Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999986140182 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993116)
  • known disease mutation: rs17125 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:33142311C>TN/A show variant in all transcripts   IGV
HGNC symbol COL11A2
Ensembl transcript ID ENST00000357486
Genbank transcript ID N/A
UniProt peptide P13942
alteration type single base exchange
alteration region CDS
DNA changes c.2360G>A
cDNA.2588G>A
g.17966G>A
AA changes G787E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 787
frameshift no
known variant Reference ID: rs121912948
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17125 (pathogenic for Deafness, autosomal dominant 13) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993116)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993116)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9870.846
4.7491
(flanking)4.7491
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased17957wt: 0.5437 / mu: 0.5827 (marginal change - not scored)wt: TGGTCTGCCTGGCTATCCTGGACGTCAGGGACCCAAGGTGA
mu: TGGTCTGCCTGGCTATCCTGGACGTCAGGAACCCAAGGTGA		 ctgg|ACGT
Acc marginally increased17956wt: 0.8842 / mu: 0.8845 (marginal change - not scored)wt: CTGGTCTGCCTGGCTATCCTGGACGTCAGGGACCCAAGGTG
mu: CTGGTCTGCCTGGCTATCCTGGACGTCAGGAACCCAAGGTG		 cctg|GACG
Donor marginally increased17963wt: 0.7001 / mu: 0.7651 (marginal change - not scored)wt: ACGTCAGGGACCCAA
mu: ACGTCAGGAACCCAA		 GTCA|ggga
Donor increased17968wt: 0.55 / mu: 0.76wt: AGGGACCCAAGGTGA
mu: AGGAACCCAAGGTGA		 GGAC|ccaa
Donor marginally increased17967wt: 0.9546 / mu: 0.9729 (marginal change - not scored)wt: CAGGGACCCAAGGTG
mu: CAGGAACCCAAGGTG		 GGGA|ccca
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      787VPGLPGYPGRQGPKGSLGFPGFPG
mutated  not conserved    787GYPGRQEPKGSLGFPGFP
Ptroglodytes  all identical  ENSPTRG00000018033  770VPGLPGYPGRQGPKGSLGFPGFP
Mmulatta  all identical  ENSMMUG00000003850  807VPGLPGYPGRQGPKGSLGFPGFP
Fcatus  all identical  ENSFCAG00000004005  435VPGLPGYPGRQGPKGSLGFPGFP
Mmusculus  all identical  ENSMUSG00000024330  761GYPGRQGPKGSLGFPGFP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000005534  875VPGLPGYPGRQGPKGSLGFPGFP
Drerio  all identical  ENSDARG00000012422  1054VPGLPGYPGRQGIKGSLGFPGFP
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000012724  1038VPGLPGYPGRQGAKGSLGFPGFP
protein features
start (aa)end (aa)featuredetails 
4871500REGIONTriple-helical region.lost
805862DOMAINCollagen-like 4.might get lost (downstream of altered splice site)
843846CONFLICTTGPR -> HGST (in Ref. 7; AAA52034).might get lost (downstream of altered splice site)
863899DOMAINCollagen-like 5.might get lost (downstream of altered splice site)
882884CONFLICTQGP -> SGS (in Ref. 7; AAA52034).might get lost (downstream of altered splice site)
10311032CONFLICTPP -> RQ (in Ref. 1; AAC50213/AAC50214/ AAC50215 and 7; AAA52034).might get lost (downstream of altered splice site)
10911091CONFLICTD -> V (in Ref. 7; AAA52034).might get lost (downstream of altered splice site)
10991156DOMAINCollagen-like 6.might get lost (downstream of altered splice site)
11241124CONFLICTA -> R (in Ref. 7; AAA52034).might get lost (downstream of altered splice site)
11271133CONFLICTEPGARGP -> GAGGLGT (in Ref. 7; AAA52034).might get lost (downstream of altered splice site)
11571172DOMAINCollagen-like 7.might get lost (downstream of altered splice site)
12531253CONFLICTP -> A (in Ref. 1; AAC50213/AAC50214/ AAC50215 and 7; AAA52034).might get lost (downstream of altered splice site)
12571257CONFLICTT -> Q (in Ref. 1; AAC50213/AAC50214/ AAC50215 and 7; AAA52034).might get lost (downstream of altered splice site)
14411499DOMAINCollagen-like 8.might get lost (downstream of altered splice site)
15011736PROPEPC-terminal propeptide. /FTId=PRO_0000005841.might get lost (downstream of altered splice site)
15411735DOMAINFibrillar collagen NC1.might get lost (downstream of altered splice site)
15521552CONFLICTE -> R (in Ref. 7; AAA52034).might get lost (downstream of altered splice site)
15711571DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15711571DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15771577DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15771577DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15941594DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
15941594DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16031603DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16031603DISULFIDInterchain (By similarity).might get lost (downstream of altered splice site)
16041604CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
16121612DISULFIDBy similarity.might get lost (downstream of altered splice site)
16551655DISULFIDBy similarity.might get lost (downstream of altered splice site)
16891689DISULFIDBy similarity.might get lost (downstream of altered splice site)
17331733DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5148 / 5148
position (AA) of stopcodon in wt / mu AA sequence 1716 / 1716
position of stopcodon in wt / mu cDNA 5376 / 5376
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 229 / 229
chromosome 6
strand -1
last intron/exon boundary 5236
theoretical NMD boundary in CDS 4957
length of CDS 5148
coding sequence (CDS) position 2360
cDNA position
(for ins/del: last normal base / first normal base)		 2588
gDNA position
(for ins/del: last normal base / first normal base)		 17966
chromosomal position
(for ins/del: last normal base / first normal base)		 33142311
original gDNA sequence snippet TGGCTATCCTGGACGTCAGGGACCCAAGGTGATGCCATGCC
altered gDNA sequence snippet TGGCTATCCTGGACGTCAGGAACCCAAGGTGATGCCATGCC
original cDNA sequence snippet TGGCTATCCTGGACGTCAGGGACCCAAGGGGTCCCTAGGAT
altered cDNA sequence snippet TGGCTATCCTGGACGTCAGGAACCCAAGGGGTCCCTAGGAT
wildtype AA sequence MERCSRCHRL LLLLPLVLGL SAAPGWAGAP PVDVLRALRF PSLPDGVRRA KGICPADVAY
RVARPAQLSA PTRQLFPGGF PKDFSLLTVV RTRPGLQAPL LTLYSAQGVR QLGLELGRPV
RFLYEDQTGR PQPPSQPVFR GLSLADGKWH RVAVAVKGQS VTLIVDCKKR VTRPLPRSAR
PVLDTHGVII FGARILDEEV FEGDVQELAI VPGVQAAYES CEQKELECEG GQRERPQNQQ
PHRAQRSPQQ QPSRLHRPQN QEPQSQPTES LYYDYEPPYY DVMTTGTTPD YQEQTDLQVP
PTADRFQAEE YGEGGTDPPE GPYDYTYGYG DDYREETELG PALSAETAHS GAAAHGPRGL
KGEKGEPAVL EPGMLVEGPP GPEGPAGLIG PPGIQGNPGP VGDPGERGPP GRAGLPGSDG
APGPPGTSLM LPFRFGSGGG DKGPVVAAQE AQAQAILQQA RLALRGPPGP MGYTGRPGPL
GQPGSPGLKG ESGDLGPQGP RGPQGLTGPP GKAGRRGRAG ADGARGMPGD PGVKGDRGFD
GLPGLPGEKG HRGDTGAQGL PGPPGEDGER GDDGEIGPRG LPGESGPRGL LGPKGPPGIP
GPPGVRGMDG PQGPKGSLGP QGEPGPPGQQ GTPGTQGLPG PQGAIGPHGE KGPQGKPGLP
GMPGSDGPPG HPGKEGPPGT KGNQGPSGPQ GPLGYPGPRG VKGVDGIRGL KGHKGEKGED
GFPGFKGDIG VKGDRGEVGV PGSRGEDGPE GPKGRTGPTG DPGPPGLMGE KGKLGVPGLP
GYPGRQGPKG SLGFPGFPGA SGEKGARGLS GKSGPRGERG PTGPRGQRGP RGATGKSGAK
GTSGGDGPHG PPGERGLPGP QGPNGFPGPK GPPGPPGKDG LPGHPGQRGE VGFQGKTGPP
GPPGVVGPQG AAGETGPMGE RGHPGPPGPP GEQGLPGTAG KEGTKGDPGP PGAPGKDGPA
GLRGFPGERG LPGTAGGPGL KGNEGPSGPP GPAGSPGERG AAGSGGPIGP PGRPGPQGPP
GAAGEKGVPG EKGPIGPTGR DGVQGPVGLP GPAGPPGVAG EDGDKGEVGD PGQKGTKGNK
GEHGPPGPPG PIGPVGQPGA AGADGEPGAR GPQGHFGAKG DEGTRGFNGP PGPIGLQGLP
GPSGEKGETG DVGPMGPPGP PGPRGPAGPN GADGPQGPPG GVGNLGPPGE KGEPGESGSP
GIQGEPGVKG PRGERGEKGE SGQPGEPGPP GPKGPTGDDG PKGNPGPVGF PGDPGPPGEG
GPRGQDGAKG DRGEDGEPGQ PGSPGPTGEN GPPGPLGKRG PAGSPGSEGR QGGKGAKGDP
GAIGAPGKTG PVGPAGPAGK PGPDGLRGLP GSVGQQGRPG ATGQAGPPGP VGPPGLPGLR
GDAGAKGEKG HPGLIGLIGP PGEQGEKGDR GLPGPQGSPG QKGEMGIPGA SGPIGPGGPP
GLPGPAGPKG AKGATGPGGP KGEKGVQGPP GHPGPPGEVI QPLPIQMPKK TRRSVDGSRL
MQEDEAIPTG GAPGSPGGLE EIFGSLDSLR EEIEQMRRPT GTQDSPARTC QDLKLCHPEL
PDGEYWVDPN QGCARDAFRV FCNFTAGGET CVTPRDDVTQ FSYVDSEGSP VGVVQLTFLR
LLSVSAHQDV SYPCSGAARD GPLRLRGANE DELSPETSPY VKEFRDGCQT QQGRTVLEVR
TPVLEQLPVL DASFSDLGAP PRRGGVLLGP VCFMG*
mutated AA sequence MERCSRCHRL LLLLPLVLGL SAAPGWAGAP PVDVLRALRF PSLPDGVRRA KGICPADVAY
RVARPAQLSA PTRQLFPGGF PKDFSLLTVV RTRPGLQAPL LTLYSAQGVR QLGLELGRPV
RFLYEDQTGR PQPPSQPVFR GLSLADGKWH RVAVAVKGQS VTLIVDCKKR VTRPLPRSAR
PVLDTHGVII FGARILDEEV FEGDVQELAI VPGVQAAYES CEQKELECEG GQRERPQNQQ
PHRAQRSPQQ QPSRLHRPQN QEPQSQPTES LYYDYEPPYY DVMTTGTTPD YQEQTDLQVP
PTADRFQAEE YGEGGTDPPE GPYDYTYGYG DDYREETELG PALSAETAHS GAAAHGPRGL
KGEKGEPAVL EPGMLVEGPP GPEGPAGLIG PPGIQGNPGP VGDPGERGPP GRAGLPGSDG
APGPPGTSLM LPFRFGSGGG DKGPVVAAQE AQAQAILQQA RLALRGPPGP MGYTGRPGPL
GQPGSPGLKG ESGDLGPQGP RGPQGLTGPP GKAGRRGRAG ADGARGMPGD PGVKGDRGFD
GLPGLPGEKG HRGDTGAQGL PGPPGEDGER GDDGEIGPRG LPGESGPRGL LGPKGPPGIP
GPPGVRGMDG PQGPKGSLGP QGEPGPPGQQ GTPGTQGLPG PQGAIGPHGE KGPQGKPGLP
GMPGSDGPPG HPGKEGPPGT KGNQGPSGPQ GPLGYPGPRG VKGVDGIRGL KGHKGEKGED
GFPGFKGDIG VKGDRGEVGV PGSRGEDGPE GPKGRTGPTG DPGPPGLMGE KGKLGVPGLP
GYPGRQEPKG SLGFPGFPGA SGEKGARGLS GKSGPRGERG PTGPRGQRGP RGATGKSGAK
GTSGGDGPHG PPGERGLPGP QGPNGFPGPK GPPGPPGKDG LPGHPGQRGE VGFQGKTGPP
GPPGVVGPQG AAGETGPMGE RGHPGPPGPP GEQGLPGTAG KEGTKGDPGP PGAPGKDGPA
GLRGFPGERG LPGTAGGPGL KGNEGPSGPP GPAGSPGERG AAGSGGPIGP PGRPGPQGPP
GAAGEKGVPG EKGPIGPTGR DGVQGPVGLP GPAGPPGVAG EDGDKGEVGD PGQKGTKGNK
GEHGPPGPPG PIGPVGQPGA AGADGEPGAR GPQGHFGAKG DEGTRGFNGP PGPIGLQGLP
GPSGEKGETG DVGPMGPPGP PGPRGPAGPN GADGPQGPPG GVGNLGPPGE KGEPGESGSP
GIQGEPGVKG PRGERGEKGE SGQPGEPGPP GPKGPTGDDG PKGNPGPVGF PGDPGPPGEG
GPRGQDGAKG DRGEDGEPGQ PGSPGPTGEN GPPGPLGKRG PAGSPGSEGR QGGKGAKGDP
GAIGAPGKTG PVGPAGPAGK PGPDGLRGLP GSVGQQGRPG ATGQAGPPGP VGPPGLPGLR
GDAGAKGEKG HPGLIGLIGP PGEQGEKGDR GLPGPQGSPG QKGEMGIPGA SGPIGPGGPP
GLPGPAGPKG AKGATGPGGP KGEKGVQGPP GHPGPPGEVI QPLPIQMPKK TRRSVDGSRL
MQEDEAIPTG GAPGSPGGLE EIFGSLDSLR EEIEQMRRPT GTQDSPARTC QDLKLCHPEL
PDGEYWVDPN QGCARDAFRV FCNFTAGGET CVTPRDDVTQ FSYVDSEGSP VGVVQLTFLR
LLSVSAHQDV SYPCSGAARD GPLRLRGANE DELSPETSPY VKEFRDGCQT QQGRTVLEVR
TPVLEQLPVL DASFSDLGAP PRRGGVLLGP VCFMG*
speed 1.19 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