Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999416 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940289)
  • known disease mutation: rs17466 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116441438A>GN/A show variant in all transcripts   IGV
HGNC symbol COL10A1
Ensembl transcript ID ENST00000243222
Genbank transcript ID NM_000493
UniProt peptide Q03692
alteration type single base exchange
alteration region CDS
DNA changes c.1841T>C
cDNA.1937T>C
g.38473T>C
AA changes L614P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 614
frameshift no
known variant Reference ID: rs111033545
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17466 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940289)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940289)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940289)
regulatory features H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.1610.366
4.4460.996
(flanking)1.9530.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased38474wt: 0.61 / mu: 0.80wt: GGCCTGTATAAGAAT
mu: GGCCCGTATAAGAAT		 CCTG|tata
Donor gained384680.38mu: TGGGTAGGCCCGTAT GGTA|ggcc
distance from splice site 1353
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      614VHVKGTHVWVGLYKNGTPVMYTYD
mutated  not conserved    614VHVKGTHVWVGPYKNGTPVMYTY
Ptroglodytes  all identical  ENSPTRG00000018524  614VHVKGTHVWVGLYKNGTPVMYTY
Mmulatta  all identical  ENSMMUG00000014642  614VHVKGTHVWVGLYKNGTPIMYTY
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000039462  614VHVKGTHVWVGLYKNGTPTMYTY
Ggallus  all identical  ENSGALG00000014965  608VHAKGTNVWVALYKNGSPVMYTY
Trubripes  all identical  ENSTRUG00000006358  549MHVNGGNALVALYKNDDAVLYSY
Drerio  all identical  ENSDARG00000054753  589ANALVALYKNGDPVMFTY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000033031  549VHVKGTNLWIALYKNGNPIMYTY
protein features
start (aa)end (aa)featuredetails 
520680REGIONNonhelical region (NC1).lost
547680DOMAINC1q.lost
595616STRANDlost
619626STRANDmight get lost (downstream of altered splice site)
634634METALCalcium.might get lost (downstream of altered splice site)
634644STRANDmight get lost (downstream of altered splice site)
649653STRANDmight get lost (downstream of altered splice site)
659663STRANDmight get lost (downstream of altered splice site)
666668STRANDmight get lost (downstream of altered splice site)
671679STRANDmight get lost (downstream of altered splice site)
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 2139 / 2139
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 97 / 97
chromosome 6
strand -1
last intron/exon boundary 251
theoretical NMD boundary in CDS 104
length of CDS 2043
coding sequence (CDS) position 1841
cDNA position
(for ins/del: last normal base / first normal base)		 1937
gDNA position
(for ins/del: last normal base / first normal base)		 38473
chromosomal position
(for ins/del: last normal base / first normal base)		 116441438
original gDNA sequence snippet GACTCATGTTTGGGTAGGCCTGTATAAGAATGGCACCCCTG
altered gDNA sequence snippet GACTCATGTTTGGGTAGGCCCGTATAAGAATGGCACCCCTG
original cDNA sequence snippet GACTCATGTTTGGGTAGGCCTGTATAAGAATGGCACCCCTG
altered cDNA sequence snippet GACTCATGTTTGGGTAGGCCCGTATAAGAATGGCACCCCTG
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 WVGPYKNGTP VMYTYDEYTK GYLDQASGSA IIDLTENDQV WLQLPNAESN
GLYSSEYVHS SFSGFLVAPM *
speed 1.02 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