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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000348749
Querying Taster for transcript #2: ENST00000261007
Querying Taster for transcript #3: ENST00000409542
Querying Taster for transcript #4: ENST00000409219
Querying Taster for transcript #5: ENST00000409323
MT speed 9.98 s - this script 7.80094 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHRNA1disease_causing0.999999999676915simple_aaeaffectedV94Msingle base exchangers137852799show file
CHRNA1disease_causing0.999999999676915simple_aaeaffectedV176Msingle base exchangers137852799show file
CHRNA1disease_causing0.999999999676915simple_aaeaffectedV176Msingle base exchangers137852799show file
CHRNA1disease_causing0.999999999676915simple_aaeaffectedV201Msingle base exchangers137852799show file
CHRNA1disease_causing0.999999999676915simple_aaeaffectedV176Msingle base exchangers137852799show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999676915      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970303)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618961C>TN/A show variant in all transcripts   IGV
HGNC symbol CHRNA1
Ensembl transcript ID ENST00000409542
Genbank transcript ID N/A
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.280G>A
cDNA.298G>A
g.10240G>A
AA changes V94M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
94
frameshift no
known variant Reference ID: rs137852799
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8721
5.8851
(flanking)2.0181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102360.95mu: GGCTCTGTCATGGCC CTCT|gtca
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      94KLGTWTYDGSVVAINPESDQPDLS
mutated  all conserved    94KLGTWTYDGSVMAINPESDQPDL
Ptroglodytes  all identical  ENSPTRG00000012658  201KLGTWTYDGSVVAINPESDQPDL
Mmulatta  all identical  ENSMMUG00000021796  200KLGTWTYDGSVVAINPESDQPDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  176KLGTWTYDGSVVAINPESDQPDL
Ggallus  all identical  ENSGALG00000009301  186KLGTWTYDGTMVVINPESDRPDL
Trubripes  all identical  ENSTRUG00000008738  197KLGTWTYDGLLVVINPDSDRPDL
Drerio  all identical  ENSDARG00000009021  176KLGTWTYDGNLVIINPDSDRPDL
Dmelanogaster  no homologue    
Celegans  all identical  K11G12.2  213VFGSWTYNSEEVRLHWYNNIQAVQL
Xtropicalis  all identical  ENSXETG00000025418  176KFGTWTYDGTLVVINPDRDRPDL
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
173173DISULFIDmight get lost (downstream of altered splice site)
186186CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
187187DISULFIDmight get lost (downstream of altered splice site)
237237DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
238238DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
256280TRANSMEMHelical.might get lost (downstream of altered splice site)
288306TRANSMEMHelical.might get lost (downstream of altered splice site)
322341TRANSMEMHelical.might get lost (downstream of altered splice site)
342453TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
415415CONFLICTP -> F (in Ref. 4; AAD14247).might get lost (downstream of altered splice site)
454472TRANSMEMHelical.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1128 / 1128
position (AA) of stopcodon in wt / mu AA sequence 376 / 376
position of stopcodon in wt / mu cDNA 1146 / 1146
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 19 / 19
chromosome 2
strand -1
last intron/exon boundary 1015
theoretical NMD boundary in CDS 946
length of CDS 1128
coding sequence (CDS) position 280
cDNA position
(for ins/del: last normal base / first normal base)
298
gDNA position
(for ins/del: last normal base / first normal base)
10240
chromosomal position
(for ins/del: last normal base / first normal base)
175618961
original gDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGTAGGT
altered gDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGTAGGT
original cDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGAAAGC
altered cDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGAAAGC
wildtype AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQNC SMKLGTWTYD GSVVAINPES DQPDLSNFME SGEWVIKESR
GWKHSVTYSC CPDTPYLDIT YHFVMQRLPL YFIVNVIIPC LLFSFLTGLV FYLPTDSGEK
MTLSISVLLS LTVFLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*
mutated AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQNC SMKLGTWTYD GSVMAINPES DQPDLSNFME SGEWVIKESR
GWKHSVTYSC CPDTPYLDIT YHFVMQRLPL YFIVNVIIPC LLFSFLTGLV FYLPTDSGEK
MTLSISVLLS LTVFLLVIVE LIPSTSSAVP LIGKYMLFTM VFVIASIIIT VIVINTHHRS
PSTHVMPNWV RKVFIDTIPN IMFFSTMKRP SREKQDKKIF TEDIDISDIS GKPGPPPMGF
HSPLIKHPEV KSAIEGIKYI AETMKSDQES NNAAAEWKYV AMVMDHILLG VFMLVCIIGT
LAVFAGRLIE LNQQG*
speed 3.08 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: 0.999999999676915      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970303)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618961C>TN/A show variant in all transcripts   IGV
HGNC symbol CHRNA1
Ensembl transcript ID ENST00000348749
Genbank transcript ID NM_000079
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.526G>A
cDNA.604G>A
g.10240G>A
AA changes V176M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
176
frameshift no
known variant Reference ID: rs137852799
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8721
5.8851
(flanking)2.0181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102360.95mu: GGCTCTGTCATGGCC CTCT|gtca
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      176KLGTWTYDGSVVAINPESDQPDLS
mutated  all conserved    176KLGTWTYDGSVMAINP
Ptroglodytes  all identical  ENSPTRG00000012658  201KLGTWTYDGSVVAINPESDQPDL
Mmulatta  all identical  ENSMMUG00000021796  200KLGTWTYDGSVVAINPESDQPDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  176KLGTWTYDGSVVAINP
Ggallus  all identical  ENSGALG00000009301  186KLGTWTYDGTMVVINP
Trubripes  all identical  ENSTRUG00000008738  197KLGTWTYDGLLVVIN
Drerio  all identical  ENSDARG00000009021  176KLGTWTYDGNLVIINPDSDRPDL
Dmelanogaster  no homologue    
Celegans  all identical  K11G12.2  213VFGSWTYNSEEVRLHWYNNIQAVQL
Xtropicalis  all identical  ENSXETG00000025418  176KFGTWTYDGTLVVINPDRDRPDL
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
186186CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
187187DISULFIDmight get lost (downstream of altered splice site)
237237DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
238238DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
256280TRANSMEMHelical.might get lost (downstream of altered splice site)
288306TRANSMEMHelical.might get lost (downstream of altered splice site)
322341TRANSMEMHelical.might get lost (downstream of altered splice site)
342453TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
415415CONFLICTP -> F (in Ref. 4; AAD14247).might get lost (downstream of altered splice site)
454472TRANSMEMHelical.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1374 / 1374
position (AA) of stopcodon in wt / mu AA sequence 458 / 458
position of stopcodon in wt / mu cDNA 1452 / 1452
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 79 / 79
chromosome 2
strand -1
last intron/exon boundary 1321
theoretical NMD boundary in CDS 1192
length of CDS 1374
coding sequence (CDS) position 526
cDNA position
(for ins/del: last normal base / first normal base)
604
gDNA position
(for ins/del: last normal base / first normal base)
10240
chromosomal position
(for ins/del: last normal base / first normal base)
175618961
original gDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGTAGGT
altered gDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGTAGGT
original cDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGAAAGC
altered cDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGAAAGC
wildtype AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKVFIDTI PNIMFFSTMK RPSREKQDKK
IFTEDIDISD ISGKPGPPPM GFHSPLIKHP EVKSAIEGIK YIAETMKSDQ ESNNAAAEWK
YVAMVMDHIL LGVFMLVCII GTLAVFAGRL IELNQQG*
mutated AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVMAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKVFIDTI PNIMFFSTMK RPSREKQDKK
IFTEDIDISD ISGKPGPPPM GFHSPLIKHP EVKSAIEGIK YIAETMKSDQ ESNNAAAEWK
YVAMVMDHIL LGVFMLVCII GTLAVFAGRL IELNQQG*
speed 1.97 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: simple_aae, prob: 0.999999999676915      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970303)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618961C>TN/A show variant in all transcripts   IGV
HGNC symbol CHRNA1
Ensembl transcript ID ENST00000409219
Genbank transcript ID N/A
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.526G>A
cDNA.544G>A
g.10240G>A
AA changes V176M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
176
frameshift no
known variant Reference ID: rs137852799
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8721
5.8851
(flanking)2.0181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102360.95mu: GGCTCTGTCATGGCC CTCT|gtca
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      176KLGTWTYDGSVVAINPESDQPDLS
mutated  all conserved    176KLGTWTYDGSVMAINP
Ptroglodytes  all identical  ENSPTRG00000012658  201KLGTWTYDGSVVAINPESDQPDL
Mmulatta  all identical  ENSMMUG00000021796  200KLGTWTYDGSVVAINPESDQPDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  176KLGTWTYDGSVVAINP
Ggallus  all identical  ENSGALG00000009301  186KLGTWTYDGTMVVINP
Trubripes  all identical  ENSTRUG00000008738  197KLGTWTYDGLLVVIN
Drerio  all identical  ENSDARG00000009021  176KLGTWTYDGNLVIINPDSDRPDL
Dmelanogaster  no homologue    
Celegans  all identical  K11G12.2  213VFGSWTYNSEEVRLHWYNNIQAVQL
Xtropicalis  all identical  ENSXETG00000025418  176KFGTWTYDGTLVVINPDRDRPDL
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
186186CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
187187DISULFIDmight get lost (downstream of altered splice site)
237237DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
238238DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
256280TRANSMEMHelical.might get lost (downstream of altered splice site)
288306TRANSMEMHelical.might get lost (downstream of altered splice site)
322341TRANSMEMHelical.might get lost (downstream of altered splice site)
342453TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
415415CONFLICTP -> F (in Ref. 4; AAD14247).might get lost (downstream of altered splice site)
454472TRANSMEMHelical.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1134 / 1134
position (AA) of stopcodon in wt / mu AA sequence 378 / 378
position of stopcodon in wt / mu cDNA 1152 / 1152
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 19 / 19
chromosome 2
strand -1
last intron/exon boundary 1021
theoretical NMD boundary in CDS 952
length of CDS 1134
coding sequence (CDS) position 526
cDNA position
(for ins/del: last normal base / first normal base)
544
gDNA position
(for ins/del: last normal base / first normal base)
10240
chromosomal position
(for ins/del: last normal base / first normal base)
175618961
original gDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGTAGGT
altered gDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGTAGGT
original cDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGAAAGC
altered cDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGAAAGC
wildtype AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKAAAEWK YVAMVMDHIL LGVFMLVCII
GTLAVFAGRL IELNQQG*
mutated AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVMAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKAAAEWK YVAMVMDHIL LGVFMLVCII
GTLAVFAGRL IELNQQG*
speed 1.45 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: 0.999999999676915      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970303)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618961C>TN/A show variant in all transcripts   IGV
HGNC symbol CHRNA1
Ensembl transcript ID ENST00000261007
Genbank transcript ID NM_001039523
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.601G>A
cDNA.668G>A
g.10240G>A
AA changes V201M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
201
frameshift no
known variant Reference ID: rs137852799
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8721
5.8851
(flanking)2.0181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102360.95mu: GGCTCTGTCATGGCC CTCT|gtca
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      201KLGTWTYDGSVVAINPESDQPDLS
mutated  all conserved    201KLGTWTYDGSVMAINPESDQPDL
Ptroglodytes  all identical  ENSPTRG00000012658  201KLGTWTYDGSVVAINPESDQPDL
Mmulatta  all identical  ENSMMUG00000021796  200KLGTWTYDGSVVAINPESDQPDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  176KLGTWTYDGSVVAINPESDQPDL
Ggallus  all identical  ENSGALG00000009301  186KLGTWTYDGTMVVINPESDRPDL
Trubripes  all identical  ENSTRUG00000008738  197KLGTWTYDGLLVVINPDSDRPDL
Drerio  all identical  ENSDARG00000009021  176YDGNLVIINPDSDRPDL
Dmelanogaster  no homologue    
Celegans  all identical  K11G12.2  213VRLHWYNNIQAVQL
Xtropicalis  all identical  ENSXETG00000025418  176KFGTWTYDGTLVVINPDRDRPDL
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
237237DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
238238DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
256280TRANSMEMHelical.might get lost (downstream of altered splice site)
288306TRANSMEMHelical.might get lost (downstream of altered splice site)
322341TRANSMEMHelical.might get lost (downstream of altered splice site)
342453TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
415415CONFLICTP -> F (in Ref. 4; AAD14247).might get lost (downstream of altered splice site)
454472TRANSMEMHelical.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1449 / 1449
position (AA) of stopcodon in wt / mu AA sequence 483 / 483
position of stopcodon in wt / mu cDNA 1516 / 1516
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 68 / 68
chromosome 2
strand -1
last intron/exon boundary 1385
theoretical NMD boundary in CDS 1267
length of CDS 1449
coding sequence (CDS) position 601
cDNA position
(for ins/del: last normal base / first normal base)
668
gDNA position
(for ins/del: last normal base / first normal base)
10240
chromosomal position
(for ins/del: last normal base / first normal base)
175618961
original gDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGTAGGT
altered gDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGTAGGT
original cDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGAAAGC
altered cDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGAAAGC
wildtype AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQGD MVDLPRPSCV TLGVPLFSHL QNEQWVDYNL KWNPDDYGGV
KKIHIPSEKI WRPDLVLYNN ADGDFAIVKF TKVLLQYTGH ITWTPPAIFK SYCEIIVTHF
PFDEQNCSMK LGTWTYDGSV VAINPESDQP DLSNFMESGE WVIKESRGWK HSVTYSCCPD
TPYLDITYHF VMQRLPLYFI VNVIIPCLLF SFLTGLVFYL PTDSGEKMTL SISVLLSLTV
FLLVIVELIP STSSAVPLIG KYMLFTMVFV IASIIITVIV INTHHRSPST HVMPNWVRKV
FIDTIPNIMF FSTMKRPSRE KQDKKIFTED IDISDISGKP GPPPMGFHSP LIKHPEVKSA
IEGIKYIAET MKSDQESNNA AAEWKYVAMV MDHILLGVFM LVCIIGTLAV FAGRLIELNQ
QG*
mutated AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQGD MVDLPRPSCV TLGVPLFSHL QNEQWVDYNL KWNPDDYGGV
KKIHIPSEKI WRPDLVLYNN ADGDFAIVKF TKVLLQYTGH ITWTPPAIFK SYCEIIVTHF
PFDEQNCSMK LGTWTYDGSV MAINPESDQP DLSNFMESGE WVIKESRGWK HSVTYSCCPD
TPYLDITYHF VMQRLPLYFI VNVIIPCLLF SFLTGLVFYL PTDSGEKMTL SISVLLSLTV
FLLVIVELIP STSSAVPLIG KYMLFTMVFV IASIIITVIV INTHHRSPST HVMPNWVRKV
FIDTIPNIMF FSTMKRPSRE KQDKKIFTED IDISDISGKP GPPPMGFHSP LIKHPEVKSA
IEGIKYIAET MKSDQESNNA AAEWKYVAMV MDHILLGVFM LVCIIGTLAV FAGRLIELNQ
QG*
speed 1.89 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
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Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999676915      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM970303)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618961C>TN/A show variant in all transcripts   IGV
HGNC symbol CHRNA1
Ensembl transcript ID ENST00000409323
Genbank transcript ID N/A
UniProt peptide P02708
alteration type single base exchange
alteration region CDS
DNA changes c.526G>A
cDNA.585G>A
g.10240G>A
AA changes V176M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS
176
frameshift no
known variant Reference ID: rs137852799
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC022

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970303)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)4.8721
5.8851
(flanking)2.0181
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102360.95mu: GGCTCTGTCATGGCC CTCT|gtca
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      176KLGTWTYDGSVVAINPESDQPDLS
mutated  all conserved    176KLGTWTYDGSVMAINP
Ptroglodytes  all identical  ENSPTRG00000012658  201KLGTWTYDGSVVAINPESDQPDL
Mmulatta  all identical  ENSMMUG00000021796  200KLGTWTYDGSVVAINPESDQPDL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  176KLGTWTYDGSVVAINP
Ggallus  all identical  ENSGALG00000009301  186KLGTWTYDGTMVVINP
Trubripes  all identical  ENSTRUG00000008738  197KLGTWTYDGLLVVIN
Drerio  all identical  ENSDARG00000009021  176KLGTWTYDGNLVIINPDSDRPDL
Dmelanogaster  no homologue    
Celegans  all identical  K11G12.2  213VFGSWTYNSEEVRLHWYNNIQAVQL
Xtropicalis  all identical  ENSXETG00000025418  176KFGTWTYDGTLVVINPDRDRPDL
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
186186CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
187187DISULFIDmight get lost (downstream of altered splice site)
237237DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
238238DISULFIDAssociated with receptor activation.might get lost (downstream of altered splice site)
256280TRANSMEMHelical.might get lost (downstream of altered splice site)
288306TRANSMEMHelical.might get lost (downstream of altered splice site)
322341TRANSMEMHelical.might get lost (downstream of altered splice site)
342453TOPO_DOMCytoplasmic.might get lost (downstream of altered splice site)
415415CONFLICTP -> F (in Ref. 4; AAD14247).might get lost (downstream of altered splice site)
454472TRANSMEMHelical.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 810 / 810
position (AA) of stopcodon in wt / mu AA sequence 270 / 270
position of stopcodon in wt / mu cDNA 869 / 869
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 60 / 60
chromosome 2
strand -1
last intron/exon boundary 600
theoretical NMD boundary in CDS 490
length of CDS 810
coding sequence (CDS) position 526
cDNA position
(for ins/del: last normal base / first normal base)
585
gDNA position
(for ins/del: last normal base / first normal base)
10240
chromosomal position
(for ins/del: last normal base / first normal base)
175618961
original gDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGTAGGT
altered gDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGTAGGT
original cDNA sequence snippet GGACCTACGACGGCTCTGTCGTGGCCATCAACCCGGAAAGC
altered cDNA sequence snippet GGACCTACGACGGCTCTGTCATGGCCATCAACCCGGAAAGC
wildtype AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG GCGCHDCCC*
mutated AA sequence MEPWPLLLLF SLCSAGLVLG SEHETRLVAK LFKDYSSVVR PVEDHRQVVE VTVGLQLIQL
INVDEVNQIV TTNVRLKQQW VDYNLKWNPD DYGGVKKIHI PSEKIWRPDL VLYNNADGDF
AIVKFTKVLL QYTGHITWTP PAIFKSYCEI IVTHFPFDEQ NCSMKLGTWT YDGSVMAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG GCGCHDCCC*
speed 1.59 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
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Problems