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 increased103872wt: 0.51 / mu: 0.85wt: AAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTA
mu: AAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTA		 cctg|GTGA
Acc increased103871wt: 0.81 / mu: 0.94wt: CAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGT
mu: CAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGT		 tcct|GGTG
Acc increased103873wt: 0.54 / mu: 0.80wt: AGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTAT
mu: AGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTAT		 ctgg|TGAT
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 1.46 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