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 4.339495 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
BEST1disease_causing_automatic0.999999999685574simple_aaeaffected0V9Msingle base exchangers28940276show file
BEST1disease_causing_automatic0.999999999685574simple_aaeaffected0V9Msingle base exchangers28940276show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28940276show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28940276show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28940276show file
BEST1disease_causing_automatic1without_aaeaffected0single base exchangers28940276show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999685574 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM111670)
  • known disease mutation at this position (HGMD CM982016)
  • known disease mutation: rs2734 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719303G>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.25G>A
cDNA.668G>A
g.2011G>A
AA changes V9M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 9
frameshift no
known variant Reference ID: rs28940276
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2734 (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 CM982016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3490.999
5.9821
(flanking)4.9391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2014wt: 0.48 / mu: 0.71wt: AAGTGGCTAATGCCC
mu: AAATGGCTAATGCCC		 GTGG|ctaa
Donor increased2013wt: 0.30 / mu: 0.77wt: CAAGTGGCTAATGCC
mu: CAAATGGCTAATGCC		 AGTG|gcta
Donor gained20070.35mu: ACAAGCCAAATGGCT AAGC|caaa
Donor gained20060.38mu: CACAAGCCAAATGGC CAAG|ccaa
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MTITYTSQVANARLGSFSRLL
mutated  all conserved    9 MTITYTSQMANARLGSFSRLLL
Ptroglodytes  all identical  ENSPTRG00000003756  9 MTITYTSQVANARLGSFSRLLL
Mmulatta  all identical  ENSMMUG00000015147  9 MTITYTSQVANARLGSFSRLLL
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  all identical  ENSMUSG00000037418  9 MTITYTNKVANARLGSFSSLLL
Ggallus  all identical  ENSGALG00000007217  9 MTVTYTNRVADARLGTFSQLLL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  9 MTVTYSRRVADARLGTFYRLLL
Dmelanogaster  all identical  FBgn0040238  9 MTITYTGEVATCRGFGCFLKLLL
Celegans  all identical  C01B12.3  9 MTVTYSLDVASSSFFCLYKLLF
Xtropicalis  all identical  ENSXETG00000006740  9 MTVTYSNRVADARLGTFSRLLL
protein features
start (aa)end (aa)featuredetails 
125TOPO_DOMCytoplasmic (Potential).lost
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 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 25
cDNA position
(for ins/del: last normal base / first normal base)		 668
gDNA position
(for ins/del: last normal base / first normal base)		 2011
chromosomal position
(for ins/del: last normal base / first normal base)		 61719303
original gDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered gDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
original cDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered cDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
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 MTITYTSQMA 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*
speed 0.68 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: 0.999999999685574 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM111670)
  • known disease mutation at this position (HGMD CM982016)
  • known disease mutation: rs2734 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719303G>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.25G>A
cDNA.138G>A
g.2011G>A
AA changes V9M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 9
frameshift no
known variant Reference ID: rs28940276
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2734 (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 CM982016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3490.999
5.9821
(flanking)4.9391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2014wt: 0.48 / mu: 0.71wt: AAGTGGCTAATGCCC
mu: AAATGGCTAATGCCC		 GTGG|ctaa
Donor increased2013wt: 0.30 / mu: 0.77wt: CAAGTGGCTAATGCC
mu: CAAATGGCTAATGCC		 AGTG|gcta
Donor gained20070.35mu: ACAAGCCAAATGGCT AAGC|caaa
Donor gained20060.38mu: CACAAGCCAAATGGC CAAG|ccaa
distance from splice site 61
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      9 MTITYTSQVANARLGSFSRLL
mutated  all conserved    9 MTITYTSQMANARLGSFSRLLL
Ptroglodytes  all identical  ENSPTRG00000003756  9 MTITYTSQVANARLGSFSRLLL
Mmulatta  all identical  ENSMMUG00000015147  9 MTITYTSQVANARLGSFSRLLL
Fcatus  no alignment  ENSFCAG00000007380  n/a
Mmusculus  all identical  ENSMUSG00000037418  9 MTITYTNKVANARLGSFSSLLL
Ggallus  all identical  ENSGALG00000007217  9 MTVTYTNRVADARLGTFSQLLL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000078331  9 MTVTYSRRVADARLGTFYRLLL
Dmelanogaster  all identical  FBgn0040238  9 MTITYTGEVATCRGFGCFLKLLL
Celegans  all identical  C01B12.3  9 MTVTYSLDVASSSFFCLYKLLF
Xtropicalis  all identical  ENSXETG00000006740  9 MTVTYSNRVADARLGTFSRLLL
protein features
start (aa)end (aa)featuredetails 
125TOPO_DOMCytoplasmic (Potential).lost
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 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 25
cDNA position
(for ins/del: last normal base / first normal base)		 138
gDNA position
(for ins/del: last normal base / first normal base)		 2011
chromosomal position
(for ins/del: last normal base / first normal base)		 61719303
original gDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered gDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
original cDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered cDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
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 MTITYTSQMA 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 *
speed 0.80 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 CM111670)
  • known disease mutation at this position (HGMD CM982016)
  • known disease mutation: rs2734 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719303G>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.2011G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28940276
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2734 (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 CM982016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3490.999
5.9821
(flanking)4.9391
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
Donor increased2014wt: 0.48 / mu: 0.71wt: AAGTGGCTAATGCCC
mu: AAATGGCTAATGCCC		 GTGG|ctaa
Donor increased2013wt: 0.30 / mu: 0.77wt: CAAGTGGCTAATGCC
mu: CAAATGGCTAATGCC		 AGTG|gcta
Donor gained20070.35mu: ACAAGCCAAATGGCT AAGC|caaa
Donor gained20060.38mu: CACAAGCCAAATGGC CAAG|ccaa
distance from splice site 1404
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)		 2011
chromosomal position
(for ins/del: last normal base / first normal base)		 61719303
original gDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered gDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
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 0.52 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
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 CM111670)
  • known disease mutation at this position (HGMD CM982016)
  • known disease mutation: rs2734 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719303G>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 intron
DNA changes g.2011G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28940276
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2734 (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 CM982016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3490.999
5.9821
(flanking)4.9391
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
Donor increased2014wt: 0.48 / mu: 0.71wt: AAGTGGCTAATGCCC
mu: AAATGGCTAATGCCC		 GTGG|ctaa
Donor increased2013wt: 0.30 / mu: 0.77wt: CAAGTGGCTAATGCC
mu: CAAATGGCTAATGCC		 AGTG|gcta
Donor gained20070.35mu: ACAAGCCAAATGGCT AAGC|caaa
Donor gained20060.38mu: CACAAGCCAAATGGC CAAG|ccaa
distance from splice site 1404
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)		 2011
chromosomal position
(for ins/del: last normal base / first normal base)		 61719303
original gDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered gDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
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 0.62 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 CM111670)
  • known disease mutation at this position (HGMD CM982016)
  • known disease mutation: rs2734 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719303G>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 5'UTR
DNA changes cDNA.605G>A
g.2011G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28940276
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2734 (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 CM982016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3490.999
5.9821
(flanking)4.9391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -53) | splice site change before start ATG (at aa -51) | splice site change before start ATG (at aa -50) |
effectgDNA positionscoredetection sequence  exon-intron border
Donor increased2014wt: 0.48 / mu: 0.71wt: AAGTGGCTAATGCCC
mu: AAATGGCTAATGCCC		 GTGG|ctaa
Donor increased2013wt: 0.30 / mu: 0.77wt: CAAGTGGCTAATGCC
mu: CAAATGGCTAATGCC		 AGTG|gcta
Donor gained20070.35mu: ACAAGCCAAATGGCT AAGC|caaa
Donor gained20060.38mu: CACAAGCCAAATGGC CAAG|ccaa
distance from splice site 61
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)		 605
gDNA position
(for ins/del: last normal base / first normal base)		 2011
chromosomal position
(for ins/del: last normal base / first normal base)		 61719303
original gDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered gDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
original cDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered cDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
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 0.58 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 CM111670)
  • known disease mutation at this position (HGMD CM982016)
  • known disease mutation: rs2734 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:61719303G>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.2011G>A
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28940276
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs2734 (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 CM982016)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)

known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM111670)
known disease mutation at this position, please check HGMD for details (HGMD ID CM982016)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3490.999
5.9821
(flanking)4.9391
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
Donor increased2014wt: 0.48 / mu: 0.71wt: AAGTGGCTAATGCCC
mu: AAATGGCTAATGCCC		 GTGG|ctaa
Donor increased2013wt: 0.30 / mu: 0.77wt: CAAGTGGCTAATGCC
mu: CAAATGGCTAATGCC		 AGTG|gcta
Donor gained20070.35mu: ACAAGCCAAATGGCT AAGC|caaa
Donor gained20060.38mu: CACAAGCCAAATGGC CAAG|ccaa
distance from splice site 1404
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)		 2011
chromosomal position
(for ins/del: last normal base / first normal base)		 61719303
original gDNA sequence snippet CCATCACTTACACAAGCCAAGTGGCTAATGCCCGCTTAGGC
altered gDNA sequence snippet CCATCACTTACACAAGCCAAATGGCTAATGCCCGCTTAGGC
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 0.72 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