEKGEPGE AGNPGPPGEA GVGGPKGERG EKGEAGPPGA AGPPGAKGPP
GDDGPKGNPG PVGFPGDPGP PGEPGPAGQD GVGGDKGEDG DPGQPGPPGP SGEAGPPGPP
GKRGPPGAAG AEGRQGEKGA KGEAGAEGPP GKTGPVGPQG PAGKPGPEGL RGIPGPVGEQ
GLPGAAGQDG PPGPMGPPGL PGLKGDPGSK GEKGHPGLIG LIGPPGEQGE KGDRGLPGTQ
GSPGAKGDGG IPGPAGPLGP PGPPGLPGPQ GPKGNKGSTG PAGQKGDSGL PGPPGSPGPP
GEVIQPLPIL SSKKTRRHTE GMQADADDNI LDYSDGMEEI FGSLNSLKQD IEHMKFPMGT
QTNPARTCKD LQLSHPDFPD GEYWIDPNQG CSGDSFKVYC NFTSGGETCI YPDKKSEGVR
ISSWPKEKPG SWFSEFKRGK LLSYLDVEGN SINMVQMTFL KLLTASARQN FTYHCHQSAA
WYDVSSGSYD KALRFLGSND EEMSYDNNPF IKTLYDGCAS RKGYEKTVIE INTPKIDQVP
IVDVMINDFG DQNQKFGFEV GPVCFLG*
speed 0.44 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
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Problems