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 increased103871wt: 0.81 / mu: 0.94wt: CAAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGT
mu: CAAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGT		 tcct|GGTG
Acc increased103872wt: 0.51 / mu: 0.85wt: AAGGTCCTCCAGGTCCTCCTGGTGATGATGGAATGAGGGTA
mu: AAGGTCCTCCAGTTCCTCCTGGTGATGATGGAATGAGGGTA		 cctg|GTGA
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 0.23 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