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 6.031332 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BEST1disease_causing_automatic0.983352210913347simple_aaeaffected0E261Ksingle base exchangers28941468show file
BEST1disease_causing_automatic0.999999999992564simple_aaeaffected0G299Esingle base exchangers28941468show file
BEST1disease_causing_automatic0.999999999999858simple_aaeaffected0G239Esingle base exchangers28941468show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28941468show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28941468show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28941468show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28941468show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.983352210913347 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM092730)
  • known disease mutation at this position (HGMD CM982028)
  • known disease mutation: rs2729 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61726998G>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.781G>A
cDNA.942G>A
g.9706G>A
AA changes E261K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 261
frameshift no
known variant Reference ID: rs28941468
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2729 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.691
5.691
(flanking)-0.9170.793
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased9704wt: 0.8836 / mu: 0.9336 (marginal change - not scored)wt: CCCTTTGGAGAGGAT
mu: CCCTTTGAAGAGGAT		 CTTT|ggag
Donor increased9702wt: 0.36 / mu: 0.87wt: ACCCCTTTGGAGAGG
mu: ACCCCTTTGAAGAGG		 CCCT|ttgg
Donor gained97070.43mu: TTTGAAGAGGATGAT TGAA|gagg
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      261LWWQSSSSTPLERMMMILRPTGLS
mutated  all conserved    261LWWQSSSSTPLKRMMMILRPTGL
Ptroglodytes  no alignment  ENSPTRG00000003756  n/a
Mmulatta  no alignment  ENSMMUG00000015147  n/a
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  no alignment  ENSMUSG00000037418  n/a
Ggallus  no alignment  ENSGALG00000007217  n/a
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000078331  n/a
Dmelanogaster  no alignment  FBgn0040238  n/a
Celegans  no alignment  C01B12.3  n/a
Xtropicalis  no alignment  ENSXETG00000006740  n/a
protein features
start (aa)end (aa)featuredetails 
250270TOPO_DOMExtracellular (Potential).lost
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 781
cDNA position
(for ins/del: last normal base / first normal base)		 942
gDNA position
(for ins/del: last normal base / first normal base)		 9706
chromosomal position
(for ins/del: last normal base / first normal base)		 61726998
original gDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered gDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
original cDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered cDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
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
YDWISIPLVY TQVVTVAVYS FFLTCLVGRQ FLNPAKAYPG HELDLVVPVF TFLQFFFYVG
WLKVGLSRAL LGWRHGQRGH GQQLPETRMQ CQERKVSRVE SSQAWWRTPV IPATREAEAG
ESLEPGRRRL WWQSSSSTPL KRMMMILRPT GLSTGICRCP CWLWMRCTRT CLGWSRTCTG
ISPSHSPPTQ LLPPSSVEPP LWAPPSTSA*
speed 1.15 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: 0.999999999992564 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM092730)
  • known disease mutation at this position (HGMD CM982028)
  • known disease mutation: rs2729 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61726998G>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.896G>A
cDNA.1539G>A
g.9706G>A
AA changes G299E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 299
frameshift no
known variant Reference ID: rs28941468
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2729 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.691
5.691
(flanking)-0.9170.793
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased9704wt: 0.8836 / mu: 0.9336 (marginal change - not scored)wt: CCCTTTGGAGAGGAT
mu: CCCTTTGAAGAGGAT		 CTTT|ggag
Donor increased9702wt: 0.36 / mu: 0.87wt: ACCCCTTTGGAGAGG
mu: ACCCCTTTGAAGAGG		 CCCT|ttgg
Donor gained97070.43mu: TTTGAAGAGGATGAT TGAA|gagg
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      299LKVAEQLINPFGEDDDDFETNWIV
mutated  not conserved    299LKVAEQLINPFEEDDDDFETNWI
Ptroglodytes  all identical  ENSPTRG00000003756  299LKVAEQLINPFGEDDDDFETNWI
Mmulatta  all identical  ENSMMUG00000015147  299LKVAEQLINPFGEDDDDFETNWI
Fcatus  all identical  ENSFCAG00000007380  329LKVAEQLINPFGEDDDDFETNWI
Mmusculus  all identical  ENSMUSG00000037418  299LKVAEQLINPFGEDDDDFETNWI
Ggallus  all identical  ENSGALG00000007217  299LKVAEQLINPFGEDDDDFETNWL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  299LKVAEQLINPFGEDDDDFETNWL
Dmelanogaster  all identical  FBgn0040238  306LINPFGEDDDDFEVNWM
Celegans  all identical  C01B12.3  302LGEDDDDFECNWI
Xtropicalis  all identical  ENSXETG00000006740  299LKVAEQLINPFGQDDDDFETNWL
protein features
start (aa)end (aa)featuredetails 
292585TOPO_DOMCytoplasmic (Potential).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 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 896
cDNA position
(for ins/del: last normal base / first normal base)		 1539
gDNA position
(for ins/del: last normal base / first normal base)		 9706
chromosomal position
(for ins/del: last normal base / first normal base)		 61726998
original gDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered gDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
original cDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered cDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
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 CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFEE
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 1.12 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: 0.999999999999858 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM092730)
  • known disease mutation at this position (HGMD CM982028)
  • known disease mutation: rs2729 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61726998G>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.716G>A
cDNA.802G>A
g.9706G>A
AA changes G239E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 239
frameshift no
known variant Reference ID: rs28941468
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2729 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.691
5.691
(flanking)-0.9170.793
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased9704wt: 0.8836 / mu: 0.9336 (marginal change - not scored)wt: CCCTTTGGAGAGGAT
mu: CCCTTTGAAGAGGAT		 CTTT|ggag
Donor increased9702wt: 0.36 / mu: 0.87wt: ACCCCTTTGGAGAGG
mu: ACCCCTTTGAAGAGG		 CCCT|ttgg
Donor gained97070.43mu: TTTGAAGAGGATGAT TGAA|gagg
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      239LKVAEQLINPFGEDDDDFETNWIV
mutated  not conserved    239LKVAEQLINPFEEDDDDFETNWI
Ptroglodytes  all identical  ENSPTRG00000003756  299LKVAEQLINPFGEDDDDFETNWI
Mmulatta  all identical  ENSMMUG00000015147  299LKVAEQLINPFGEDDDDFETNWI
Fcatus  all identical  ENSFCAG00000007380  329LKVAEQLINPFGEDDDDFETNWI
Mmusculus  all identical  ENSMUSG00000037418  299LKVAEQLINPFGEDDDDFETNWI
Ggallus  all identical  ENSGALG00000007217  299LKVAEQLINPFGEDDDDFETNWL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  299LKVAEQLINPFGEDDDDFETNWL
Dmelanogaster  all identical  FBgn0040238  306NPFGEDDDDFEVNWM
Celegans  all identical  C01B12.3  302GEDDDDFECNWI
Xtropicalis  all identical  ENSXETG00000006740  299LKVAEQLINPFGQD
protein features
start (aa)end (aa)featuredetails 
229249INTRAMEMPotential.lost
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 716
cDNA position
(for ins/del: last normal base / first normal base)		 802
gDNA position
(for ins/del: last normal base / first normal base)		 9706
chromosomal position
(for ins/del: last normal base / first normal base)		 61726998
original gDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered gDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
original cDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered cDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
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 CGHLYAYDWI SIPLVYTQVV
TVAVYSFFLT CLVGRQFLNP AKAYPGHELD LVVPVFTFLQ FFFYVGWLKV AEQLINPFEE
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 1.12 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 CM092730)
  • known disease mutation at this position (HGMD CM982028)
  • known disease mutation: rs2729 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61726998G>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.9706G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28941468
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2729 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.691
5.691
(flanking)-0.9170.793
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased9704wt: 0.8836 / mu: 0.9336 (marginal change - not scored)wt: CCCTTTGGAGAGGAT
mu: CCCTTTGAAGAGGAT		 CTTT|ggag
Donor increased9702wt: 0.36 / mu: 0.87wt: ACCCCTTTGGAGAGG
mu: ACCCCTTTGAAGAGG		 CCCT|ttgg
Donor gained97070.43mu: TTTGAAGAGGATGAT TGAA|gagg
distance from splice site 2729
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)		 9706
chromosomal position
(for ins/del: last normal base / first normal base)		 61726998
original gDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered gDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
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 0.94 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: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM092730)
  • known disease mutation at this position (HGMD CM982028)
  • known disease mutation: rs2729 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61726998G>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 intron
DNA changes g.9706G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28941468
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2729 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.691
5.691
(flanking)-0.9170.793
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased9704wt: 0.8836 / mu: 0.9336 (marginal change - not scored)wt: CCCTTTGGAGAGGAT
mu: CCCTTTGAAGAGGAT		 CTTT|ggag
Donor increased9702wt: 0.36 / mu: 0.87wt: ACCCCTTTGGAGAGG
mu: ACCCCTTTGAAGAGG		 CCCT|ttgg
Donor gained97070.43mu: TTTGAAGAGGATGAT TGAA|gagg
distance from splice site 2062
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
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 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 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)		 9706
chromosomal position
(for ins/del: last normal base / first normal base)		 61726998
original gDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered gDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
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 N/A
speed 0.85 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 CM092730)
  • known disease mutation at this position (HGMD CM982028)
  • known disease mutation: rs2729 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61726998G>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 intron
DNA changes g.9706G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28941468
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2729 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.691
5.691
(flanking)-0.9170.793
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased9704wt: 0.8836 / mu: 0.9336 (marginal change - not scored)wt: CCCTTTGGAGAGGAT
mu: CCCTTTGAAGAGGAT		 CTTT|ggag
Donor increased9702wt: 0.36 / mu: 0.87wt: ACCCCTTTGGAGAGG
mu: ACCCCTTTGAAGAGG		 CCCT|ttgg
Donor gained97070.43mu: TTTGAAGAGGATGAT TGAA|gagg
distance from splice site 366
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
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)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 9706
chromosomal position
(for ins/del: last normal base / first normal base)		 61726998
original gDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered gDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
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 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 0.53 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 CM092730)
  • known disease mutation at this position (HGMD CM982028)
  • known disease mutation: rs2729 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61726998G>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.9706G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28941468
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2729 (pathogenic for Vitelliform macular dystrophy type 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092730)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982028)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.691
5.691
(flanking)-0.9170.793
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 marginally increased9704wt: 0.8836 / mu: 0.9336 (marginal change - not scored)wt: CCCTTTGGAGAGGAT
mu: CCCTTTGAAGAGGAT		 CTTT|ggag
Donor increased9702wt: 0.36 / mu: 0.87wt: ACCCCTTTGGAGAGG
mu: ACCCCTTTGAAGAGG		 CCCT|ttgg
Donor gained97070.43mu: TTTGAAGAGGATGAT TGAA|gagg
distance from splice site 2729
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)		 9706
chromosomal position
(for ins/del: last normal base / first normal base)		 61726998
original gDNA sequence snippet GCAGCTCATCAACCCCTTTGGAGAGGATGATGATGATTTTG
altered gDNA sequence snippet GCAGCTCATCAACCCCTTTGAAGAGGATGATGATGATTTTG
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 0.85 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