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 0 s - this script 4.469336 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHRNA1disease_causing_automatic0.999999981988793simple_aaeaffected0G198Ssingle base exchangers137852801show file
CHRNA1disease_causing_automatic0.999999981988793simple_aaeaffected0G91Ssingle base exchangers137852801show file
CHRNA1disease_causing_automatic0.999999998892747simple_aaeaffected0G173Ssingle base exchangers137852801show file
CHRNA1disease_causing_automatic0.999999998892747simple_aaeaffected0G173Ssingle base exchangers137852801show file
CHRNA1disease_causing_automatic0.999999998892747simple_aaeaffected0G173Ssingle base exchangers137852801show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999981988793 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950258)
  • known disease mutation: rs18379 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618970C>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.592G>A
cDNA.659G>A
g.10231G>A
AA changes G198S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 198
frameshift no
known variant Reference ID: rs137852801
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs18379 (pathogenic for Lethal multiple pterygium syndrome|Congenital myasthenic syndrome 1A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
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)4.6291
4.6291
(flanking)-0.8390.588
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102310.31mu: ACGACAGCTCTGTCG GACA|gctc
Donor gained102270.32mu: ACCTACGACAGCTCT CTAC|gaca
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      198CSMKLGTWTYDGSVVAINPESDQP
mutated  not conserved    198CSMKLGTWTYDSSVVAINPESDQ
Ptroglodytes  all identical  ENSPTRG00000012658  198CSMKLGTWTYDGSVVAINPESDQ
Mmulatta  all identical  ENSMMUG00000021796  197CSMKLGTWTYDGSVVAINPESDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  173CSMKLGTWTYDGSVVAINPESDQ
Ggallus  all identical  ENSGALG00000009301  183CSMKLGTWTYDGTMVVINPESDR
Trubripes  all identical  ENSTRUG00000008738  194CSMKLGTWTYDGLLVVINPDSDR
Drerio  all identical  ENSDARG00000009021  173YDGNLVIINPDSDR
Dmelanogaster  no homologue    
Celegans  not conserved  K11G12.2  210CTLVFGSWTYNSEE
Xtropicalis  all identical  ENSXETG00000025418  173SMKFGTWTYDGTLVVINPDRDR
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 592
cDNA position
(for ins/del: last normal base / first normal base)		 659
gDNA position
(for ins/del: last normal base / first normal base)		 10231
chromosomal position
(for ins/del: last normal base / first normal base)		 175618970
original gDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered gDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
original cDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered cDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
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 LGTWTYDSSV 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*
speed 0.71 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: 0.999999981988793 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950258)
  • known disease mutation: rs18379 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618970C>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.271G>A
cDNA.289G>A
g.10231G>A
AA changes G91S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 91
frameshift no
known variant Reference ID: rs137852801
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs18379 (pathogenic for Lethal multiple pterygium syndrome|Congenital myasthenic syndrome 1A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
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)4.6291
4.6291
(flanking)-0.8390.588
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102310.31mu: ACGACAGCTCTGTCG GACA|gctc
Donor gained102270.32mu: ACCTACGACAGCTCT CTAC|gaca
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      91CSMKLGTWTYDGSVVAINPESDQP
mutated  not conserved    91CSMKLGTWTYDSSVVAINPESDQ
Ptroglodytes  all identical  ENSPTRG00000012658  198CSMKLGTWTYDGSVVAINPESDQ
Mmulatta  all identical  ENSMMUG00000021796  197CSMKLGTWTYDGSVVAINPESDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  173CSMKLGTWTYDGSVVAINPESDQ
Ggallus  all identical  ENSGALG00000009301  183CSMKLGTWTYDGTMVVINPESDR
Trubripes  all identical  ENSTRUG00000008738  194CSMKLGTWTYDGLLVVINPDSDR
Drerio  all identical  ENSDARG00000009021  173CSMKLGTWTYDGNLVIINPDSDR
Dmelanogaster  no homologue    
Celegans  not conserved  K11G12.2  210CTLVFGSWTYNSEEVRLHWYNNIQA
Xtropicalis  all identical  ENSXETG00000025418  173CSMKFGTWTYDGTLVVINPDRDR
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 271
cDNA position
(for ins/del: last normal base / first normal base)		 289
gDNA position
(for ins/del: last normal base / first normal base)		 10231
chromosomal position
(for ins/del: last normal base / first normal base)		 175618970
original gDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered gDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
original cDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered cDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
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 SSVVAINPES 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 0.75 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: 0.999999998892747 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950258)
  • known disease mutation: rs18379 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618970C>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.517G>A
cDNA.595G>A
g.10231G>A
AA changes G173S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 173
frameshift no
known variant Reference ID: rs137852801
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs18379 (pathogenic for Lethal multiple pterygium syndrome|Congenital myasthenic syndrome 1A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
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)4.6291
4.6291
(flanking)-0.8390.588
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102310.31mu: ACGACAGCTCTGTCG GACA|gctc
Donor gained102270.32mu: ACCTACGACAGCTCT CTAC|gaca
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      173CSMKLGTWTYDGSVVAINPESDQP
mutated  not conserved    173CSMKLGTWTYDSSVVAINP
Ptroglodytes  all identical  ENSPTRG00000012658  198CSMKLGTWTYDGSVVAINPESDQ
Mmulatta  all identical  ENSMMUG00000021796  197CSMKLGTWTYDGSVVAINPESDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  173CSMKLGTWTYDGSVVAINP
Ggallus  all identical  ENSGALG00000009301  183CSMKLGTWTYDGTMVVINP
Trubripes  all identical  ENSTRUG00000008738  194CSMKLGTWTYDGLLVVIN
Drerio  all identical  ENSDARG00000009021  173CSMKLGTWTYDGNLVIINPDSDR
Dmelanogaster  no homologue    
Celegans  not conserved  K11G12.2  210CTLVFGSWTYNSEEVRLHWYNNIQA
Xtropicalis  all identical  ENSXETG00000025418  173CSMKFGTWTYDGTLVVINPDRDR
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
173173DISULFIDlost
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 517
cDNA position
(for ins/del: last normal base / first normal base)		 595
gDNA position
(for ins/del: last normal base / first normal base)		 10231
chromosomal position
(for ins/del: last normal base / first normal base)		 175618970
original gDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered gDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
original cDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered cDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
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 YDSSVVAINP
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 0.75 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: 0.999999998892747 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950258)
  • known disease mutation: rs18379 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618970C>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.517G>A
cDNA.535G>A
g.10231G>A
AA changes G173S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 173
frameshift no
known variant Reference ID: rs137852801
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs18379 (pathogenic for Lethal multiple pterygium syndrome|Congenital myasthenic syndrome 1A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
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)4.6291
4.6291
(flanking)-0.8390.588
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102310.31mu: ACGACAGCTCTGTCG GACA|gctc
Donor gained102270.32mu: ACCTACGACAGCTCT CTAC|gaca
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      173CSMKLGTWTYDGSVVAINPESDQP
mutated  not conserved    173CSMKLGTWTYDSSVVAINP
Ptroglodytes  all identical  ENSPTRG00000012658  198CSMKLGTWTYDGSVVAINPESDQ
Mmulatta  all identical  ENSMMUG00000021796  197CSMKLGTWTYDGSVVAINPESDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  173CSMKLGTWTYDGSVVAINP
Ggallus  all identical  ENSGALG00000009301  183CSMKLGTWTYDGTMVVINP
Trubripes  all identical  ENSTRUG00000008738  194CSMKLGTWTYDGLLVVIN
Drerio  all identical  ENSDARG00000009021  173CSMKLGTWTYDGNLVIINPDSDR
Dmelanogaster  no homologue    
Celegans  not conserved  K11G12.2  210CTLVFGSWTYNSEEVRLHWYNNIQA
Xtropicalis  all identical  ENSXETG00000025418  173CSMKFGTWTYDGTLVVINPDRDR
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
173173DISULFIDlost
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 517
cDNA position
(for ins/del: last normal base / first normal base)		 535
gDNA position
(for ins/del: last normal base / first normal base)		 10231
chromosomal position
(for ins/del: last normal base / first normal base)		 175618970
original gDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered gDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
original cDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered cDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
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 YDSSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG EKMTLSISVL LSLTVFLLVI VELIPSTSSA VPLIGKYMLF
TMVFVIASII ITVIVINTHH RSPSTHVMPN WVRKAAAEWK YVAMVMDHIL LGVFMLVCII
GTLAVFAGRL IELNQQG*
speed 0.91 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: 0.999999998892747 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM950258)
  • known disease mutation: rs18379 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:175618970C>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.517G>A
cDNA.576G>A
g.10231G>A
AA changes G173S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 173
frameshift no
known variant Reference ID: rs137852801
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs18379 (pathogenic for Lethal multiple pterygium syndrome|Congenital myasthenic syndrome 1A) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)

known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
known disease mutation at this position, please check HGMD for details (HGMD ID CM950258)
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)4.6291
4.6291
(flanking)-0.8390.588
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained102310.31mu: ACGACAGCTCTGTCG GACA|gctc
Donor gained102270.32mu: ACCTACGACAGCTCT CTAC|gaca
distance from splice site 24
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      173CSMKLGTWTYDGSVVAINPESDQP
mutated  not conserved    173CSMKLGTWTYDSSVVAINP
Ptroglodytes  all identical  ENSPTRG00000012658  198CSMKLGTWTYDGSVVAINPESDQ
Mmulatta  all identical  ENSMMUG00000021796  197CSMKLGTWTYDGSVVAINPESDQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000027107  173CSMKLGTWTYDGSVVAINP
Ggallus  all identical  ENSGALG00000009301  183CSMKLGTWTYDGTMVVINP
Trubripes  all identical  ENSTRUG00000008738  194CSMKLGTWTYDGLLVVIN
Drerio  all identical  ENSDARG00000009021  173CSMKLGTWTYDGNLVIINPDSDR
Dmelanogaster  no homologue    
Celegans  not conserved  K11G12.2  210CTLVFGSWTYNSEEVRLHWYNNIQA
Xtropicalis  all identical  ENSXETG00000025418  173CSMKFGTWTYDGTLVVINPDRDR
protein features
start (aa)end (aa)featuredetails 
21255TOPO_DOMExtracellular.lost
173173DISULFIDlost
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 517
cDNA position
(for ins/del: last normal base / first normal base)		 576
gDNA position
(for ins/del: last normal base / first normal base)		 10231
chromosomal position
(for ins/del: last normal base / first normal base)		 175618970
original gDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered gDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
original cDNA sequence snippet TGGGCACCTGGACCTACGACGGCTCTGTCGTGGCCATCAAC
altered cDNA sequence snippet TGGGCACCTGGACCTACGACAGCTCTGTCGTGGCCATCAAC
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 YDSSVVAINP
ESDQPDLSNF MESGEWVIKE SRGWKHSVTY SCCPDTPYLD ITYHFVMQRL PLYFIVNVII
PCLLFSFLTG LVFYLPTDSG GCGCHDCCC*
speed 0.76 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