Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000319550
Querying Taster for transcript #2: ENST00000327673
Querying Taster for transcript #3: ENST00000243222
MT speed 4.35 s - this script 7.068816 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COL10A1disease_causing_automatic0.999999999316074simple_aae0Y597Csingle base exchangers111033554show file
COL10A1disease_causing_automatic0.999999999316074simple_aae0Y597Csingle base exchangers111033554show file
NT5DC1disease_causing_automatic1without_aae0single base exchangers111033554show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999316074 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983417)
  • known disease mutation: rs17480 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116441489T>CN/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.1790A>G
cDNA.2198A>G
g.38422A>G
AA changes Y597C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS
597
frameshift no
known variant Reference ID: rs111033554
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17480 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6691
4.7841
(flanking)4.7841
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 increased38433wt: 0.7705 / mu: 0.8362 (marginal change - not scored)wt: CAGGAATATACTATTTTTCATACCACGTGCATGTGAAAGGG
mu: CAGGAATATGCTATTTTTCATACCACGTGCATGTGAAAGGG
 tcat|ACCA
distance from splice site 1301
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      597TGIFTCQIPGIYYFSYHVHVKGTH
mutated  not conserved    597TGIFTCQIPGICYFS
Ptroglodytes  all identical  ENSPTRG00000018524  597TGIFTCRIPGIYYFS
Mmulatta  all identical  ENSMMUG00000014642  597TGIFTCRIPGIYYFS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000039462  597SGIFTCKIPGIYYFS
Ggallus  all identical  ENSGALG00000014965  590TGIFTCRIPGLYYF
Trubripes  all identical  ENSTRUG00000006358  530SGIFSCQIPGLY
Drerio  all identical  ENSDARG00000054753  572TGIFTCHIPGIYYFSYSMHVNG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000033031  532SGLYYFSYHVHVKGT
protein features
start (aa)end (aa)featuredetails 
520680REGIONNonhelical region (NC1).lost
547680DOMAINC1q.lost
595616STRANDlost
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 1790
cDNA position
(for ins/del: last normal base / first normal base)
2198
gDNA position
(for ins/del: last normal base / first normal base)
38422
chromosomal position
(for ins/del: last normal base / first normal base)
116441489
original gDNA sequence snippet TTGTCAGATACCAGGAATATACTATTTTTCATACCACGTGC
altered gDNA sequence snippet TTGTCAGATACCAGGAATATGCTATTTTTCATACCACGTGC
original cDNA sequence snippet TTGTCAGATACCAGGAATATACTATTTTTCATACCACGTGC
altered cDNA sequence snippet TTGTCAGATACCAGGAATATGCTATTTTTCATACCACGTGC
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 CQIPGICYFS
YHVHVKGTHV WVGLYKNGTP VMYTYDEYTK GYLDQASGSA IIDLTENDQV WLQLPNAESN
GLYSSEYVHS SFSGFLVAPM *
speed 1.61 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
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999316074 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM983417)
  • known disease mutation: rs17480 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116441489T>CN/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.1790A>G
cDNA.1886A>G
g.38422A>G
AA changes Y597C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS
597
frameshift no
known variant Reference ID: rs111033554
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17480 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6691
4.7841
(flanking)4.7841
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 increased38433wt: 0.7705 / mu: 0.8362 (marginal change - not scored)wt: CAGGAATATACTATTTTTCATACCACGTGCATGTGAAAGGG
mu: CAGGAATATGCTATTTTTCATACCACGTGCATGTGAAAGGG
 tcat|ACCA
distance from splice site 1404
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      597TGIFTCQIPGIYYFSYHVHVKGTH
mutated  not conserved    597TGIFTCQIPGICYFS
Ptroglodytes  all identical  ENSPTRG00000018524  597TGIFTCRIPGIYYFS
Mmulatta  all identical  ENSMMUG00000014642  597TGIFTCRIPGIYYFS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000039462  597SGIFTCKIPGIYYFS
Ggallus  all identical  ENSGALG00000014965  590TGIFTCRIPGLYYF
Trubripes  all identical  ENSTRUG00000006358  530SGIFSCQIPGLY
Drerio  all identical  ENSDARG00000054753  572TGIFTCHIPGIYYFSYSMHVNG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000033031  532SGLYYFSYHVHVKGT
protein features
start (aa)end (aa)featuredetails 
520680REGIONNonhelical region (NC1).lost
547680DOMAINC1q.lost
595616STRANDlost
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 1790
cDNA position
(for ins/del: last normal base / first normal base)
1886
gDNA position
(for ins/del: last normal base / first normal base)
38422
chromosomal position
(for ins/del: last normal base / first normal base)
116441489
original gDNA sequence snippet TTGTCAGATACCAGGAATATACTATTTTTCATACCACGTGC
altered gDNA sequence snippet TTGTCAGATACCAGGAATATGCTATTTTTCATACCACGTGC
original cDNA sequence snippet TTGTCAGATACCAGGAATATACTATTTTTCATACCACGTGC
altered cDNA sequence snippet TTGTCAGATACCAGGAATATGCTATTTTTCATACCACGTGC
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 CQIPGICYFS
YHVHVKGTHV WVGLYKNGTP VMYTYDEYTK GYLDQASGSA IIDLTENDQV WLQLPNAESN
GLYSSEYVHS SFSGFLVAPM *
speed 1.48 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
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM983417)
  • known disease mutation: rs17480 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116441489T>CN/A show variant in all transcripts   IGV
HGNC symbol NT5DC1
Ensembl transcript ID ENST00000319550
Genbank transcript ID NM_152729
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.19478T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs111033554
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17480 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983417)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6691
4.7841
(flanking)4.7841
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased19476wt: 0.6409 / mu: 0.6629 (marginal change - not scored)wt: AAAATAGTATATTCC
mu: AAAATAGCATATTCC
 AATA|gtat
distance from splice site 2381
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 83 / 83
chromosome 6
strand 1
last intron/exon boundary 1335
theoretical NMD boundary in CDS 1202
length of CDS 1368
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)
N/A
gDNA position
(for ins/del: last normal base / first normal base)
19478
chromosomal position
(for ins/del: last normal base / first normal base)
116441489
original gDNA sequence snippet GCACGTGGTATGAAAAATAGTATATTCCTGGTATCTGACAA
altered gDNA sequence snippet GCACGTGGTATGAAAAATAGCATATTCCTGGTATCTGACAA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MAQHFSLAAC DVVGFDLDHT LCRYNLPESA PLIYNSFAQF LVKEKGYDKE LLNVTPEDWD
FCCKGLALDL EDGNFLKLAN NGTVLRASHG TKMMTPEVLA EAYGKKEWKH FLSDTGMACR
SGKYYFYDNY FDLPGALLCA RVVDYLTKLN NGQKTFDFWK DIVAAIQHNY KMSAFKENCG
IYFPEIKRDP GRYLHSCPES VKKWLRQLKN AGKILLLITS SHSDYCRLLC EYILGNDFTD
LFDIVITNAL KPGFFSHLPS QRPFRTLEND EEQEALPSLD KPGWYSQGNA VHLYELLKKM
TGKPEPKVVY FGDSMHSDIF PARHYSNWET VLILEELRGD EGTRSQRPEE SEPLEKKGKY
EGPKAKPLNT SSKKWGSFFI DSVLGLENTE DSLVYTWSCK RISTYSTIAI PSIEAIAELP
LDYKFTRFSS SNSKTAGYYP NPPLVLSSDE TLISK*
mutated AA sequence N/A
speed 1.26 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
back to results table

Problems