Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999724019723      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs17477 (probable pathogenic)
  • known disease mutation at this position (HGMD CM960316)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116441268A>GN/A show variant in all transcripts   IGV
HGNC symbol COL10A1
Ensembl transcript ID ENST00000327673
Genbank transcript ID N/A
UniProt peptide Q03692
alteration type single base exchange
alteration region CDS
DNA changes c.2011T>C
cDNA.2419T>C
g.38643T>C
AA changes S671P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 671
frameshift no
known variant Reference ID: rs111033552
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs17477 (probable pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960316)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960316)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960316)
regulatory features H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.311
1.1310.993
(flanking)-0.1870.965
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 increased38644wt: 0.2905 / mu: 0.3153 (marginal change - not scored)wt: CTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTGG
mu: CTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTGG		 cctc|TTTC
Acc marginally increased38650wt: 0.9043 / mu: 0.9148 (marginal change - not scored)wt: GTATGTCCACTCCTCTTTCTCAGGATTCCTAGTGGCTCCAA
mu: GTATGTCCACTCCCCTTTCTCAGGATTCCTAGTGGCTCCAA		 tctc|AGGA
Acc gained386350.34mu: CCTATACTCCTCTGAGTATGTCCACTCCCCTTTCTCAGGAT atgt|CCAC
distance from splice site 1080
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      671NGLYSSEYVHSSFSGFLVAPM*
mutated  not conserved    671GLYSSEYVHSPFSGFLVAPM
Ptroglodytes  all identical  ENSPTRG00000018524  671GLYSSEYVHSSFSGFLVAPM
Mmulatta  all identical  ENSMMUG00000014642  671GLYSSEYVHSSFSGFLVAPM
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000039462  671GLYSSEYVHSSFSGFLVAPM
Ggallus  all identical  ENSGALG00000014965  665NGLYSSEYVHSSFSGFLFA
Trubripes  all identical  ENSTRUG00000006358  606NGIFADHNVHCSFSGFLIASM
Drerio  all identical  ENSDARG00000054753  646VHCSFSGFLIA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000033031  606NGLYSSDYIHSSFSGFL
protein features
start (aa)end (aa)featuredetails 
520680REGIONNonhelical region (NC1).lost
547680DOMAINC1q.lost
666668STRANDmight get lost (downstream of altered splice site)
671679STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2043 / 2043
position (AA) of stopcodon in wt / mu AA sequence 681 / 681
position of stopcodon in wt / mu cDNA 2451 / 2451
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 409 / 409
chromosome 6
strand -1
last intron/exon boundary 563
theoretical NMD boundary in CDS 104
length of CDS 2043
coding sequence (CDS) position 2011
cDNA position
(for ins/del: last normal base / first normal base)		 2419
gDNA position
(for ins/del: last normal base / first normal base)		 38643
chromosomal position
(for ins/del: last normal base / first normal base)		 116441268
original gDNA sequence snippet CCTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTG
altered gDNA sequence snippet CCTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTG
original cDNA sequence snippet CCTCTGAGTATGTCCACTCCTCTTTCTCAGGATTCCTAGTG
altered cDNA sequence snippet CCTCTGAGTATGTCCACTCCCCTTTCTCAGGATTCCTAGTG
wildtype AA sequence MLPQIPFLLL VSLNLVHGVF YAERYQMPTG IKGPLPNTKT QFFIPYTIKS KGIAVRGEQG
TPGPPGPAGP RGHPGPSGPP GKPGYGSPGL QGEPGLPGPP GPSAVGKPGV PGLPGKPGER
GPYGPKGDVG PAGLPGPRGP PGPPGIPGPA GISVPGKPGQ QGPTGAPGPR GFPGEKGAPG
VPGMNGQKGE MGYGAPGRPG ERGLPGPQGP TGPSGPPGVG KRGENGVPGQ PGIKGDRGFP
GEMGPIGPPG PQGPPGERGP EGIGKPGAAG APGQPGIPGT KGLPGAPGIA GPPGPPGFGK
PGLPGLKGER GPAGLPGGPG AKGEQGPAGL PGKPGLTGPP GNMGPQGPKG IPGSHGLPGP
KGETGPAGPA GYPGAKGERG SPGSDGKPGY PGKPGLDGPK GNPGLPGPKG DPGVGGPPGL
PGPVGPAGAK GMPGHNGEAG PRGAPGIPGT RGPIGPPGIP GFPGSKGDPG SPGPPGPAGI
ATKGLNGPTG PPGPPGPRGH SGEPGLPGPP GPPGPPGQAV MPEGFIKAGQ RPSLSGTPLV
SANQGVTGMP VSAFTVILSK AYPAIGTPIP FDKILYNRQQ HYDPRTGIFT CQIPGIYYFS
YHVHVKGTHV WVGLYKNGTP VMYTYDEYTK GYLDQASGSA IIDLTENDQV WLQLPNAESN
GLYSSEYVHS SFSGFLVAPM *
mutated AA sequence MLPQIPFLLL VSLNLVHGVF YAERYQMPTG IKGPLPNTKT QFFIPYTIKS KGIAVRGEQG
TPGPPGPAGP RGHPGPSGPP GKPGYGSPGL QGEPGLPGPP GPSAVGKPGV PGLPGKPGER
GPYGPKGDVG PAGLPGPRGP PGPPGIPGPA GISVPGKPGQ QGPTGAPGPR GFPGEKGAPG
VPGMNGQKGE MGYGAPGRPG ERGLPGPQGP TGPSGPPGVG KRGENGVPGQ PGIKGDRGFP
GEMGPIGPPG PQGPPGERGP EGIGKPGAAG APGQPGIPGT KGLPGAPGIA GPPGPPGFGK
PGLPGLKGER GPAGLPGGPG AKGEQGPAGL PGKPGLTGPP GNMGPQGPKG IPGSHGLPGP
KGETGPAGPA GYPGAKGERG SPGSDGKPGY PGKPGLDGPK GNPGLPGPKG DPGVGGPPGL
PGPVGPAGAK GMPGHNGEAG PRGAPGIPGT RGPIGPPGIP GFPGSKGDPG SPGPPGPAGI
ATKGLNGPTG PPGPPGPRGH SGEPGLPGPP GPPGPPGQAV MPEGFIKAGQ RPSLSGTPLV
SANQGVTGMP VSAFTVILSK AYPAIGTPIP FDKILYNRQQ HYDPRTGIFT CQIPGIYYFS
YHVHVKGTHV WVGLYKNGTP VMYTYDEYTK GYLDQASGSA IIDLTENDQV WLQLPNAESN
GLYSSEYVHS PFSGFLVAPM *
speed 0.77 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