Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999952853343 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993117)
  • known disease mutation: rs17124 (pathogenic)
  • protein features (might be) affected
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:33139540G>AN/A show variant in all transcripts   IGV
HGNC symbol COL11A2
Ensembl transcript ID ENST00000361917
Genbank transcript ID NM_080679
UniProt peptide P13942
alteration type single base exchange
alteration region CDS
DNA changes c.2779C>T
cDNA.3007C>T
g.20737C>T
AA changes R927C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 927
frameshift no
known variant Reference ID: rs121912947
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17124 (pathogenic for Deafness, autosomal dominant 13|not provided|Rare genetic deafness) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993117)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993117)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993117)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7951
1.0281
(flanking)0.3691
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 increased20733wt: 0.6427 / mu: 0.6680 (marginal change - not scored)wt: GGGGGACCCATTGGTCCGCCAGGGCGCCCAGGCCCGCAGGG
mu: GGGGGACCCATTGGTCCGCCAGGGTGCCCAGGCCCGCAGGG		 gcca|GGGC
Donor marginally increased20742wt: 0.6115 / mu: 0.6703 (marginal change - not scored)wt: CGCCCAGGCCCGCAG
mu: TGCCCAGGCCCGCAG		 CCCA|ggcc
distance from splice site 51
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      927AGSGGPIGPPGRPGPQGPPGAAGE
mutated  not conserved    927AGSGGPIGPPGCPGPQGPPGAAG
Ptroglodytes  all identical  ENSPTRG00000018033  996AGSGGPIGPPGRPGPQGPPGAAG
Mmulatta  all identical  ENSMMUG00000003850  1033AGSGGPIGPPGRPGPQGPPGAAG
Fcatus  all identical  ENSFCAG00000004005  661AGSGGPIGPPGRPGPQGPPGAAG
Mmusculus  all identical  ENSMUSG00000024330  987AGSGGPIGPPGRPGPQGPPGAAG
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000005534  1101SGTAGPVGPPGRPG
Drerio  all identical  ENSDARG00000012422  1280AGTAGPVGPPGRPGPQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000012724  1264PGQGGPIGPPGRPGPQGPAGAAG
protein features
start (aa)end (aa)featuredetails 
4871500REGIONTriple-helical region.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4890 / 4890
position (AA) of stopcodon in wt / mu AA sequence 1630 / 1630
position of stopcodon in wt / mu cDNA 5118 / 5118
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 4978
theoretical NMD boundary in CDS 4699
length of CDS 4890
coding sequence (CDS) position 2779
cDNA position
(for ins/del: last normal base / first normal base)		 3007
gDNA position
(for ins/del: last normal base / first normal base)		 20737
chromosomal position
(for ins/del: last normal base / first normal base)		 33139540
original gDNA sequence snippet GACCCATTGGTCCGCCAGGGCGCCCAGGCCCGCAGGGTCCC
altered gDNA sequence snippet GACCCATTGGTCCGCCAGGGTGCCCAGGCCCGCAGGGTCCC
original cDNA sequence snippet GACCCATTGGTCCGCCAGGGCGCCCAGGCCCGCAGGGTCCC
altered cDNA sequence snippet GACCCATTGGTCCGCCAGGGTGCCCAGGCCCGCAGGGTCCC
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 QEPQSQAAHG 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 QEPQSQAAHG 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 PIGPPGCPGP 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 1.28 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