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 0 s - this script 3.774858 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COL10A1disease_causing_automatic0.993089594532534simple_aaeaffected0G18Esingle base exchangers111033551show file
COL10A1disease_causing_automatic0.993089594532534simple_aaeaffected0G18Esingle base exchangers111033551show file
NT5DC1disease_causing_automatic1without_aae0single base exchangers111033551show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.993089594532534 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970340)
  • known disease mutation: rs17476 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116446603C>TN/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.53G>A
cDNA.461G>A
g.33308G>A
AA changes G18E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 18
frameshift no
known variant Reference ID: rs111033551
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17476 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2380.112
2.2030.996
(flanking)3.0731
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 increased33308wt: 0.6850 / mu: 0.7199 (marginal change - not scored)wt: ATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGAT
mu: ATCCTTGAACTTGGTTCATGAAGTGTTTTACGCTGAACGAT		 atgg|AGTG
Donor increased33304wt: 0.82 / mu: 0.98wt: TGGTTCATGGAGTGT
mu: TGGTTCATGAAGTGT		 GTTC|atgg
Donor marginally increased33306wt: 0.7513 / mu: 0.8469 (marginal change - not scored)wt: GTTCATGGAGTGTTT
mu: GTTCATGAAGTGTTT		 TCAT|ggag
distance from splice site 102
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      18FLLLVSLNLVHGVFYAERYQMPTG
mutated  not conserved    18FLLLVSLNLVHEVFYAERYQMPT
Ptroglodytes  all identical  ENSPTRG00000018524  18FLLLVSLNLVHGVFYAERYQTPT
Mmulatta  all identical  ENSMMUG00000014642  18FLLLVSLNLVHGVFYAERYQTPT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000039462  18FLLLMFLTLVHGMFYAERYQTPT
Ggallus  all identical  ENSGALG00000014965  18LLLLFCLNIVHGSDGYFSERYQKQS
Trubripes  no alignment  ENSTRUG00000006358  n/a
Drerio  all identical  ENSDARG00000054753  20LLLVALTAAHG----ERYVVKK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000033031  n/a
protein features
start (aa)end (aa)featuredetails 
118SIGNALPotential.lost
1956REGIONNonhelical region (NC2).might get lost (downstream of altered splice site)
57519REGIONTriple-helical region.might get lost (downstream of altered splice site)
500500CONFLICTH -> P (in Ref. 1; CAA42933).might get lost (downstream of altered splice site)
520680REGIONNonhelical region (NC1).might get lost (downstream of altered splice site)
547680DOMAINC1q.might get lost (downstream of altered splice site)
553557STRANDmight get lost (downstream of altered splice site)
560562STRANDmight get lost (downstream of altered splice site)
573576STRANDmight get lost (downstream of altered splice site)
584586TURNmight get lost (downstream of altered splice site)
595616STRANDmight get lost (downstream of altered splice site)
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 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 53
cDNA position
(for ins/del: last normal base / first normal base)		 461
gDNA position
(for ins/del: last normal base / first normal base)		 33308
chromosomal position
(for ins/del: last normal base / first normal base)		 116446603
original gDNA sequence snippet ATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGAT
altered gDNA sequence snippet ATCCTTGAACTTGGTTCATGAAGTGTTTTACGCTGAACGAT
original cDNA sequence snippet ATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGAT
altered cDNA sequence snippet ATCCTTGAACTTGGTTCATGAAGTGTTTTACGCTGAACGAT
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 VSLNLVHEVF 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 *
speed 0.87 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: 0.993089594532534 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970340)
  • known disease mutation: rs17476 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116446603C>TN/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.53G>A
cDNA.149G>A
g.33308G>A
AA changes G18E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 18
frameshift no
known variant Reference ID: rs111033551
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17476 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2380.112
2.2030.996
(flanking)3.0731
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 increased33308wt: 0.6850 / mu: 0.7199 (marginal change - not scored)wt: ATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGAT
mu: ATCCTTGAACTTGGTTCATGAAGTGTTTTACGCTGAACGAT		 atgg|AGTG
Donor increased33304wt: 0.82 / mu: 0.98wt: TGGTTCATGGAGTGT
mu: TGGTTCATGAAGTGT		 GTTC|atgg
Donor marginally increased33306wt: 0.7513 / mu: 0.8469 (marginal change - not scored)wt: GTTCATGGAGTGTTT
mu: GTTCATGAAGTGTTT		 TCAT|ggag
distance from splice site 68
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      18FLLLVSLNLVHGVFYAERYQMPTG
mutated  not conserved    18FLLLVSLNLVHEVFYAERYQMPT
Ptroglodytes  all identical  ENSPTRG00000018524  18FLLLVSLNLVHGVFYAERYQTPT
Mmulatta  all identical  ENSMMUG00000014642  18FLLLVSLNLVHGVFYAERYQTPT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000039462  18FLLLMFLTLVHGMFYAERYQTPT
Ggallus  all identical  ENSGALG00000014965  18LLLLFCLNIVHGSDGYFSERYQKQS
Trubripes  no alignment  ENSTRUG00000006358  n/a
Drerio  all identical  ENSDARG00000054753  20LLLVALTAAHG----ERYVVKK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000033031  n/a
protein features
start (aa)end (aa)featuredetails 
118SIGNALPotential.lost
1956REGIONNonhelical region (NC2).might get lost (downstream of altered splice site)
57519REGIONTriple-helical region.might get lost (downstream of altered splice site)
500500CONFLICTH -> P (in Ref. 1; CAA42933).might get lost (downstream of altered splice site)
520680REGIONNonhelical region (NC1).might get lost (downstream of altered splice site)
547680DOMAINC1q.might get lost (downstream of altered splice site)
553557STRANDmight get lost (downstream of altered splice site)
560562STRANDmight get lost (downstream of altered splice site)
573576STRANDmight get lost (downstream of altered splice site)
584586TURNmight get lost (downstream of altered splice site)
595616STRANDmight get lost (downstream of altered splice site)
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 53
cDNA position
(for ins/del: last normal base / first normal base)		 149
gDNA position
(for ins/del: last normal base / first normal base)		 33308
chromosomal position
(for ins/del: last normal base / first normal base)		 116446603
original gDNA sequence snippet ATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGAT
altered gDNA sequence snippet ATCCTTGAACTTGGTTCATGAAGTGTTTTACGCTGAACGAT
original cDNA sequence snippet ATCCTTGAACTTGGTTCATGGAGTGTTTTACGCTGAACGAT
altered cDNA sequence snippet ATCCTTGAACTTGGTTCATGAAGTGTTTTACGCTGAACGAT
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 VSLNLVHEVF 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 *
speed 0.94 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 CM970340)
  • known disease mutation: rs17476 (pathogenic)
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116446603C>TN/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.24592C>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs111033551
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17476 (pathogenic for Metaphyseal chondrodysplasia, Schmid type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970340)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2380.112
2.2030.996
(flanking)3.0731
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 increased24597wt: 0.9957 / mu: 0.9959 (marginal change - not scored)wt: CCATGAACCAAGTTC
mu: TCATGAACCAAGTTC		 ATGA|acca
distance from splice site 7495
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)		 24592
chromosomal position
(for ins/del: last normal base / first normal base)		 116446603
original gDNA sequence snippet ATCGTTCAGCGTAAAACACTCCATGAACCAAGTTCAAGGAT
altered gDNA sequence snippet ATCGTTCAGCGTAAAACACTTCATGAACCAAGTTCAAGGAT
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 0.11 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

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