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 ENST00000374714
Genbank transcript ID N/A
UniProt peptide P13942
alteration type single base exchange
alteration region CDS
DNA changes c.3022C>T
cDNA.3250C>T
g.20737C>T
AA changes R1008C Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1008
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      1008AGSGGPIGPPGRPGPQGPPGAAGE
mutated  not conserved    1008AGSGGPIGPPGCPGPQGPPGAAG
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  1101GPPGRPGPQGPPGPAG
Drerio  all identical  ENSDARG00000012422  1280AGTAGPVGPPGRPGPQGPPGTSG
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 5133 / 5133
position (AA) of stopcodon in wt / mu AA sequence 1711 / 1711
position of stopcodon in wt / mu cDNA 5361 / 5361
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 5221
theoretical NMD boundary in CDS 4942
length of CDS 5133
coding sequence (CDS) position 3022
cDNA position
(for ins/del: last normal base / first normal base)		 3250
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 QEPQSQDPTP GEEEEILESS LLPPLEEEQT DLQVPPTADR
FQAEEYGEGG TDPPEGPYDY TYGYGDDYRE ETELGPALSA ETAHSGAAAH GPRGLKGEKG
EPAVLEPGML VEGPPGPEGP AGLIGPPGIQ GNPGPVGDPG ERGPPGRAGL PGSDGAPGPP
GTSLMLPFRF GSGGGDKGPV VAAQEAQAQA ILQQARLALR GPPGPMGYTG RPGPLGQPGS
PGLKGESGDL GPQGPRGPQG LTGPPGKAGR RGRAGADGAR GMPGDPGVKG DRGFDGLPGL
PGEKGHRGDT GAQGLPGPPG EDGERGDDGE IGPRGLPGES GPRGLLGPKG PPGIPGPPGV
RGMDGPQGPK GSLGPQGEPG PPGQQGTPGT QGLPGPQGAI GPHGEKGPQG KPGLPGMPGS
DGPPGHPGKE GPPGTKGNQG PSGPQGPLGY PGPRGVKGVD GIRGLKGHKG EKGEDGFPGF
KGDIGVKGDR GEVGVPGSRG EDGPEGPKGR TGPTGDPGPP GLMGEKGKLG VPGLPGYPGR
QGPKGSLGFP GFPGASGEKG ARGLSGKSGP RGERGPTGPR GQRGPRGATG KSGAKGTSGG
DGPHGPPGER GLPGPQGPNG FPGPKGPPGP PGKDGLPGHP GQRGEVGFQG KTGPPGPPGV
VGPQGAAGET GPMGERGHPG PPGPPGEQGL PGTAGKEGTK GDPGPPGAPG KDGPAGLRGF
PGERGLPGTA GGPGLKGNEG PSGPPGPAGS PGERGAAGSG GPIGPPGRPG PQGPPGAAGE
KGVPGEKGPI GPTGRDGVQG PVGLPGPAGP PGVAGEDGDK GEVGDPGQKG TKGNKGEHGP
PGPPGPIGPV GQPGAAGADG EPGARGPQGH FGAKGDEGTR GFNGPPGPIG LQGLPGPSGE
KGETGDVGPM GPPGPPGPRG PAGPNGADGP QGPPGGVGNL GPPGEKGEPG ESGSPGIQGE
PGVKGPRGER GEKGESGQPG EPGPPGPKGP TGDDGPKGNP GPVGFPGDPG PPGEGGPRGQ
DGAKGDRGED GEPGQPGSPG PTGENGPPGP LGKRGPAGSP GSEGRQGGKG AKGDPGAIGA
PGKTGPVGPA GPAGKPGPDG LRGLPGSVGQ QGRPGATGQA GPPGPVGPPG LPGLRGDAGA
KGEKGHPGLI GLIGPPGEQG EKGDRGLPGP QGSPGQKGEM GIPGASGPIG PGGPPGLPGP
AGPKGAKGAT GPGGPKGEKG VQGPPGHPGP PGEVIQPLPI QMPKKTRRSV DGSRLMQEDE
AIPTGGAPGS PGGLEEIFGS LDSLREEIEQ MRRPTGTQDS PARTCQDLKL CHPELPDGEY
WVDPNQGCAR DAFRVFCNFT AGGETCVTPR DDVTQFSYVD SEGSPVGVVQ LTFLRLLSVS
AHQDVSYPCS GAARDGPLRL RGANEDELSP ETSPYVKEFR DGCQTQQGRT VLEVRTPVLE
QLPVLDASFS DLGAPPRRGG VLLGPVCFMG *
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 QEPQSQDPTP GEEEEILESS LLPPLEEEQT DLQVPPTADR
FQAEEYGEGG TDPPEGPYDY TYGYGDDYRE ETELGPALSA ETAHSGAAAH GPRGLKGEKG
EPAVLEPGML VEGPPGPEGP AGLIGPPGIQ GNPGPVGDPG ERGPPGRAGL PGSDGAPGPP
GTSLMLPFRF GSGGGDKGPV VAAQEAQAQA ILQQARLALR GPPGPMGYTG RPGPLGQPGS
PGLKGESGDL GPQGPRGPQG LTGPPGKAGR RGRAGADGAR GMPGDPGVKG DRGFDGLPGL
PGEKGHRGDT GAQGLPGPPG EDGERGDDGE IGPRGLPGES GPRGLLGPKG PPGIPGPPGV
RGMDGPQGPK GSLGPQGEPG PPGQQGTPGT QGLPGPQGAI GPHGEKGPQG KPGLPGMPGS
DGPPGHPGKE GPPGTKGNQG PSGPQGPLGY PGPRGVKGVD GIRGLKGHKG EKGEDGFPGF
KGDIGVKGDR GEVGVPGSRG EDGPEGPKGR TGPTGDPGPP GLMGEKGKLG VPGLPGYPGR
QGPKGSLGFP GFPGASGEKG ARGLSGKSGP RGERGPTGPR GQRGPRGATG KSGAKGTSGG
DGPHGPPGER GLPGPQGPNG FPGPKGPPGP PGKDGLPGHP GQRGEVGFQG KTGPPGPPGV
VGPQGAAGET GPMGERGHPG PPGPPGEQGL PGTAGKEGTK GDPGPPGAPG KDGPAGLRGF
PGERGLPGTA GGPGLKGNEG PSGPPGPAGS PGERGAAGSG GPIGPPGCPG PQGPPGAAGE
KGVPGEKGPI GPTGRDGVQG PVGLPGPAGP PGVAGEDGDK GEVGDPGQKG TKGNKGEHGP
PGPPGPIGPV GQPGAAGADG EPGARGPQGH FGAKGDEGTR GFNGPPGPIG LQGLPGPSGE
KGETGDVGPM GPPGPPGPRG PAGPNGADGP QGPPGGVGNL GPPGEKGEPG ESGSPGIQGE
PGVKGPRGER GEKGESGQPG EPGPPGPKGP TGDDGPKGNP GPVGFPGDPG PPGEGGPRGQ
DGAKGDRGED GEPGQPGSPG PTGENGPPGP LGKRGPAGSP GSEGRQGGKG AKGDPGAIGA
PGKTGPVGPA GPAGKPGPDG LRGLPGSVGQ QGRPGATGQA GPPGPVGPPG LPGLRGDAGA
KGEKGHPGLI GLIGPPGEQG EKGDRGLPGP QGSPGQKGEM GIPGASGPIG PGGPPGLPGP
AGPKGAKGAT GPGGPKGEKG VQGPPGHPGP PGEVIQPLPI QMPKKTRRSV DGSRLMQEDE
AIPTGGAPGS PGGLEEIFGS LDSLREEIEQ MRRPTGTQDS PARTCQDLKL CHPELPDGEY
WVDPNQGCAR DAFRVFCNFT AGGETCVTPR DDVTQFSYVD SEGSPVGVVQ LTFLRLLSVS
AHQDVSYPCS GAARDGPLRL RGANEDELSP ETSPYVKEFR DGCQTQQGRT VLEVRTPVLE
QLPVLDASFS DLGAPPRRGG VLLGPVCFMG *
speed 1.23 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