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: ENST00000264499
Querying Taster for transcript #2: ENST00000506636
MT speed 0 s - this script 3.561708 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BBS7disease_causing_automatic0.998632544620822simple_aaeaffected0H323Rsingle base exchangers119466001show file
BBS7disease_causing_automatic0.998632544620822simple_aaeaffected0H323Rsingle base exchangers119466001show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.998632544620822 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030645)
  • known disease mutation: rs3015 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:122768628T>CN/A show variant in all transcripts   IGV
HGNC symbol BBS7
Ensembl transcript ID ENST00000264499
Genbank transcript ID NM_176824
UniProt peptide Q8IWZ6
alteration type single base exchange
alteration region CDS
DNA changes c.968A>G
cDNA.1152A>G
g.23025A>G
AA changes H323R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 323
frameshift no
known variant Reference ID: rs119466001
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs3015 (pathogenic for Bardet-Biedl syndrome 7|Bardet-Biedl syndrome|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030645)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030645)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030645)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6290.883
4.6750.99
(flanking)2.8280.982
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained230240.84mu: CCATTCGTAAGGAAA ATTC|gtaa
distance from splice site 34
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      323GWVTGLTTEPIHKESGPGEELKIN
mutated  not conserved    323GWVTGLTTEPIRKESGPGEELKI
Ptroglodytes  all identical  ENSPTRG00000016411  310GWVTGLTTEPIHKESGPGEELKI
Mmulatta  all identical  ENSMMUG00000009819  323GWVTGLTTEPIHKESGPGEELKF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000037325  323GWVTGLTTEPTHKESGPGEELKL
Ggallus  all conserved  ENSGALG00000011880  323GWLTGLTTELAYREGGSGEELKL
Trubripes  not conserved  ENSTRUG00000007380  323GWVTGLTTEPQKAEVGPGNEIKM
Drerio  not conserved  ENSDARG00000059911  323GWVSGLTTEPQQMVAGPGEEIKM
Dmelanogaster  no homologue    
Celegans  not conserved  Y75B8A.12  325GWLFSLA-----KTSRPMIENLPV
Xtropicalis  all identical  ENSXETG00000031279  323GWVTGLTTEPIHKEAGPGQELKM
protein features
start (aa)end (aa)featuredetails 
469469CONFLICTQ -> L (in Ref. 1; AAO16025/AAO16026 and 2; BAA91767).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2148 / 2148
position (AA) of stopcodon in wt / mu AA sequence 716 / 716
position of stopcodon in wt / mu cDNA 2332 / 2332
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 185 / 185
chromosome 4
strand -1
last intron/exon boundary 2199
theoretical NMD boundary in CDS 1964
length of CDS 2148
coding sequence (CDS) position 968
cDNA position
(for ins/del: last normal base / first normal base)		 1152
gDNA position
(for ins/del: last normal base / first normal base)		 23025
chromosomal position
(for ins/del: last normal base / first normal base)		 122768628
original gDNA sequence snippet TCTGACAACAGAGCCCATTCATAAGGAAAGTGGACCAGGAG
altered gDNA sequence snippet TCTGACAACAGAGCCCATTCGTAAGGAAAGTGGACCAGGAG
original cDNA sequence snippet TCTGACAACAGAGCCCATTCATAAGGAAAGTGGACCAGGAG
altered cDNA sequence snippet TCTGACAACAGAGCCCATTCGTAAGGAAAGTGGACCAGGAG
wildtype AA sequence MDLILNRMDY LQVGVTSQKT MKLIPASRHR ATQKVVIGDH DGVVMCFGMK KGEAAAVFKT
LPGPKIARLE LGGVINTPQE KIFIAAASEI RGFTKRGKQF LSFETNLTES IKAMHISGSD
LFLSASYIYN HYCDCKDQHY YLSGDKINDV ICLPVERLSR ITPVLACQDR VLRVLQGSDV
MYAVEVPGPP TVLALHNGNG GDSGEDLLFG TSDGKLALIQ ITTSKPVRKW EIQNEKKRGG
ILCIDSFDIV GDGVKDLLVG RDDGMVEVYS FDNANEPVLR FDQMLSESVT SIQGGCVGKD
SYDEIVVSTY SGWVTGLTTE PIHKESGPGE ELKINQEMQN KISSLRNELE HLQYKVLQER
ENYQQSSQSS KAKSAVPSFG INDKFTLNKD DASYSLILEV QTAIDNVLIQ SDVPIDLLDV
DKNSAVVSFS SCDSESNDNF LLATYRCQAD TTRLELKIRS IEGQYGTLQA YVTPRIQPKT
CQVRQYHIKP LSLHQRTHFI DHDRPMNTLT LTGQFSFAEV HSWVVFCLPE VPEKPPAGEC
VTFYFQNTFL DTQLESTYRK GEGVFKSDNI STISILKDVL SKEATKRKIN LNISYEINEV
SVKHTLKLIH PKLEYQLLLA KKVQLIDALK ELQIHEGNTN FLIPEYHCIL EEADHLQEEY
KKQPAHLERL YGMITDLFID KFKFKGTNVK TKVPLLLEIL DSYDQNALIS FFDAA*
mutated AA sequence MDLILNRMDY LQVGVTSQKT MKLIPASRHR ATQKVVIGDH DGVVMCFGMK KGEAAAVFKT
LPGPKIARLE LGGVINTPQE KIFIAAASEI RGFTKRGKQF LSFETNLTES IKAMHISGSD
LFLSASYIYN HYCDCKDQHY YLSGDKINDV ICLPVERLSR ITPVLACQDR VLRVLQGSDV
MYAVEVPGPP TVLALHNGNG GDSGEDLLFG TSDGKLALIQ ITTSKPVRKW EIQNEKKRGG
ILCIDSFDIV GDGVKDLLVG RDDGMVEVYS FDNANEPVLR FDQMLSESVT SIQGGCVGKD
SYDEIVVSTY SGWVTGLTTE PIRKESGPGE ELKINQEMQN KISSLRNELE HLQYKVLQER
ENYQQSSQSS KAKSAVPSFG INDKFTLNKD DASYSLILEV QTAIDNVLIQ SDVPIDLLDV
DKNSAVVSFS SCDSESNDNF LLATYRCQAD TTRLELKIRS IEGQYGTLQA YVTPRIQPKT
CQVRQYHIKP LSLHQRTHFI DHDRPMNTLT LTGQFSFAEV HSWVVFCLPE VPEKPPAGEC
VTFYFQNTFL DTQLESTYRK GEGVFKSDNI STISILKDVL SKEATKRKIN LNISYEINEV
SVKHTLKLIH PKLEYQLLLA KKVQLIDALK ELQIHEGNTN FLIPEYHCIL EEADHLQEEY
KKQPAHLERL YGMITDLFID KFKFKGTNVK TKVPLLLEIL DSYDQNALIS FFDAA*
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: simple_aae, prob: 0.998632544620822 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030645)
  • known disease mutation: rs3015 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:122768628T>CN/A show variant in all transcripts   IGV
HGNC symbol BBS7
Ensembl transcript ID ENST00000506636
Genbank transcript ID NM_018190
UniProt peptide Q8IWZ6
alteration type single base exchange
alteration region CDS
DNA changes c.968A>G
cDNA.1105A>G
g.23025A>G
AA changes H323R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 323
frameshift no
known variant Reference ID: rs119466001
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs3015 (pathogenic for Bardet-Biedl syndrome 7|Bardet-Biedl syndrome|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030645)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030645)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030645)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6290.883
4.6750.99
(flanking)2.8280.982
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained230240.84mu: CCATTCGTAAGGAAA ATTC|gtaa
distance from splice site 34
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      323GWVTGLTTEPIHKESGPGEELKIN
mutated  not conserved    323GWVTGLTTEPIRKESGPGEELKI
Ptroglodytes  all identical  ENSPTRG00000016411  310GWVTGLTTEPIHKESGPGEELKI
Mmulatta  all identical  ENSMMUG00000009819  323GWVTGLTTEPIHKESGPGEELKF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000037325  323GWVTGLTTEPTHKESGPGEELKL
Ggallus  all conserved  ENSGALG00000011880  323GWLTGLTTELAYREGGSGEELKL
Trubripes  not conserved  ENSTRUG00000007380  323GWVTGLTTEPQKAEVGPGNEIKM
Drerio  not conserved  ENSDARG00000059911  323GWVSGLTTEPQQMVAGPGEEIKM
Dmelanogaster  no homologue    
Celegans  not conserved  Y75B8A.12  325GWLFSLA-----KTSRPMIENLPV
Xtropicalis  all identical  ENSXETG00000031279  323GWVTGLTTEPIHKEAGPGQELKM
protein features
start (aa)end (aa)featuredetails 
469469CONFLICTQ -> L (in Ref. 1; AAO16025/AAO16026 and 2; BAA91767).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2019 / 2019
position (AA) of stopcodon in wt / mu AA sequence 673 / 673
position of stopcodon in wt / mu cDNA 2156 / 2156
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 138 / 138
chromosome 4
strand -1
last intron/exon boundary 2028
theoretical NMD boundary in CDS 1840
length of CDS 2019
coding sequence (CDS) position 968
cDNA position
(for ins/del: last normal base / first normal base)		 1105
gDNA position
(for ins/del: last normal base / first normal base)		 23025
chromosomal position
(for ins/del: last normal base / first normal base)		 122768628
original gDNA sequence snippet TCTGACAACAGAGCCCATTCATAAGGAAAGTGGACCAGGAG
altered gDNA sequence snippet TCTGACAACAGAGCCCATTCGTAAGGAAAGTGGACCAGGAG
original cDNA sequence snippet TCTGACAACAGAGCCCATTCATAAGGAAAGTGGACCAGGAG
altered cDNA sequence snippet TCTGACAACAGAGCCCATTCGTAAGGAAAGTGGACCAGGAG
wildtype AA sequence MDLILNRMDY LQVGVTSQKT MKLIPASRHR ATQKVVIGDH DGVVMCFGMK KGEAAAVFKT
LPGPKIARLE LGGVINTPQE KIFIAAASEI RGFTKRGKQF LSFETNLTES IKAMHISGSD
LFLSASYIYN HYCDCKDQHY YLSGDKINDV ICLPVERLSR ITPVLACQDR VLRVLQGSDV
MYAVEVPGPP TVLALHNGNG GDSGEDLLFG TSDGKLALIQ ITTSKPVRKW EIQNEKKRGG
ILCIDSFDIV GDGVKDLLVG RDDGMVEVYS FDNANEPVLR FDQMLSESVT SIQGGCVGKD
SYDEIVVSTY SGWVTGLTTE PIHKESGPGE ELKINQEMQN KISSLRNELE HLQYKVLQER
ENYQQSSQSS KAKSAVPSFG INDKFTLNKD DASYSLILEV QTAIDNVLIQ SDVPIDLLDV
DKNSAVVSFS SCDSESNDNF LLATYRCQAD TTRLELKIRS IEGQYGTLQA YVTPRIQPKT
CQVRQYHIKP LSLHQRTHFI DHDRPMNTLT LTGQFSFAEV HSWVVFCLPE VPEKPPAGEC
VTFYFQNTFL DTQLESTYRK GEGVFKSDNI STISILKDVL SKEATKRKIN LNISYEINEV
SVKHTLKLIH PKLEYQLLLA KKVQLIDALK ELQIHEGNTN FLIPEYHCIL EEADHLQEEY
KKQPAHLERL YG*
mutated AA sequence MDLILNRMDY LQVGVTSQKT MKLIPASRHR ATQKVVIGDH DGVVMCFGMK KGEAAAVFKT
LPGPKIARLE LGGVINTPQE KIFIAAASEI RGFTKRGKQF LSFETNLTES IKAMHISGSD
LFLSASYIYN HYCDCKDQHY YLSGDKINDV ICLPVERLSR ITPVLACQDR VLRVLQGSDV
MYAVEVPGPP TVLALHNGNG GDSGEDLLFG TSDGKLALIQ ITTSKPVRKW EIQNEKKRGG
ILCIDSFDIV GDGVKDLLVG RDDGMVEVYS FDNANEPVLR FDQMLSESVT SIQGGCVGKD
SYDEIVVSTY SGWVTGLTTE PIRKESGPGE ELKINQEMQN KISSLRNELE HLQYKVLQER
ENYQQSSQSS KAKSAVPSFG INDKFTLNKD DASYSLILEV QTAIDNVLIQ SDVPIDLLDV
DKNSAVVSFS SCDSESNDNF LLATYRCQAD TTRLELKIRS IEGQYGTLQA YVTPRIQPKT
CQVRQYHIKP LSLHQRTHFI DHDRPMNTLT LTGQFSFAEV HSWVVFCLPE VPEKPPAGEC
VTFYFQNTFL DTQLESTYRK GEGVFKSDNI STISILKDVL SKEATKRKIN LNISYEINEV
SVKHTLKLIH PKLEYQLLLA KKVQLIDALK ELQIHEGNTN FLIPEYHCIL EEADHLQEEY
KKQPAHLERL YG*
speed 0.67 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