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 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      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 1.26 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