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 6 transcript(s)...
Querying Taster for transcript #1: ENST00000378043
Querying Taster for transcript #2: ENST00000534553
Querying Taster for transcript #3: ENST00000449131
Querying Taster for transcript #4: ENST00000435278
Querying Taster for transcript #5: ENST00000378042
Querying Taster for transcript #6: ENST00000301774
MT speed 0 s - this script 2.592776 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BEST1disease_causing_automatic3.66510069254309e-06simple_aaeaffected0L41Psingle base exchangers121918288show file
BEST1disease_causing_automatic3.66510069254309e-06simple_aaeaffected0L41Psingle base exchangers121918288show file
BEST1disease_causing_automatic1.64248094990322e-05without_aaeaffected0single base exchangers121918288show file
BEST1disease_causing_automatic1.64248094990322e-05without_aaeaffected0single base exchangers121918288show file
BEST1disease_causing_automatic1.64248094990322e-05without_aaeaffected0single base exchangers121918288show file
BEST1disease_causing_automatic0.000279645328818828without_aaeaffected0single base exchangers121918288show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 3.66510069254309e-06 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033071)
  • known disease mutation: rs2743 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719400T>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000378043
Genbank transcript ID NM_004183
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.122T>C
cDNA.765T>C
g.2108T>C
AA changes L41P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 41
frameshift no
known variant Reference ID: rs121918288
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2743 (pathogenic for Bestrophinopathy, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9770
1.4360.002
(flanking)-0.1810
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 increased2109wt: 0.5853 / mu: 0.6336 (marginal change - not scored)wt: GAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTT
mu: GAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTT		 gctc|TGCT
Acc increased2112wt: 0.33 / mu: 0.39wt: TTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTTTAT
mu: TTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTTTAT		 ctgc|TACT
Acc increased2105wt: 0.57 / mu: 0.66wt: TGGCGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCC
mu: TGGCGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCC		 tcct|GCTC
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      41KLLYGEFLIFLLCYYIIRFIYRLA
mutated  not conserved    41KLLYGEFLIFLPCYYIIRFIYRL
Ptroglodytes  all identical  ENSPTRG00000003756  41KLLYGEFLIFLLCYYIIRFIYRL
Mmulatta  all identical  ENSMMUG00000015147  41KLLYGEFFIFLLCYYIIRFIYRL
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  not conserved  ENSMUSG00000037418  41KLLYGEFLVFIFLYYSIRGLYRM
Ggallus  not conserved  ENSGALG00000007217  41KLLYSEFLIFISLYFAISLVYRL
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000078331  41KLLYRELLIFTVMYCIISITYRC
Dmelanogaster  not conserved  FBgn0040238  41KLVWLDLLAFLTIYYAINMVYRF
Celegans  not conserved  C01B12.3  41KSVWAELVVWLCLYAVLSVIYRC
Xtropicalis  not conserved  ENSXETG00000006740  41KLLYREFLIFISCYFIISVTYRF
protein features
start (aa)end (aa)featuredetails 
2646TRANSMEMHelical; (Potential).lost
4770TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7191TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
92178TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
179199TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
200228TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
229249INTRAMEMPotential.might get lost (downstream of altered splice site)
250270TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
271291TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
292585TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
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 2401 / 2401
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 644 / 644
chromosome 11
strand 1
last intron/exon boundary 2383
theoretical NMD boundary in CDS 1689
length of CDS 1758
coding sequence (CDS) position 122
cDNA position
(for ins/del: last normal base / first normal base)		 765
gDNA position
(for ins/del: last normal base / first normal base)		 2108
chromosomal position
(for ins/del: last normal base / first normal base)		 61719400
original gDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered gDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
original cDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered cDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
wildtype AA sequence MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR DEAHS*
mutated AA sequence MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL PCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR DEAHS*
speed 0.16 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: 3.66510069254309e-06 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM033071)
  • known disease mutation: rs2743 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719400T>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000435278
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.122T>C
cDNA.235T>C
g.2108T>C
AA changes L41P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 41
frameshift no
known variant Reference ID: rs121918288
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2743 (pathogenic for Bestrophinopathy, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9770
1.4360.002
(flanking)-0.1810
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 increased2109wt: 0.5853 / mu: 0.6336 (marginal change - not scored)wt: GAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTT
mu: GAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTT		 gctc|TGCT
Acc increased2112wt: 0.33 / mu: 0.39wt: TTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTTTAT
mu: TTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTTTAT		 ctgc|TACT
Acc increased2105wt: 0.57 / mu: 0.66wt: TGGCGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCC
mu: TGGCGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCC		 tcct|GCTC
distance from splice site 31
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      41KLLYGEFLIFLLCYYIIRFIYRLA
mutated  not conserved    41KLLYGEFLIFLPCYYIIRFIYRL
Ptroglodytes  all identical  ENSPTRG00000003756  41KLLYGEFLIFLLCYYIIRFIYRL
Mmulatta  all identical  ENSMMUG00000015147  41KLLYGEFFIFLLCYYIIRFIYRL
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  not conserved  ENSMUSG00000037418  41KLLYGEFLVFIFLYYSIRGLYRM
Ggallus  not conserved  ENSGALG00000007217  41KLLYSEFLIFISLYFAISLVYRL
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000078331  41KLLYRELLIFTVMYCIISITYRC
Dmelanogaster  not conserved  FBgn0040238  41KLVWLDLLAFLTIYYAINMVYRF
Celegans  not conserved  C01B12.3  41KSVWAELVVWLCLYAVLSVIYRC
Xtropicalis  not conserved  ENSXETG00000006740  41KLLYREFLIFISCYFIISVTYRF
protein features
start (aa)end (aa)featuredetails 
2646TRANSMEMHelical; (Potential).lost
4770TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7191TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
92178TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
179199TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
200228TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
229249INTRAMEMPotential.might get lost (downstream of altered splice site)
250270TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
271291TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
292585TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 813 / 813
position (AA) of stopcodon in wt / mu AA sequence 271 / 271
position of stopcodon in wt / mu cDNA 926 / 926
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 114 / 114
chromosome 11
strand 1
last intron/exon boundary 828
theoretical NMD boundary in CDS 664
length of CDS 813
coding sequence (CDS) position 122
cDNA position
(for ins/del: last normal base / first normal base)		 235
gDNA position
(for ins/del: last normal base / first normal base)		 2108
chromosomal position
(for ins/del: last normal base / first normal base)		 61719400
original gDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered gDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
original cDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered cDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
wildtype AA sequence MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQPE
QRGDGVPAQS GGRGGCSRWH HWPLPRPAVP *
mutated AA sequence MTITYTSQVA NARLGSFSRL LLCWRGSIYK LLYGEFLIFL PCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQPE
QRGDGVPAQS GGRGGCSRWH HWPLPRPAVP *
speed 0.16 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: without_aae, prob: 1.64248094990322e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM033071)
  • known disease mutation: rs2743 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719400T>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000534553
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region intron
DNA changes g.2108T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121918288
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2743 (pathogenic for Bestrophinopathy, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9770
1.4360.002
(flanking)-0.1810
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -69) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased2109wt: 0.5853 / mu: 0.6336 (marginal change - not scored)wt: GAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTT
mu: GAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTT		 gctc|TGCT
Acc increased2112wt: 0.33 / mu: 0.39wt: TTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTTTAT
mu: TTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTTTAT		 ctgc|TACT
Acc increased2105wt: 0.57 / mu: 0.66wt: TGGCGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCC
mu: TGGCGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCC		 tcct|GCTC
distance from splice site 1501
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
125TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
2646TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
4770TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7191TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
92178TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
179199TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
200228TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
229249INTRAMEMPotential.might get lost (downstream of altered splice site)
250270TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
271291TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
292585TOPO_DOMCytoplasmic (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 577 / 577
chromosome 11
strand 1
last intron/exon boundary 740
theoretical NMD boundary in CDS 113
length of CDS 168
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)		 2108
chromosomal position
(for ins/del: last normal base / first normal base)		 61719400
original gDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered gDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAA*
mutated AA sequence N/A
speed 0.16 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: without_aae, prob: 1.64248094990322e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM033071)
  • known disease mutation: rs2743 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719400T>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000449131
Genbank transcript ID NM_001139443
UniProt peptide O76090
alteration type single base exchange
alteration region intron
DNA changes g.2108T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121918288
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2743 (pathogenic for Bestrophinopathy, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9770
1.4360.002
(flanking)-0.1810
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -8) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased2109wt: 0.5853 / mu: 0.6336 (marginal change - not scored)wt: GAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTT
mu: GAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTT		 gctc|TGCT
Acc increased2112wt: 0.33 / mu: 0.39wt: TTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTTTAT
mu: TTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTTTAT		 ctgc|TACT
Acc increased2105wt: 0.57 / mu: 0.66wt: TGGCGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCC
mu: TGGCGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCC		 tcct|GCTC
distance from splice site 1501
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
125TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
2646TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
4770TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7191TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
92178TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
179199TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
200228TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
229249INTRAMEMPotential.might get lost (downstream of altered splice site)
250270TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
271291TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
292585TOPO_DOMCytoplasmic (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 87 / 87
chromosome 11
strand 1
last intron/exon boundary 1007
theoretical NMD boundary in CDS 870
length of CDS 1815
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)		 2108
chromosomal position
(for ins/del: last normal base / first normal base)		 61719400
original gDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered gDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFGE
DDDDFETNWI VDRNLQVSLL AVDEMHQDLP RMEPDMYWNK PEPQPPYTAA SAQFRRASFM
GSTFNISLNK EEMEFQPNQE DEEDAHAGII GRFLGLQSHD HHPPRANSRT KLLWPKRESL
LHEGLPKNHK AAKQNVRGQE DNKAWKLKAV DAFKSAPLYQ RPGYYSAPQT PLSPTPMFFP
LEPSAPSKLH SVTGIDTKDK SLKTVSSGAK KSFELLSESD GALMEHPEVS QVRRKTVEFN
LTDMPEIPEN HLKEPLEQSP TNIHTTLKDH MDPYWALENR SVLHLNQGHC IALCPTPASL
ALSLPFLHNF LGFHHCQSTL DLRPALAWGI YLATFTGILG KCSGPFLTSP WYHPEDFLGP
GEGR*
mutated AA sequence N/A
speed 0.21 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: without_aae, prob: 1.64248094990322e-05 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM033071)
  • known disease mutation: rs2743 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719400T>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000301774
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region intron
DNA changes g.2108T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121918288
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2743 (pathogenic for Bestrophinopathy, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9770
1.4360.002
(flanking)-0.1810
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -129) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased2109wt: 0.5853 / mu: 0.6336 (marginal change - not scored)wt: GAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTT
mu: GAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTT		 gctc|TGCT
Acc increased2112wt: 0.33 / mu: 0.39wt: TTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTTTAT
mu: TTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTTTAT		 ctgc|TACT
Acc increased2105wt: 0.57 / mu: 0.66wt: TGGCGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCC
mu: TGGCGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCC		 tcct|GCTC
distance from splice site 1501
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
125TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
2646TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
4770TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7191TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
92178TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
179199TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
200228TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
229249INTRAMEMPotential.might get lost (downstream of altered splice site)
250270TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
271291TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
292585TOPO_DOMCytoplasmic (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 756 / 756
chromosome 11
strand 1
last intron/exon boundary 740
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 879
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)		 2108
chromosomal position
(for ins/del: last normal base / first normal base)		 61719400
original gDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered gDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MEFQPNQEDE EDAHAGIIGR FLGLQSHDHH PPRANSRTKL LWPKRESLLH EGLPKNHKAA
KQNVRGQEDN KAWKLKAVDA FKSAPLYQRP GYYSAPQTPL SPTPMFFPLE PSAPSKLHSV
TGIDTKDKSL KTVSSGAKKS FELLSESDGA LMEHPEVSQV RRKTVEFNLT DMPEIPENHL
KEPLEQSPTN IHTTLKDHMD PYWALENRSV LHLNQGHCIA LCPTPASLAL SLPFLHNFLG
FHHCQSTLDL RPALAWGIYL ATFTGILGKC SGPFLTSPWY HPEDFLGPGE GR*
mutated AA sequence N/A
speed 0.14 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: without_aae, prob: 0.000279645328818828 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM033071)
  • known disease mutation: rs2743 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719400T>CN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000378042
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.702T>C
g.2108T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs121918288
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2743 (pathogenic for Bestrophinopathy, autosomal recessive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)

known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
known disease mutation at this position, please check HGMD for details (HGMD ID CM033071)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.9770
1.4360.002
(flanking)-0.1810
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -20) | splice site change before start ATG (at aa -18) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased2109wt: 0.5853 / mu: 0.6336 (marginal change - not scored)wt: GAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTT
mu: GAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTT		 gctc|TGCT
Acc increased2112wt: 0.33 / mu: 0.39wt: TTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCTTTAT
mu: TTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCTTTAT		 ctgc|TACT
Acc increased2105wt: 0.57 / mu: 0.66wt: TGGCGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCC
mu: TGGCGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCC		 tcct|GCTC
distance from splice site 31
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
125TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
2646TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
4770TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7191TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
92178TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
179199TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
200228TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
229249INTRAMEMPotential.might get lost (downstream of altered splice site)
250270TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
271291TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
292585TOPO_DOMCytoplasmic (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 761 / 761
chromosome 11
strand 1
last intron/exon boundary 2239
theoretical NMD boundary in CDS 1428
length of CDS 1497
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 702
gDNA position
(for ins/del: last normal base / first normal base)		 2108
chromosomal position
(for ins/del: last normal base / first normal base)		 61719400
original gDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered gDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
original cDNA sequence snippet CGAGTTCTTAATCTTCCTGCTCTGCTACTACATCATCCGCT
altered cDNA sequence snippet CGAGTTCTTAATCTTCCTGCCCTGCTACTACATCATCCGCT
wildtype AA sequence MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV SLLAVDEMHQ
DLPRMEPDMY WNKPEPQPPY TAASAQFRRA SFMGSTFNIS LNKEEMEFQP NQEDEEDAHA
GIIGRFLGLQ SHDHHPPRAN SRTKLLWPKR ESLLHEGLPK NHKAAKQNVR GQEDNKAWKL
KAVDAFKSAP LYQRPGYYSA PQTPLSPTPM FFPLEPSAPS KLHSVTGIDT KDKSLKTVSS
GAKKSFELLS ESDGALMEHP EVSQVRRKTV EFNLTDMPEI PENHLKEPLE QSPTNIHTTL
KDHMDPYWAL ENRDEAHS*
mutated AA sequence N/A
speed 0.22 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