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 ENST00000374713
Genbank transcript ID N/A
UniProt peptide P13942
alteration type single base exchange
alteration region CDS
DNA changes c.2282G>A
cDNA.2510G>A
g.17966G>A
AA changes G761E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 761
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      761VPGLPGYPGRQGPKGSLGFPGFPG
mutated  not conserved    761VPGLPGYPGRQEPKGSLGFPGFP
Ptroglodytes  all identical  ENSPTRG00000018033  770VPGLPGYPGRQGPKGSLGFPGFP
Mmulatta  all identical  ENSMMUG00000003850  807VPGLPGYPGRQGPKGSLGFPGFP
Fcatus  all identical  ENSFCAG00000004005  435VPGLPGYPGRQGPKGSLGFPGFP
Mmusculus  all identical  ENSMUSG00000024330  761VPGLPGYPGRQGPKGSLGFPGFP
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 5070 / 5070
position (AA) of stopcodon in wt / mu AA sequence 1690 / 1690
position of stopcodon in wt / mu cDNA 5298 / 5298
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 5158
theoretical NMD boundary in CDS 4879
length of CDS 5070
coding sequence (CDS) position 2282
cDNA position
(for ins/del: last normal base / first normal base)		 2510
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 QEPQSQEQTD LQVPPTADRF QAEEYGEGGT DPPEGPYDYT
YGYGDDYREE TELGPALSAE TAHSGAAAHG PRGLKGEKGE PAVLEPGMLV EGPPGPEGPA
GLIGPPGIQG NPGPVGDPGE RGPPGRAGLP GSDGAPGPPG TSLMLPFRFG SGGGDKGPVV
AAQEAQAQAI LQQARLALRG PPGPMGYTGR PGPLGQPGSP GLKGESGDLG PQGPRGPQGL
TGPPGKAGRR GRAGADGARG MPGDPGVKGD RGFDGLPGLP GEKGHRGDTG AQGLPGPPGE
DGERGDDGEI GPRGLPGESG PRGLLGPKGP PGIPGPPGVR GMDGPQGPKG SLGPQGEPGP
PGQQGTPGTQ GLPGPQGAIG PHGEKGPQGK PGLPGMPGSD GPPGHPGKEG PPGTKGNQGP
SGPQGPLGYP GPRGVKGVDG IRGLKGHKGE KGEDGFPGFK GDIGVKGDRG EVGVPGSRGE
DGPEGPKGRT GPTGDPGPPG LMGEKGKLGV PGLPGYPGRQ GPKGSLGFPG FPGASGEKGA
RGLSGKSGPR GERGPTGPRG QRGPRGATGK SGAKGTSGGD GPHGPPGERG LPGPQGPNGF
PGPKGPPGPP GKDGLPGHPG QRGEVGFQGK TGPPGPPGVV GPQGAAGETG PMGERGHPGP
PGPPGEQGLP GTAGKEGTKG DPGPPGAPGK DGPAGLRGFP GERGLPGTAG GPGLKGNEGP
SGPPGPAGSP GERGAAGSGG PIGPPGRPGP QGPPGAAGEK GVPGEKGPIG PTGRDGVQGP
VGLPGPAGPP GVAGEDGDKG EVGDPGQKGT KGNKGEHGPP GPPGPIGPVG QPGAAGADGE
PGARGPQGHF GAKGDEGTRG FNGPPGPIGL QGLPGPSGEK GETGDVGPMG PPGPPGPRGP
AGPNGADGPQ GPPGGVGNLG PPGEKGEPGE SGSPGIQGEP GVKGPRGERG EKGESGQPGE
PGPPGPKGPT GDDGPKGNPG PVGFPGDPGP PGEGGPRGQD GAKGDRGEDG EPGQPGSPGP
TGENGPPGPL GKRGPAGSPG SEGRQGGKGA KGDPGAIGAP GKTGPVGPAG PAGKPGPDGL
RGLPGSVGQQ GRPGATGQAG PPGPVGPPGL PGLRGDAGAK GEKGHPGLIG LIGPPGEQGE
KGDRGLPGPQ GSPGQKGEMG IPGASGPIGP GGPPGLPGPA GPKGAKGATG PGGPKGEKGV
QGPPGHPGPP GEVIQPLPIQ MPKKTRRSVD GSRLMQEDEA IPTGGAPGSP GGLEEIFGSL
DSLREEIEQM RRPTGTQDSP ARTCQDLKLC HPELPDGEYW VDPNQGCARD AFRVFCNFTA
GGETCVTPRD DVTQFSYVDS EGSPVGVVQL TFLRLLSVSA HQDVSYPCSG AARDGPLRLR
GANEDELSPE TSPYVKEFRD GCQTQQGRTV LEVRTPVLEQ LPVLDASFSD LGAPPRRGGV
LLGPVCFMG*
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 QEPQSQEQTD LQVPPTADRF QAEEYGEGGT DPPEGPYDYT
YGYGDDYREE TELGPALSAE TAHSGAAAHG PRGLKGEKGE PAVLEPGMLV EGPPGPEGPA
GLIGPPGIQG NPGPVGDPGE RGPPGRAGLP GSDGAPGPPG TSLMLPFRFG SGGGDKGPVV
AAQEAQAQAI LQQARLALRG PPGPMGYTGR PGPLGQPGSP GLKGESGDLG PQGPRGPQGL
TGPPGKAGRR GRAGADGARG MPGDPGVKGD RGFDGLPGLP GEKGHRGDTG AQGLPGPPGE
DGERGDDGEI GPRGLPGESG PRGLLGPKGP PGIPGPPGVR GMDGPQGPKG SLGPQGEPGP
PGQQGTPGTQ GLPGPQGAIG PHGEKGPQGK PGLPGMPGSD GPPGHPGKEG PPGTKGNQGP
SGPQGPLGYP GPRGVKGVDG IRGLKGHKGE KGEDGFPGFK GDIGVKGDRG EVGVPGSRGE
DGPEGPKGRT GPTGDPGPPG LMGEKGKLGV PGLPGYPGRQ EPKGSLGFPG FPGASGEKGA
RGLSGKSGPR GERGPTGPRG QRGPRGATGK SGAKGTSGGD GPHGPPGERG LPGPQGPNGF
PGPKGPPGPP GKDGLPGHPG QRGEVGFQGK TGPPGPPGVV GPQGAAGETG PMGERGHPGP
PGPPGEQGLP GTAGKEGTKG DPGPPGAPGK DGPAGLRGFP GERGLPGTAG GPGLKGNEGP
SGPPGPAGSP GERGAAGSGG PIGPPGRPGP QGPPGAAGEK GVPGEKGPIG PTGRDGVQGP
VGLPGPAGPP GVAGEDGDKG EVGDPGQKGT KGNKGEHGPP GPPGPIGPVG QPGAAGADGE
PGARGPQGHF GAKGDEGTRG FNGPPGPIGL QGLPGPSGEK GETGDVGPMG PPGPPGPRGP
AGPNGADGPQ GPPGGVGNLG PPGEKGEPGE SGSPGIQGEP GVKGPRGERG EKGESGQPGE
PGPPGPKGPT GDDGPKGNPG PVGFPGDPGP PGEGGPRGQD GAKGDRGEDG EPGQPGSPGP
TGENGPPGPL GKRGPAGSPG SEGRQGGKGA KGDPGAIGAP GKTGPVGPAG PAGKPGPDGL
RGLPGSVGQQ GRPGATGQAG PPGPVGPPGL PGLRGDAGAK GEKGHPGLIG LIGPPGEQGE
KGDRGLPGPQ GSPGQKGEMG IPGASGPIGP GGPPGLPGPA GPKGAKGATG PGGPKGEKGV
QGPPGHPGPP GEVIQPLPIQ MPKKTRRSVD GSRLMQEDEA IPTGGAPGSP GGLEEIFGSL
DSLREEIEQM RRPTGTQDSP ARTCQDLKLC HPELPDGEYW VDPNQGCARD AFRVFCNFTA
GGETCVTPRD DVTQFSYVDS EGSPVGVVQL TFLRLLSVSA HQDVSYPCSG AARDGPLRLR
GANEDELSPE TSPYVKEFRD GCQTQQGRTV LEVRTPVLEQ LPVLDASFSD LGAPPRRGGV
LLGPVCFMG*
speed 0.76 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