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: ENST00000017003
Querying Taster for transcript #2: ENST00000507602
MT speed 0 s - this script 2.349639 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
XYLT2polymorphism_automatic4.40952052649379e-10simple_aaeaffectedT801Rsingle base exchangers6504649show file
XYLT2polymorphism_automatic0.00205268013131399without_aaeaffectedsingle base exchangers6504649show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999559048 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM064361)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:48437456C>GN/A show variant in all transcripts   IGV
HGNC symbol XYLT2
Ensembl transcript ID ENST00000017003
Genbank transcript ID NM_022167
UniProt peptide Q9H1B5
alteration type single base exchange
alteration region CDS
DNA changes c.2402C>G
cDNA.2451C>G
g.14004C>G
AA changes T801R Score: 71 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 801
frameshift no
known variant Reference ID: rs6504649
databasehomozygous (G/G)heterozygousallele carriers
1000G1988611059
ExAC73051815725462

known disease mutation at this position, please check HGMD for details (HGMD ID CM064361)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0910
1.7520.004
(flanking)-2.4280
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased14003wt: 0.24 / mu: 0.91wt: GGCACACACAGCTCA
mu: GGCACAGACAGCTCA		 CACA|caca
Donor gained139980.38mu: CCAGCGGCACAGACA AGCG|gcac
distance from splice site 127
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      801PELAEEAAQRHTQLTGPALEAWTD
mutated  not conserved    801PELAEEAAQRHRQLTGPALEAWT
Ptroglodytes  all identical  ENSPTRG00000009395  801PELAEEAAQRHTQLTGPALEAWT
Mmulatta  all identical  ENSMMUG00000017226  801PELAEEAAQRHTQLTGPALEAWT
Fcatus  not conserved  ENSFCAG00000012330  756PEPAEEAARRHAELTGPALEAWT
Mmusculus  all identical  ENSMUSG00000020868  801AEALEEAARRHTELTGSALEAWT
Ggallus  not conserved  ENSGALG00000007702  794PEEAEVAAARKAQLTGRALDEWA
Trubripes  not conserved  ENSTRUG00000008009  815QEPAMQEARRKAQLVDQPLQEWV
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0015360  815FTMREESLAKGKML-GQELHSWI
Celegans  no alignment  Y50D4C.4  n/a
Xtropicalis  all conserved  ENSXETG00000006839  726RVEAEREAKGKSELLGKELEAWT
protein features
start (aa)end (aa)featuredetails 
37865TOPO_DOMLumenal (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2598 / 2598
position (AA) of stopcodon in wt / mu AA sequence 866 / 866
position of stopcodon in wt / mu cDNA 2647 / 2647
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 50 / 50
chromosome 17
strand 1
last intron/exon boundary 2325
theoretical NMD boundary in CDS 2225
length of CDS 2598
coding sequence (CDS) position 2402
cDNA position
(for ins/del: last normal base / first normal base)		 2451
gDNA position
(for ins/del: last normal base / first normal base)		 14004
chromosomal position
(for ins/del: last normal base / first normal base)		 48437456
original gDNA sequence snippet GGAGGCTGCCCAGCGGCACACACAGCTCACAGGCCCTGCGC
altered gDNA sequence snippet GGAGGCTGCCCAGCGGCACAGACAGCTCACAGGCCCTGCGC
original cDNA sequence snippet GGAGGCTGCCCAGCGGCACACACAGCTCACAGGCCCTGCGC
altered cDNA sequence snippet GGAGGCTGCCCAGCGGCACAGACAGCTCACAGGCCCTGCGC
wildtype AA sequence MVASARVQKL VRRYKLAIAT ALAILLLQGL VVWSFSGLEE DEAGEKGRQR KPRPLDPGEG
SKDTDSSAGR RGSTGRRHGR WRGRAESPGV PVAKVVRAVT SRQRASRRVP PAPPPEAPGR
QNLSGAAAGE ALVGAAGFPP HGDTGSVEGA PQPTDNGFTP KCEIVGKDAL SALARASTKQ
CQQEIANVVC LHQAGSLMPK AVPRHCQLTG KMSPGIQWDE SQAQQPMDGP PVRIAYMLVV
HGRAIRQLKR LLKAVYHEQH FFYIHVDKRS DYLHREVVEL AQGYDNVRVT PWRMVTIWGG
ASLLRMYLRS MRDLLEVPGW AWDFFINLSA TDYPTRTNEE LVAFLSKNRD KNFLKSHGRD
NSRFIKKQGL DRLFHECDSH MWRLGERQIP AGIVVDGGSD WFVLTRSFVE YVVYTDDPLV
AQLRQFYTYT LLPAESFFHT VLENSLACET LVDNNLRVTN WNRKLGCKCQ YKHIVDWCGC
SPNDFKPQDF LRLQQVSRPT FFARKFESTV NQEVLEILDF HLYGSYPPGT PALKAYWENT
YDAADGPSGL SDVMLTAYTA FARLSLHHAA TAAPPMGTPL CRFEPRGLPS SVHLYFYDDH
FQGYLVTQAV QPSAQGPAET LEMWLMPQGS LKLLGRSDQA SRLQSLEVGT DWDPKERLFR
NFGGLLGPLD EPVAVQRWAR GPNLTATVVW IDPTYVVATS YDITVDTETE VTQYKPPLSR
PLRPGPWTVR LLQFWEPLGE TRFLVLPLTF NRKLPLRKDD ASWLHAGPPH NEYMEQSFQG
LSSILNLPQP ELAEEAAQRH TQLTGPALEA WTDRELSSFW SVAGLCAIGP SPCPSLEPCR
LTSWSSLSPD PKSELGPVKA DGRLR*
mutated AA sequence MVASARVQKL VRRYKLAIAT ALAILLLQGL VVWSFSGLEE DEAGEKGRQR KPRPLDPGEG
SKDTDSSAGR RGSTGRRHGR WRGRAESPGV PVAKVVRAVT SRQRASRRVP PAPPPEAPGR
QNLSGAAAGE ALVGAAGFPP HGDTGSVEGA PQPTDNGFTP KCEIVGKDAL SALARASTKQ
CQQEIANVVC LHQAGSLMPK AVPRHCQLTG KMSPGIQWDE SQAQQPMDGP PVRIAYMLVV
HGRAIRQLKR LLKAVYHEQH FFYIHVDKRS DYLHREVVEL AQGYDNVRVT PWRMVTIWGG
ASLLRMYLRS MRDLLEVPGW AWDFFINLSA TDYPTRTNEE LVAFLSKNRD KNFLKSHGRD
NSRFIKKQGL DRLFHECDSH MWRLGERQIP AGIVVDGGSD WFVLTRSFVE YVVYTDDPLV
AQLRQFYTYT LLPAESFFHT VLENSLACET LVDNNLRVTN WNRKLGCKCQ YKHIVDWCGC
SPNDFKPQDF LRLQQVSRPT FFARKFESTV NQEVLEILDF HLYGSYPPGT PALKAYWENT
YDAADGPSGL SDVMLTAYTA FARLSLHHAA TAAPPMGTPL CRFEPRGLPS SVHLYFYDDH
FQGYLVTQAV QPSAQGPAET LEMWLMPQGS LKLLGRSDQA SRLQSLEVGT DWDPKERLFR
NFGGLLGPLD EPVAVQRWAR GPNLTATVVW IDPTYVVATS YDITVDTETE VTQYKPPLSR
PLRPGPWTVR LLQFWEPLGE TRFLVLPLTF NRKLPLRKDD ASWLHAGPPH NEYMEQSFQG
LSSILNLPQP ELAEEAAQRH RQLTGPALEA WTDRELSSFW SVAGLCAIGP SPCPSLEPCR
LTSWSSLSPD PKSELGPVKA DGRLR*
speed 0.32 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: 0.997947319868686 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM064361)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:48437456C>GN/A show variant in all transcripts   IGV
HGNC symbol XYLT2
Ensembl transcript ID ENST00000507602
Genbank transcript ID N/A
UniProt peptide Q9H1B5
alteration type single base exchange
alteration region intron
DNA changes g.14004C>G
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs6504649
databasehomozygous (G/G)heterozygousallele carriers
1000G1988611059
ExAC73051815725462

known disease mutation at this position, please check HGMD for details (HGMD ID CM064361)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0910
1.7520.004
(flanking)-2.4280
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased14003wt: 0.24 / mu: 0.91wt: GGCACACACAGCTCA
mu: GGCACAGACAGCTCA		 CACA|caca
Donor gained139980.38mu: CCAGCGGCACAGACA AGCG|gcac
distance from splice site 2843
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
37865TOPO_DOMLumenal (Potential).might get lost (downstream of altered splice site)
683683CARBOHYDN-linked (GlcNAc...) (Potential).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 7 / 7
chromosome 17
strand 1
last intron/exon boundary 1948
theoretical NMD boundary in CDS 1891
length of CDS 2031
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)		 14004
chromosomal position
(for ins/del: last normal base / first normal base)		 48437456
original gDNA sequence snippet GGAGGCTGCCCAGCGGCACACACAGCTCACAGGCCCTGCGC
altered gDNA sequence snippet GGAGGCTGCCCAGCGGCACAGACAGCTCACAGGCCCTGCGC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVASARVQKL VRRYKLAIAT ALAILLLQGL VVWSFSGLEE DEAGEKGRQR KPRPLDPGEG
SKDTDSSAGR RGSTGRRHGR WRGRAESPGV PVAKVVRAVT SRQRASRRVP PAPPPEAPGR
QNLSGAAAGE ALVGAAGFPP HGDTGSVEGA PQPTDNGFTP KCEIVGKDAL SALARASTKQ
CQQEIANVVC LHQAGSLMPK AVPRHCQLTG KMSPGIQWDE SQAQQPMDGP PVRIAYMLVV
HGRAIRQLKR LLKAVYHEQH FFYIHVDKRS DYLHREVVEL AQGYDNVRVT PWRMVTIWGG
ASLLRMYLRS MRDLLEVPGW AWDFFINLSA TDYPTRTNEE LVAFLSKNRD KNFLKSHGRD
NSRFIKKQGL DRLFHECDSH MWRLGERQIP AGIVVDGGSD WFVLTRSFVE YVVYTDDPLV
AQLRQFYTYT LLPAESFFHT VLENSLACET LVDNNLRVTN WNRKLGCKCQ YKHIVDWCGC
SPNDFKPQDF LRLQQVSRPT FFARKFESTV NQEVLEILDF HLYGSYPPGT PALKAYWENT
YDAADGPSGL SDVMLTAYTA FARLSLHHAA TAAPPMGTPL CRFEPRGLPS SVHLYFYDDH
FQGYLVTQAV QPSAQGPAET LEMWLMPQGS LKLLGRSDQA SRLQSLENRG LSMLPRLVSN
SWPQAVLPLQ PPKALG*
mutated AA sequence N/A
speed 0.27 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