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: ENST00000352690
Querying Taster for transcript #2: ENST00000283285
Querying Taster for transcript #3: ENST00000438817
MT speed 0 s - this script 4.621344 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CD96disease_causing_automatic1.23780724281198e-11simple_aae0T264Msingle base exchangers119477056show file
CD96disease_causing_automatic1.23780724281198e-11simple_aae0T264Msingle base exchangers119477056show file
CD96disease_causing_automatic2.05550067872172e-11simple_aae0T280Msingle base exchangers119477056show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 1.23780724281198e-11 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM074083)
  • known disease mutation: rs4640 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:111304209C>TN/A show variant in all transcripts   IGV
HGNC symbol CD96
Ensembl transcript ID ENST00000352690
Genbank transcript ID NM_005816
UniProt peptide P40200
alteration type single base exchange
alteration region CDS
DNA changes c.791C>T
cDNA.961C>T
g.43284C>T
AA changes T264M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 264
frameshift no
known variant Reference ID: rs119477056
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs4640 (pathogenic for C syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Jund, Transcription Factor, Jund TF binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2460.001
-0.8940
(flanking)0.4290.004
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 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      264PEIPVIVENNSTDVLVERRFTCLL
mutated  not conserved    264PEIPVIVENNSMDVLVERRFTCL
Ptroglodytes  all identical  ENSPTRG00000015205  280PEIPVIVENNSTDVLVERRFTCL
Mmulatta  all identical  ENSMMUG00000000688  281PEIPMIVENNSTDVLVERTFTCL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000022657  261PEILMTVENSTMDVLGERVFTCL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
22519TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1710 / 1710
position (AA) of stopcodon in wt / mu AA sequence 570 / 570
position of stopcodon in wt / mu cDNA 1880 / 1880
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 171 / 171
chromosome 3
strand 1
last intron/exon boundary 1772
theoretical NMD boundary in CDS 1551
length of CDS 1710
coding sequence (CDS) position 791
cDNA position
(for ins/del: last normal base / first normal base)		 961
gDNA position
(for ins/del: last normal base / first normal base)		 43284
chromosomal position
(for ins/del: last normal base / first normal base)		 111304209
original gDNA sequence snippet GATTGTGGAAAATAACTCCACGGATGTCTTGGTAGAGGTGA
altered gDNA sequence snippet GATTGTGGAAAATAACTCCATGGATGTCTTGGTAGAGGTGA
original cDNA sequence snippet GATTGTGGAAAATAACTCCACGGATGTCTTGGTAGAGAGAA
altered cDNA sequence snippet GATTGTGGAAAATAACTCCATGGATGTCTTGGTAGAGAGAA
wildtype AA sequence MEKKWKYCAV YYIIQIHFVK GVWEKTVNTE ENVYATLGSD VNLTCQTQTV GFFVQMQWSK
VTNKIDLIAV YHPQYGFYCA YGRPCESLVT FTETPENGSK WTLHLRNMSC SVSGRYECML
VLYPEGIQTK IYNLLIQTHV TADEWNSNHT IEIEINQTLE IPCFQNSSSK ISSEFTYAWS
VEDNGTQETL ISQNHLISNS TLLKDRVKLG TDYRLHLSPV QIFDDGRKFS CHIRVGPNKI
LRSSTTVKVF AKPEIPVIVE NNSTDVLVER RFTCLLKNVF PKANITWFID GSFLHDEKEG
IYITNEERKG KDGFLELKSV LTRVHSNKPA QSDNLTIWCM ALSPVPGNKV WNISSEKITF
LLGSEISSTD PPLSVTESTL DTQPSPASSV SPARYPATSS VTLVDVSALR PNTTPQPSNS
SMTTRGFNYP WTSSGTDTKK SVSRIPSETY SSSPSGAGST LHDNVFTSTA RAFSEVPTTA
NGSTKTNHVH ITGIVVNKPK DGMSWPVIVA ALLFCCMILF GLGVRKWCQY QKEIMERPPP
FKPPPPPIKY TCIQEPNESD LPYHEMETL*
mutated AA sequence MEKKWKYCAV YYIIQIHFVK GVWEKTVNTE ENVYATLGSD VNLTCQTQTV GFFVQMQWSK
VTNKIDLIAV YHPQYGFYCA YGRPCESLVT FTETPENGSK WTLHLRNMSC SVSGRYECML
VLYPEGIQTK IYNLLIQTHV TADEWNSNHT IEIEINQTLE IPCFQNSSSK ISSEFTYAWS
VEDNGTQETL ISQNHLISNS TLLKDRVKLG TDYRLHLSPV QIFDDGRKFS CHIRVGPNKI
LRSSTTVKVF AKPEIPVIVE NNSMDVLVER RFTCLLKNVF PKANITWFID GSFLHDEKEG
IYITNEERKG KDGFLELKSV LTRVHSNKPA QSDNLTIWCM ALSPVPGNKV WNISSEKITF
LLGSEISSTD PPLSVTESTL DTQPSPASSV SPARYPATSS VTLVDVSALR PNTTPQPSNS
SMTTRGFNYP WTSSGTDTKK SVSRIPSETY SSSPSGAGST LHDNVFTSTA RAFSEVPTTA
NGSTKTNHVH ITGIVVNKPK DGMSWPVIVA ALLFCCMILF GLGVRKWCQY QKEIMERPPP
FKPPPPPIKY TCIQEPNESD LPYHEMETL*
speed 1.31 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: 1.23780724281198e-11 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM074083)
  • known disease mutation: rs4640 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:111304209C>TN/A show variant in all transcripts   IGV
HGNC symbol CD96
Ensembl transcript ID ENST00000438817
Genbank transcript ID N/A
UniProt peptide P40200
alteration type single base exchange
alteration region CDS
DNA changes c.791C>T
cDNA.890C>T
g.43284C>T
AA changes T264M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 264
frameshift no
known variant Reference ID: rs119477056
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs4640 (pathogenic for C syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Jund, Transcription Factor, Jund TF binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2460.001
-0.8940
(flanking)0.4290.004
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 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      264PEIPVIVENNSTDVLVERRFTCLL
mutated  not conserved    264PEIPVIVENNSMDVLVERRFTCL
Ptroglodytes  all identical  ENSPTRG00000015205  280PEIPVIVENNSTDVLVERRFTCL
Mmulatta  all identical  ENSMMUG00000000688  281PEIPMIVENNSTDVLVERTFTCL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000022657  261PEILMTVENSTMDVLGERVFTCL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
22519TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1209 / 1209
position (AA) of stopcodon in wt / mu AA sequence 403 / 403
position of stopcodon in wt / mu cDNA 1308 / 1308
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 100 / 100
chromosome 3
strand 1
last intron/exon boundary 1187
theoretical NMD boundary in CDS 1037
length of CDS 1209
coding sequence (CDS) position 791
cDNA position
(for ins/del: last normal base / first normal base)		 890
gDNA position
(for ins/del: last normal base / first normal base)		 43284
chromosomal position
(for ins/del: last normal base / first normal base)		 111304209
original gDNA sequence snippet GATTGTGGAAAATAACTCCACGGATGTCTTGGTAGAGGTGA
altered gDNA sequence snippet GATTGTGGAAAATAACTCCATGGATGTCTTGGTAGAGGTGA
original cDNA sequence snippet GATTGTGGAAAATAACTCCACGGATGTCTTGGTAGAGAGAA
altered cDNA sequence snippet GATTGTGGAAAATAACTCCATGGATGTCTTGGTAGAGAGAA
wildtype AA sequence MEKKWKYCAV YYIIQIHFVK GVWEKTVNTE ENVYATLGSD VNLTCQTQTV GFFVQMQWSK
VTNKIDLIAV YHPQYGFYCA YGRPCESLVT FTETPENGSK WTLHLRNMSC SVSGRYECML
VLYPEGIQTK IYNLLIQTHV TADEWNSNHT IEIEINQTLE IPCFQNSSSK ISSEFTYAWS
VEDNGTQETL ISQNHLISNS TLLKDRVKLG TDYRLHLSPV QIFDDGRKFS CHIRVGPNKI
LRSSTTVKVF AKPEIPVIVE NNSTDVLVER RFTCLLKNVF PKANITWFID GSFLHDEKEG
IYITNEERKG KDGFLELKSV LTRVHSNKPA QSDNLTIWCM ALSPVPGNKV WNISSEKITF
LLGSEISSTD PPLSVTESTL DTQPSPASSV SPASKNVFTL SY*
mutated AA sequence MEKKWKYCAV YYIIQIHFVK GVWEKTVNTE ENVYATLGSD VNLTCQTQTV GFFVQMQWSK
VTNKIDLIAV YHPQYGFYCA YGRPCESLVT FTETPENGSK WTLHLRNMSC SVSGRYECML
VLYPEGIQTK IYNLLIQTHV TADEWNSNHT IEIEINQTLE IPCFQNSSSK ISSEFTYAWS
VEDNGTQETL ISQNHLISNS TLLKDRVKLG TDYRLHLSPV QIFDDGRKFS CHIRVGPNKI
LRSSTTVKVF AKPEIPVIVE NNSMDVLVER RFTCLLKNVF PKANITWFID GSFLHDEKEG
IYITNEERKG KDGFLELKSV LTRVHSNKPA QSDNLTIWCM ALSPVPGNKV WNISSEKITF
LLGSEISSTD PPLSVTESTL DTQPSPASSV SPASKNVFTL SY*
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: 2.05550067872172e-11 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM074083)
  • known disease mutation: rs4640 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:111304209C>TN/A show variant in all transcripts   IGV
HGNC symbol CD96
Ensembl transcript ID ENST00000283285
Genbank transcript ID NM_198196
UniProt peptide P40200
alteration type single base exchange
alteration region CDS
DNA changes c.839C>T
cDNA.970C>T
g.43284C>T
AA changes T280M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 280
frameshift no
known variant Reference ID: rs119477056
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs4640 (pathogenic for C syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074083)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Jund, Transcription Factor, Jund TF binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.2460.001
-0.8940
(flanking)0.4290.004
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 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      280PEIPVIVENNSTDVLVERRFTCLL
mutated  not conserved    280PEIPVIVENNSMDVLVERRFTCL
Ptroglodytes  all identical  ENSPTRG00000015205  280PEIPVIVENNSTDVLVERRFTCL
Mmulatta  all identical  ENSMMUG00000000688  281PEIPMIVENNSTDVLVERTFTCL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000022657  261PEILMTVENSTMDVLGERVFTCL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
22519TOPO_DOMExtracellular (Potential).lost
269375DOMAINIg-like C2-type.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1758 / 1758
position (AA) of stopcodon in wt / mu AA sequence 586 / 586
position of stopcodon in wt / mu cDNA 1889 / 1889
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 132 / 132
chromosome 3
strand 1
last intron/exon boundary 1781
theoretical NMD boundary in CDS 1599
length of CDS 1758
coding sequence (CDS) position 839
cDNA position
(for ins/del: last normal base / first normal base)		 970
gDNA position
(for ins/del: last normal base / first normal base)		 43284
chromosomal position
(for ins/del: last normal base / first normal base)		 111304209
original gDNA sequence snippet GATTGTGGAAAATAACTCCACGGATGTCTTGGTAGAGGTGA
altered gDNA sequence snippet GATTGTGGAAAATAACTCCATGGATGTCTTGGTAGAGGTGA
original cDNA sequence snippet GATTGTGGAAAATAACTCCACGGATGTCTTGGTAGAGAGAA
altered cDNA sequence snippet GATTGTGGAAAATAACTCCATGGATGTCTTGGTAGAGAGAA
wildtype AA sequence MEKKWKYCAV YYIIQIHFVK GVWEKTVNTE ENVYATLGSD VNLTCQTQTV GFFVQMQWSK
VTNKIDLIAV YHPQYGFYCA YGRPCESLVT FTETPENGSK WTLHLRNMSC SVSGRYECML
VLYPEGIQTK IYNLLIQTHV TADEWNSNHT IEIEINQTLE IPCFQNSSSK ISSEFTYAWS
VENSSTDSWV LLSKGIKEDN GTQETLISQN HLISNSTLLK DRVKLGTDYR LHLSPVQIFD
DGRKFSCHIR VGPNKILRSS TTVKVFAKPE IPVIVENNST DVLVERRFTC LLKNVFPKAN
ITWFIDGSFL HDEKEGIYIT NEERKGKDGF LELKSVLTRV HSNKPAQSDN LTIWCMALSP
VPGNKVWNIS SEKITFLLGS EISSTDPPLS VTESTLDTQP SPASSVSPAR YPATSSVTLV
DVSALRPNTT PQPSNSSMTT RGFNYPWTSS GTDTKKSVSR IPSETYSSSP SGAGSTLHDN
VFTSTARAFS EVPTTANGST KTNHVHITGI VVNKPKDGMS WPVIVAALLF CCMILFGLGV
RKWCQYQKEI MERPPPFKPP PPPIKYTCIQ EPNESDLPYH EMETL*
mutated AA sequence MEKKWKYCAV YYIIQIHFVK GVWEKTVNTE ENVYATLGSD VNLTCQTQTV GFFVQMQWSK
VTNKIDLIAV YHPQYGFYCA YGRPCESLVT FTETPENGSK WTLHLRNMSC SVSGRYECML
VLYPEGIQTK IYNLLIQTHV TADEWNSNHT IEIEINQTLE IPCFQNSSSK ISSEFTYAWS
VENSSTDSWV LLSKGIKEDN GTQETLISQN HLISNSTLLK DRVKLGTDYR LHLSPVQIFD
DGRKFSCHIR VGPNKILRSS TTVKVFAKPE IPVIVENNSM DVLVERRFTC LLKNVFPKAN
ITWFIDGSFL HDEKEGIYIT NEERKGKDGF LELKSVLTRV HSNKPAQSDN LTIWCMALSP
VPGNKVWNIS SEKITFLLGS EISSTDPPLS VTESTLDTQP SPASSVSPAR YPATSSVTLV
DVSALRPNTT PQPSNSSMTT RGFNYPWTSS GTDTKKSVSR IPSETYSSSP SGAGSTLHDN
VFTSTARAFS EVPTTANGST KTNHVHITGI VVNKPKDGMS WPVIVAALLF CCMILFGLGV
RKWCQYQKEI MERPPPFKPP PPPIKYTCIQ EPNESDLPYH EMETL*
speed 0.52 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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