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 3.85 s - this script 5.798895 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
COL10A1polymorphism_automatic4.00185830029542e-08simple_aaeaffectedM27Tsingle base exchangers1064583show file
COL10A1polymorphism_automatic4.00185830029542e-08simple_aaeaffectedM27Tsingle base exchangers1064583show file
NT5DC1polymorphism_automatic0.988568170878278without_aaeaffectedsingle base exchangers1064583show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999959981417 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116446576A>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.80T>C
cDNA.176T>C
g.33335T>C
AA changes M27T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS
27
frameshift no
known variant Reference ID: rs1064583
databasehomozygous (G/G)heterozygousallele carriers
1000G60010311631
ExAC97891318922978
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8350.142
1.3510.574
(flanking)0.840.634
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased33329wt: 0.54 / mu: 0.63wt: ACGATACCAAATGCC
mu: ACGATACCAAACGCC
 GATA|ccaa
Donor increased33330wt: 0.71 / mu: 0.83wt: CGATACCAAATGCCC
mu: CGATACCAAACGCCC
 ATAC|caaa
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      27VHGVFYAERYQMPTGIKGPLPNTK
mutated  not conserved    27VHGVFYAERYQTPTGIKGPLPNT
Ptroglodytes  not conserved  ENSPTRG00000018524  27VHGVFYAERYQTPTGIKGPLPNT
Mmulatta  not conserved  ENSMMUG00000014642  27VHGVFYAERYQTPTGIKGPLPNT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000039462  27VHGMFYAERYQTPTGIKGPLASP
Ggallus  not conserved  ENSGALG00000014965  27VHGSDGYFSERYQKQSSIKGP----
Trubripes  no alignment  ENSTRUG00000006358  n/a
Drerio  all conserved  ENSDARG00000054753  29AHG----ERYVVKKVMKAPQ---
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000033031  n/a
protein features
start (aa)end (aa)featuredetails 
1956REGIONNonhelical region (NC2).lost
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 80
cDNA position
(for ins/del: last normal base / first normal base)
176
gDNA position
(for ins/del: last normal base / first normal base)
33335
chromosomal position
(for ins/del: last normal base / first normal base)
116446576
original gDNA sequence snippet TTACGCTGAACGATACCAAATGCCCACAGGCATAAAAGGCC
altered gDNA sequence snippet TTACGCTGAACGATACCAAACGCCCACAGGCATAAAAGGCC
original cDNA sequence snippet TTACGCTGAACGATACCAAATGCCCACAGGCATAAAAGGCC
altered cDNA sequence snippet TTACGCTGAACGATACCAAACGCCCACAGGCATAAAAGGCC
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 YAERYQTPTG 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 1.49 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

polymorphism

Model: simple_aae, prob: 0.999999959981417 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116446576A>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.80T>C
cDNA.488T>C
g.33335T>C
AA changes M27T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS
27
frameshift no
known variant Reference ID: rs1064583
databasehomozygous (G/G)heterozygousallele carriers
1000G60010311631
ExAC97891318922978
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8350.142
1.3510.574
(flanking)0.840.634
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased33329wt: 0.54 / mu: 0.63wt: ACGATACCAAATGCC
mu: ACGATACCAAACGCC
 GATA|ccaa
Donor increased33330wt: 0.71 / mu: 0.83wt: CGATACCAAATGCCC
mu: CGATACCAAACGCCC
 ATAC|caaa
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      27VHGVFYAERYQMPTGIKGPLPNTK
mutated  not conserved    27VHGVFYAERYQTPTGIKGPLPNT
Ptroglodytes  not conserved  ENSPTRG00000018524  27VHGVFYAERYQTPTGIKGPLPNT
Mmulatta  not conserved  ENSMMUG00000014642  27VHGVFYAERYQTPTGIKGPLPNT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000039462  27VHGMFYAERYQTPTGIKGPLASP
Ggallus  not conserved  ENSGALG00000014965  27VHGSDGYFSERYQKQSSIKGP----
Trubripes  no alignment  ENSTRUG00000006358  n/a
Drerio  all conserved  ENSDARG00000054753  29AHG----ERYVVKKVMKAPQ---
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000033031  n/a
protein features
start (aa)end (aa)featuredetails 
1956REGIONNonhelical region (NC2).lost
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 80
cDNA position
(for ins/del: last normal base / first normal base)
488
gDNA position
(for ins/del: last normal base / first normal base)
33335
chromosomal position
(for ins/del: last normal base / first normal base)
116446576
original gDNA sequence snippet TTACGCTGAACGATACCAAATGCCCACAGGCATAAAAGGCC
altered gDNA sequence snippet TTACGCTGAACGATACCAAACGCCCACAGGCATAAAAGGCC
original cDNA sequence snippet TTACGCTGAACGATACCAAATGCCCACAGGCATAAAAGGCC
altered cDNA sequence snippet TTACGCTGAACGATACCAAACGCCCACAGGCATAAAAGGCC
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 YAERYQTPTG 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 1.35 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

polymorphism

Model: without_aae, prob: 0.0114318291217216 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:116446576A>GN/A show variant in all transcripts   IGV
HGNC symbol NT5DC1
Ensembl transcript ID ENST00000319550
Genbank transcript ID NM_152729
UniProt peptide Q5TFE4
alteration type single base exchange
alteration region intron
DNA changes g.24565A>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS
N/A
frameshift N/A
known variant Reference ID: rs1064583
databasehomozygous (G/G)heterozygousallele carriers
1000G60010311631
ExAC97891318922978
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8350.142
1.3510.574
(flanking)0.840.634
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 increased24558wt: 0.7780 / mu: 0.8055 (marginal change - not scored)wt: GGTAGTGGGCCTTTTATGCCTGTGGGCATTTGGTATCGTTC
mu: GGTAGTGGGCCTTTTATGCCTGTGGGCGTTTGGTATCGTTC
 gcct|GTGG
Acc increased24556wt: 0.47 / mu: 0.58wt: TGGGTAGTGGGCCTTTTATGCCTGTGGGCATTTGGTATCGT
mu: TGGGTAGTGGGCCTTTTATGCCTGTGGGCGTTTGGTATCGT
 atgc|CTGT
distance from splice site 7468
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
N/A
protein features
start (aa)end (aa)featuredetails 
313313METALMagnesium (By similarity).might get lost (downstream of altered splice site)
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)
24565
chromosomal position
(for ins/del: last normal base / first normal base)
116446576
original gDNA sequence snippet GGCCTTTTATGCCTGTGGGCATTTGGTATCGTTCAGCGTAA
altered gDNA sequence snippet GGCCTTTTATGCCTGTGGGCGTTTGGTATCGTTCAGCGTAA
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 1.01 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