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 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      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 0.79 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