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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000367922
Querying Taster for transcript #2: ENST00000367921
MT speed 2.85 s - this script 6.300614 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DDR2disease_causing_automatic0.999999998523426simple_aae0T713Isingle base exchangers121964865show file
DDR2disease_causing_automatic0.999999998523426simple_aae0T713Isingle base exchangers121964865show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998523426 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM090155)
  • known disease mutation: rs12315 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:162746015C>TN/A show variant in all transcripts   IGV
HGNC symbol DDR2
Ensembl transcript ID ENST00000367922
Genbank transcript ID NM_001014796
UniProt peptide Q16832
alteration type single base exchange
alteration region CDS
DNA changes c.2138C>T
cDNA.2576C>T
g.144853C>T
AA changes T713I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
713
frameshift no
known variant Reference ID: rs121964865
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs12315 (pathogenic for Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM090155)

known disease mutation at this position, please check HGMD for details (HGMD ID CM090155)
known disease mutation at this position, please check HGMD for details (HGMD ID CM090155)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.71
5.6911
(flanking)-0.6280.813
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 90
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      713SSLNFVHRDLATRNCLVGKNYTIK
mutated  not conserved    713SSLNFVHRDLAIRNCLVGK
Ptroglodytes  all identical  ENSPTRG00000001603  713SSLNFVHRDLATRNCLVGK
Mmulatta  all identical  ENSMMUG00000009330  713SSLNFVHRDLATRNCLVGK
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026674  713SSLNFVHRDLATRNCLVGK
Ggallus  all identical  ENSGALG00000002687  718SSLNFVHRDLATR
Trubripes  all identical  ENSTRUG00000018340  749SSLNFVHRDLATRNCLVGKNFTX
Drerio  all identical  ENSDARG00000051913  725SSLNFVHRDLATRNC
Dmelanogaster  all identical  FBgn0053531  905RDLATRSCIIGPELCV
Celegans  not conserved  F11D5.3  658ESCNFVHRDIAARNCLVDGEGNV
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
422855TOPO_DOMCytoplasmic (Potential).lost
563849DOMAINProtein kinase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2568 / 2568
position (AA) of stopcodon in wt / mu AA sequence 856 / 856
position of stopcodon in wt / mu cDNA 3006 / 3006
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 439 / 439
chromosome 1
strand 1
last intron/exon boundary 2872
theoretical NMD boundary in CDS 2383
length of CDS 2568
coding sequence (CDS) position 2138
cDNA position
(for ins/del: last normal base / first normal base)
2576
gDNA position
(for ins/del: last normal base / first normal base)
144853
chromosomal position
(for ins/del: last normal base / first normal base)
162746015
original gDNA sequence snippet TGTTCACCGAGATCTGGCCACACGAAACTGTTTAGTGGGTA
altered gDNA sequence snippet TGTTCACCGAGATCTGGCCATACGAAACTGTTTAGTGGGTA
original cDNA sequence snippet TGTTCACCGAGATCTGGCCACACGAAACTGTTTAGTGGGTA
altered cDNA sequence snippet TGTTCACCGAGATCTGGCCATACGAAACTGTTTAGTGGGTA
wildtype AA sequence MILIPRMLLV LFLLLPILSS AKAQVNPAIC RYPLGMSGGQ IPDEDITASS QWSESTAAKY
GRLDSEEGDG AWCPEIPVEP DDLKEFLQID LHTLHFITLV GTQGRHAGGH GIEFAPMYKI
NYSRDGTRWI SWRNRHGKQV LDGNSNPYDI FLKDLEPPIV ARFVRFIPVT DHSMNVCMRV
ELYGCVWLDG LVSYNAPAGQ QFVLPGGSII YLNDSVYDGA VGYSMTEGLG QLTDGVSGLD
DFTQTHEYHV WPGYDYVGWR NESATNGYIE IMFEFDRIRN FTTMKVHCNN MFAKGVKIFK
EVQCYFRSEA SEWEPNAISF PLVLDDVNPS ARFVTVPLHH RMASAIKCQY HFADTWMMFS
EITFQSDAAM YNNSEALPTS PMAPTTYDPM LKVDDSNTRI LIGCLVAIIF ILLAIIVIIL
WRQFWQKMLE KASRRMLDDE MTVSLSLPSD SSMFNNNRSS SPSEQGSNST YDRIFPLRPD
YQEPSRLIRK LPEFAPGEEE SGCSGVVKPV QPSGPEGVPH YAEADIVNLQ GVTGGNTYSV
PAVTMDLLSG KDVAVEEFPR KLLTFKEKLG EGQFGEVHLC EVEGMEKFKD KDFALDVSAN
QPVLVAVKML RADANKNARN DFLKEIKIMS RLKDPNIIHL LAVCITDDPL CMITEYMENG
DLNQFLSRHE PPNSSSSDVR TVSYTNLKFM ATQIASGMKY LSSLNFVHRD LATRNCLVGK
NYTIKIADFG MSRNLYSGDY YRIQGRAVLP IRWMSWESIL LGKFTTASDV WAFGVTLWET
FTFCQEQPYS QLSDEQVIEN TGEFFRDQGR QTYLPQPAIC PDSVYKLMLS CWRRDTKNRP
SFQEIHLLLL QQGDE*
mutated AA sequence MILIPRMLLV LFLLLPILSS AKAQVNPAIC RYPLGMSGGQ IPDEDITASS QWSESTAAKY
GRLDSEEGDG AWCPEIPVEP DDLKEFLQID LHTLHFITLV GTQGRHAGGH GIEFAPMYKI
NYSRDGTRWI SWRNRHGKQV LDGNSNPYDI FLKDLEPPIV ARFVRFIPVT DHSMNVCMRV
ELYGCVWLDG LVSYNAPAGQ QFVLPGGSII YLNDSVYDGA VGYSMTEGLG QLTDGVSGLD
DFTQTHEYHV WPGYDYVGWR NESATNGYIE IMFEFDRIRN FTTMKVHCNN MFAKGVKIFK
EVQCYFRSEA SEWEPNAISF PLVLDDVNPS ARFVTVPLHH RMASAIKCQY HFADTWMMFS
EITFQSDAAM YNNSEALPTS PMAPTTYDPM LKVDDSNTRI LIGCLVAIIF ILLAIIVIIL
WRQFWQKMLE KASRRMLDDE MTVSLSLPSD SSMFNNNRSS SPSEQGSNST YDRIFPLRPD
YQEPSRLIRK LPEFAPGEEE SGCSGVVKPV QPSGPEGVPH YAEADIVNLQ GVTGGNTYSV
PAVTMDLLSG KDVAVEEFPR KLLTFKEKLG EGQFGEVHLC EVEGMEKFKD KDFALDVSAN
QPVLVAVKML RADANKNARN DFLKEIKIMS RLKDPNIIHL LAVCITDDPL CMITEYMENG
DLNQFLSRHE PPNSSSSDVR TVSYTNLKFM ATQIASGMKY LSSLNFVHRD LAIRNCLVGK
NYTIKIADFG MSRNLYSGDY YRIQGRAVLP IRWMSWESIL LGKFTTASDV WAFGVTLWET
FTFCQEQPYS QLSDEQVIEN TGEFFRDQGR QTYLPQPAIC PDSVYKLMLS CWRRDTKNRP
SFQEIHLLLL QQGDE*
speed 1.30 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: 0.999999998523426 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM090155)
  • known disease mutation: rs12315 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:162746015C>TN/A show variant in all transcripts   IGV
HGNC symbol DDR2
Ensembl transcript ID ENST00000367921
Genbank transcript ID NM_006182
UniProt peptide Q16832
alteration type single base exchange
alteration region CDS
DNA changes c.2138C>T
cDNA.2491C>T
g.144853C>T
AA changes T713I Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS
713
frameshift no
known variant Reference ID: rs121964865
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs12315 (pathogenic for Spondyloepimetaphyseal dysplasia-short limb-abnormal calcification syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM090155)

known disease mutation at this position, please check HGMD for details (HGMD ID CM090155)
known disease mutation at this position, please check HGMD for details (HGMD ID CM090155)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.71
5.6911
(flanking)-0.6280.813
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 90
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      713SSLNFVHRDLATRNCLVGKNYTIK
mutated  not conserved    713SSLNFVHRDLAIRNCLVGK
Ptroglodytes  all identical  ENSPTRG00000001603  713SSLNFVHRDLATRNCLVGK
Mmulatta  all identical  ENSMMUG00000009330  713SSLNFVHRDLATRNCLVGK
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026674  713SSLNFVHRDLATRNCLVGK
Ggallus  all identical  ENSGALG00000002687  718SSLNFVHRDLATR
Trubripes  all identical  ENSTRUG00000018340  749SSLNFVHRDLATRNCLVGKNFTX
Drerio  all identical  ENSDARG00000051913  725SSLNFVHRDLATRNC
Dmelanogaster  all identical  FBgn0053531  905RDLATRSCIIGPELCV
Celegans  not conserved  F11D5.3  658ESCNFVHRDIAARNCLVDGEGNV
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
422855TOPO_DOMCytoplasmic (Potential).lost
563849DOMAINProtein kinase.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2568 / 2568
position (AA) of stopcodon in wt / mu AA sequence 856 / 856
position of stopcodon in wt / mu cDNA 2921 / 2921
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 354 / 354
chromosome 1
strand 1
last intron/exon boundary 2787
theoretical NMD boundary in CDS 2383
length of CDS 2568
coding sequence (CDS) position 2138
cDNA position
(for ins/del: last normal base / first normal base)
2491
gDNA position
(for ins/del: last normal base / first normal base)
144853
chromosomal position
(for ins/del: last normal base / first normal base)
162746015
original gDNA sequence snippet TGTTCACCGAGATCTGGCCACACGAAACTGTTTAGTGGGTA
altered gDNA sequence snippet TGTTCACCGAGATCTGGCCATACGAAACTGTTTAGTGGGTA
original cDNA sequence snippet TGTTCACCGAGATCTGGCCACACGAAACTGTTTAGTGGGTA
altered cDNA sequence snippet TGTTCACCGAGATCTGGCCATACGAAACTGTTTAGTGGGTA
wildtype AA sequence MILIPRMLLV LFLLLPILSS AKAQVNPAIC RYPLGMSGGQ IPDEDITASS QWSESTAAKY
GRLDSEEGDG AWCPEIPVEP DDLKEFLQID LHTLHFITLV GTQGRHAGGH GIEFAPMYKI
NYSRDGTRWI SWRNRHGKQV LDGNSNPYDI FLKDLEPPIV ARFVRFIPVT DHSMNVCMRV
ELYGCVWLDG LVSYNAPAGQ QFVLPGGSII YLNDSVYDGA VGYSMTEGLG QLTDGVSGLD
DFTQTHEYHV WPGYDYVGWR NESATNGYIE IMFEFDRIRN FTTMKVHCNN MFAKGVKIFK
EVQCYFRSEA SEWEPNAISF PLVLDDVNPS ARFVTVPLHH RMASAIKCQY HFADTWMMFS
EITFQSDAAM YNNSEALPTS PMAPTTYDPM LKVDDSNTRI LIGCLVAIIF ILLAIIVIIL
WRQFWQKMLE KASRRMLDDE MTVSLSLPSD SSMFNNNRSS SPSEQGSNST YDRIFPLRPD
YQEPSRLIRK LPEFAPGEEE SGCSGVVKPV QPSGPEGVPH YAEADIVNLQ GVTGGNTYSV
PAVTMDLLSG KDVAVEEFPR KLLTFKEKLG EGQFGEVHLC EVEGMEKFKD KDFALDVSAN
QPVLVAVKML RADANKNARN DFLKEIKIMS RLKDPNIIHL LAVCITDDPL CMITEYMENG
DLNQFLSRHE PPNSSSSDVR TVSYTNLKFM ATQIASGMKY LSSLNFVHRD LATRNCLVGK
NYTIKIADFG MSRNLYSGDY YRIQGRAVLP IRWMSWESIL LGKFTTASDV WAFGVTLWET
FTFCQEQPYS QLSDEQVIEN TGEFFRDQGR QTYLPQPAIC PDSVYKLMLS CWRRDTKNRP
SFQEIHLLLL QQGDE*
mutated AA sequence MILIPRMLLV LFLLLPILSS AKAQVNPAIC RYPLGMSGGQ IPDEDITASS QWSESTAAKY
GRLDSEEGDG AWCPEIPVEP DDLKEFLQID LHTLHFITLV GTQGRHAGGH GIEFAPMYKI
NYSRDGTRWI SWRNRHGKQV LDGNSNPYDI FLKDLEPPIV ARFVRFIPVT DHSMNVCMRV
ELYGCVWLDG LVSYNAPAGQ QFVLPGGSII YLNDSVYDGA VGYSMTEGLG QLTDGVSGLD
DFTQTHEYHV WPGYDYVGWR NESATNGYIE IMFEFDRIRN FTTMKVHCNN MFAKGVKIFK
EVQCYFRSEA SEWEPNAISF PLVLDDVNPS ARFVTVPLHH RMASAIKCQY HFADTWMMFS
EITFQSDAAM YNNSEALPTS PMAPTTYDPM LKVDDSNTRI LIGCLVAIIF ILLAIIVIIL
WRQFWQKMLE KASRRMLDDE MTVSLSLPSD SSMFNNNRSS SPSEQGSNST YDRIFPLRPD
YQEPSRLIRK LPEFAPGEEE SGCSGVVKPV QPSGPEGVPH YAEADIVNLQ GVTGGNTYSV
PAVTMDLLSG KDVAVEEFPR KLLTFKEKLG EGQFGEVHLC EVEGMEKFKD KDFALDVSAN
QPVLVAVKML RADANKNARN DFLKEIKIMS RLKDPNIIHL LAVCITDDPL CMITEYMENG
DLNQFLSRHE PPNSSSSDVR TVSYTNLKFM ATQIASGMKY LSSLNFVHRD LAIRNCLVGK
NYTIKIADFG MSRNLYSGDY YRIQGRAVLP IRWMSWESIL LGKFTTASDV WAFGVTLWET
FTFCQEQPYS QLSDEQVIEN TGEFFRDQGR QTYLPQPAIC PDSVYKLMLS CWRRDTKNRP
SFQEIHLLLL QQGDE*
speed 1.55 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