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 7 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: ENST00000526988
Querying Taster for transcript #5: ENST00000435278
Querying Taster for transcript #6: ENST00000378042
Querying Taster for transcript #7: ENST00000301774
MT speed 0 s - this script 7.121042 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BEST1disease_causing_automatic0.999999999613727simple_aaeaffected0Y227Nsingle base exchangers28941469show file
BEST1disease_causing_automatic0.999999999613727simple_aaeaffected0Y167Nsingle base exchangers28941469show file
BEST1disease_causing_automatic0.999999999613727simple_aaeaffected0Y121Nsingle base exchangers28941469show file
BEST1disease_causing_automatic0.999999999613727simple_aaeaffected0Y227Nsingle base exchangers28941469show file
BEST1disease_causing_automatic0.999999999613727simple_aaeaffected0Y167Nsingle base exchangers28941469show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28941469show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28941469show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999613727 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM982025)
  • known disease mutation: rs2731 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61724901T>AN/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.679T>A
cDNA.1322T>A
g.7609T>A
AA changes Y227N Score: 142 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 227
frameshift no
known variant Reference ID: rs28941469
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2731 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9071
4.9051
(flanking)4.9051
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained76050.98mu: CTGTATGCCAACGAC GTAT|gcca
Donor gained76130.38mu: CAACGACTGGATTAG ACGA|ctgg
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      227TLRTQCGHLYAYDWISIPLVYTQV
mutated  not conserved    227TLRTQCGHLYANDWISIPLVYTQ
Ptroglodytes  all identical  ENSPTRG00000003756  227TLRTQCGHLYAYDWISIPLVYTQ
Mmulatta  all identical  ENSMMUG00000015147  227TLRTQCGHLYAYDWISIPLVYTQ
Fcatus  all identical  ENSFCAG00000007380  257VLRTQCGLLFAYDWISIPLVYTQ
Mmusculus  all identical  ENSMUSG00000037418  227TLRTQCGQLYAYDWISIPLVYTQ
Ggallus  all identical  ENSGALG00000007217  227TLRSQCGRLYGYDWISIPLVYTQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  227TLRSQCMRLYGYDWISLPLVYTQ
Dmelanogaster  all identical  FBgn0040238  229KFRGQCGLLISYDTISVPLVY
Celegans  all conserved  C01B12.3  227QFRVNILSLTLFDWVPVPLVYTQ
Xtropicalis  all identical  ENSXETG00000006740  227SLRTQCGRLYGYDWISVPLVYTQ
protein features
start (aa)end (aa)featuredetails 
200228TOPO_DOMExtracellular (Potential).lost
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 679
cDNA position
(for ins/del: last normal base / first normal base)		 1322
gDNA position
(for ins/del: last normal base / first normal base)		 7609
chromosomal position
(for ins/del: last normal base / first normal base)		 61724901
original gDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered gDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
original cDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered cDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
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 LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYANDWI 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 1.21 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: simple_aae, prob: 0.999999999613727 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM982025)
  • known disease mutation: rs2731 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61724901T>AN/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 CDS
DNA changes c.499T>A
cDNA.585T>A
g.7609T>A
AA changes Y167N Score: 142 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 167
frameshift no
known variant Reference ID: rs28941469
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2731 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9071
4.9051
(flanking)4.9051
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained76050.98mu: CTGTATGCCAACGAC GTAT|gcca
Donor gained76130.38mu: CAACGACTGGATTAG ACGA|ctgg
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      167TLRTQCGHLYAYDWISIPLVYTQV
mutated  not conserved    167TLRTQCGHLYANDWISIPLVYTQ
Ptroglodytes  all identical  ENSPTRG00000003756  227TLRTQCGHLYAYDWISIPLVYTQ
Mmulatta  all identical  ENSMMUG00000015147  227TLRTQCGHLYAYDWISIPLVYTQ
Fcatus  all identical  ENSFCAG00000007380  257VLRTQCGLLFAYDWISIPLVYTQ
Mmusculus  all identical  ENSMUSG00000037418  227TLRTQCGQLYAYDWISIPLVYTQ
Ggallus  all identical  ENSGALG00000007217  227TLRSQCGRLYGYDWISIPLVYTQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  227TLRSQCMRLYGYDWISLPLVYTQ
Dmelanogaster  all identical  FBgn0040238  231KFRGQCGLLISYDTISVPLVYTQ
Celegans  all conserved  C01B12.3  227QFRVNILSLTLFDWVPVPLVYTQ
Xtropicalis  all identical  ENSXETG00000006740  227SLRTQCGRLYGYDWISVPLVYTQ
protein features
start (aa)end (aa)featuredetails 
92178TOPO_DOMCytoplasmic (Potential).lost
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 1815 / 1815
position (AA) of stopcodon in wt / mu AA sequence 605 / 605
position of stopcodon in wt / mu cDNA 1901 / 1901
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 499
cDNA position
(for ins/del: last normal base / first normal base)		 585
gDNA position
(for ins/del: last normal base / first normal base)		 7609
chromosomal position
(for ins/del: last normal base / first normal base)		 61724901
original gDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered gDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
original cDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered cDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
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 MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYANDWI 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*
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: 0.999999999613727 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM982025)
  • known disease mutation: rs2731 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61724901T>AN/A show variant in all transcripts   IGV
HGNC symbol BEST1
Ensembl transcript ID ENST00000526988
Genbank transcript ID N/A
UniProt peptide O76090
alteration type single base exchange
alteration region CDS
DNA changes c.361T>A
cDNA.522T>A
g.7609T>A
AA changes Y121N Score: 142 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 121
frameshift no
known variant Reference ID: rs28941469
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2731 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9071
4.9051
(flanking)4.9051
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained76050.98mu: CTGTATGCCAACGAC GTAT|gcca
Donor gained76130.38mu: CAACGACTGGATTAG ACGA|ctgg
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      121TLRTQCGHLYAYDWISIPLVYTQV
mutated  not conserved    121NDWISIPLVYTQ
Ptroglodytes  all identical  ENSPTRG00000003756  227YDWISIPLVYTQ
Mmulatta  all identical  ENSMMUG00000015147  227YDWISIPLVYTQ
Fcatus  all identical  ENSFCAG00000007380  257VLRTQCGLLFAYDWISIPLVYTQ
Mmusculus  all identical  ENSMUSG00000037418  227YDWISIPLVYTQ
Ggallus  all identical  ENSGALG00000007217  227YDWISIPLVYTQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  227TLRSQCMRLYGYDWISLPLVYTQ
Dmelanogaster  all identical  FBgn0040238  231YDTISVPLVYTQ
Celegans  all conserved  C01B12.3  227QFRVNILSLTLFDW
Xtropicalis  all identical  ENSXETG00000006740  227YDWISVPLVYTQ
protein features
start (aa)end (aa)featuredetails 
92178TOPO_DOMCytoplasmic (Potential).lost
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 990 / 990
position (AA) of stopcodon in wt / mu AA sequence 330 / 330
position of stopcodon in wt / mu cDNA 1151 / 1151
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 162 / 162
chromosome 11
strand 1
last intron/exon boundary 1147
theoretical NMD boundary in CDS 935
length of CDS 990
coding sequence (CDS) position 361
cDNA position
(for ins/del: last normal base / first normal base)		 522
gDNA position
(for ins/del: last normal base / first normal base)		 7609
chromosomal position
(for ins/del: last normal base / first normal base)		 61724901
original gDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered gDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
original cDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered cDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
wildtype AA sequence MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAGFMTPA
EHKQLEKLSL PHNMFWVPWV WFANLSMKAW LGGRIRDPIL LQSLLNEMNT LRTQCGHLYA
YDWISIPLVY TQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL ERMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*
mutated AA sequence MSLVSGFVEG KDEQGRLLRR TLIRYANLGN VLILRSVSTA VYKRFPSAQH LVQAGFMTPA
EHKQLEKLSL PHNMFWVPWV WFANLSMKAW LGGRIRDPIL LQSLLNEMNT LRTQCGHLYA
NDWISIPLVY TQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL ERMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*
speed 1.21 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: simple_aae, prob: 0.999999999613727 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM982025)
  • known disease mutation: rs2731 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61724901T>AN/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.679T>A
cDNA.792T>A
g.7609T>A
AA changes Y227N Score: 142 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 227
frameshift no
known variant Reference ID: rs28941469
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2731 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9071
4.9051
(flanking)4.9051
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained76050.98mu: CTGTATGCCAACGAC GTAT|gcca
Donor gained76130.38mu: CAACGACTGGATTAG ACGA|ctgg
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      227TLRTQCGHLYAYDWISIPLVYTQP
mutated  not conserved    227TLRTQCGHLYANDWISIPLVYTQ
Ptroglodytes  all identical  ENSPTRG00000003756  227TLRTQCGHLYAYDWISIPLVYTQ
Mmulatta  all identical  ENSMMUG00000015147  227TLRTQCGHLYAYDWISIPLVYTQ
Fcatus  all identical  ENSFCAG00000007380  257VLRTQCGLLFAYDWISIPLVYTQ
Mmusculus  all identical  ENSMUSG00000037418  227TLRTQCGQLYAYDWISIPLVYTQ
Ggallus  all identical  ENSGALG00000007217  227TLRSQCGRLYGYDWISIPLVYTQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  227TLRSQCMRLYGYDWISLPLVYTQ
Dmelanogaster  all identical  FBgn0040238  229KFRGQCGLLISYDTISVPLVY
Celegans  all conserved  C01B12.3  227QFRVNILSLTLFDWVPVPLVYTQ
Xtropicalis  all identical  ENSXETG00000006740  227SLRTQCGRLYGYDWISVPLVYTQ
protein features
start (aa)end (aa)featuredetails 
200228TOPO_DOMExtracellular (Potential).lost
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 679
cDNA position
(for ins/del: last normal base / first normal base)		 792
gDNA position
(for ins/del: last normal base / first normal base)		 7609
chromosomal position
(for ins/del: last normal base / first normal base)		 61724901
original gDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered gDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
original cDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered cDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
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 LCYYIIRFIY RLALTEEQQL
MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYANDWI SIPLVYTQPE
QRGDGVPAQS GGRGGCSRWH HWPLPRPAVP *
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: simple_aae, prob: 0.999999999613727 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM982025)
  • known disease mutation: rs2731 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61724901T>AN/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 CDS
DNA changes c.499T>A
cDNA.1259T>A
g.7609T>A
AA changes Y167N Score: 142 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 167
frameshift no
known variant Reference ID: rs28941469
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2731 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9071
4.9051
(flanking)4.9051
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained76050.98mu: CTGTATGCCAACGAC GTAT|gcca
Donor gained76130.38mu: CAACGACTGGATTAG ACGA|ctgg
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      167TLRTQCGHLYAYDWISIPLVYTQV
mutated  not conserved    167TLRTQCGHLYANDWISIPLVYTQ
Ptroglodytes  all identical  ENSPTRG00000003756  227TLRTQCGHLYAYDWISIPLVYTQ
Mmulatta  all identical  ENSMMUG00000015147  227TLRTQCGHLYAYDWISIPLVYTQ
Fcatus  all identical  ENSFCAG00000007380  257VLRTQCGLLFAYDWISIPLVYTQ
Mmusculus  all identical  ENSMUSG00000037418  227TLRTQCGQLYAYDWISIPLVYTQ
Ggallus  all identical  ENSGALG00000007217  227TLRSQCGRLYGYDWISIPLVYTQ
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  227TLRSQCMRLYGYDWISLPLVYTQ
Dmelanogaster  all identical  FBgn0040238  231KFRGQCGLLISYDTISVPLVYTQ
Celegans  all conserved  C01B12.3  227QFRVNILSLTLFDWVPVPLVYTQ
Xtropicalis  all identical  ENSXETG00000006740  227SLRTQCGRLYGYDWISVPLVYTQ
protein features
start (aa)end (aa)featuredetails 
92178TOPO_DOMCytoplasmic (Potential).lost
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 1497 / 1497
position (AA) of stopcodon in wt / mu AA sequence 499 / 499
position of stopcodon in wt / mu cDNA 2257 / 2257
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 499
cDNA position
(for ins/del: last normal base / first normal base)		 1259
gDNA position
(for ins/del: last normal base / first normal base)		 7609
chromosomal position
(for ins/del: last normal base / first normal base)		 61724901
original gDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered gDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
original cDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered cDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
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 MFEKLTLYCD SYIQLIPISF VLGFYVTLVV TRWWNQYENL PWPDRLMSLV SGFVEGKDEQ
GRLLRRTLIR YANLGNVLIL RSVSTAVYKR FPSAQHLVQA GFMTPAEHKQ LEKLSLPHNM
FWVPWVWFAN LSMKAWLGGR IRDPILLQSL LNEMNTLRTQ CGHLYANDWI 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*
speed 1.19 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 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM982025)
  • known disease mutation: rs2731 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61724901T>AN/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.7609T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28941469
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2731 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9071
4.9051
(flanking)4.9051
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained76050.98mu: CTGTATGCCAACGAC GTAT|gcca
Donor gained76130.38mu: CAACGACTGGATTAG ACGA|ctgg
distance from splice site 1478
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
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)		 7609
chromosomal position
(for ins/del: last normal base / first normal base)		 61724901
original gDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered gDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
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 0.97 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 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM982025)
  • known disease mutation: rs2731 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61724901T>AN/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.7609T>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28941469
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2731 (pathogenic for Retinal dystrophy|Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982025)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9071
4.9051
(flanking)4.9051
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -4) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor gained76050.98mu: CTGTATGCCAACGAC GTAT|gcca
Donor gained76130.38mu: CAACGACTGGATTAG ACGA|ctgg
distance from splice site 1478
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)		 7609
chromosomal position
(for ins/del: last normal base / first normal base)		 61724901
original gDNA sequence snippet AGTGTGGACACCTGTATGCCTACGACTGGATTAGTATCCCA
altered gDNA sequence snippet AGTGTGGACACCTGTATGCCAACGACTGGATTAGTATCCCA
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 0.11 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