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MutationTaster - study a chromosomal position

 MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000370263
MT speed 0 s - this script 2.87169 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CHRNA4disease_causing_automatic0.999999999840228simple_aaeaffected0S284Lsingle base exchangers28931591show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999999840228 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM001964)
  • known disease mutation: rs17500 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:61981912G>AN/A show variant in all transcripts   IGV
HGNC symbol CHRNA4
Ensembl transcript ID ENST00000370263
Genbank transcript ID NM_000744
UniProt peptide P43681
alteration type single base exchange
alteration region CDS
DNA changes c.851C>T
cDNA.1073C>T
g.27842C>T
AA changes S284L Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 284
frameshift no
known variant Reference ID: rs28931591
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17500 (pathogenic for Seizures|Epilepsy, nocturnal frontal lobe, type 1|Autosomal dominant nocturnal frontal lobe epilepsy|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001964)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001964)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001964)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0030.987
5.8661
(flanking)4.8871
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased27853wt: 0.7477 / mu: 0.8022 (marginal change - not scored)wt: TGCTGCTGTCGCTCACCGTCTTCCTGCTGCTCATCACCGAG
mu: TGCTGCTGTTGCTCACCGTCTTCCTGCTGCTCATCACCGAG		 gtct|TCCT
Acc increased27851wt: 0.22 / mu: 0.41wt: CGTGCTGCTGTCGCTCACCGTCTTCCTGCTGCTCATCACCG
mu: CGTGCTGCTGTTGCTCACCGTCTTCCTGCTGCTCATCACCG		 ccgt|CTTC
Acc increased27850wt: 0.74 / mu: 0.82wt: CCGTGCTGCTGTCGCTCACCGTCTTCCTGCTGCTCATCACC
mu: CCGTGCTGCTGTTGCTCACCGTCTTCCTGCTGCTCATCACC		 accg|TCTT
Acc gained278400.31mu: CTGTGCATCTCCGTGCTGCTGTTGCTCACCGTCTTCCTGCT gctg|TTGC
distance from splice site 468
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      284EKITLCISVLLSLTVFLLLITEII
mutated  not conserved    284EKITLCISVLLLLTVFLLLITEI
Ptroglodytes  all identical  ENSPTRG00000013735  272EKITLCISVLLSLTVFLLLITEI
Mmulatta  all identical  ENSMMUG00000015916  259EKITLCISVLLSLTVFLLLITEI
Fcatus  not conserved  ENSFCAG00000008921  228------------------LIGEY
Mmusculus  all identical  ENSMUSG00000027577  286EKVTLCISVLLSLTVFLLLITEI
Ggallus  all identical  ENSGALG00000005801  279EKITLCISVLLSLTVFLLLITEI
Trubripes  all identical  ENSTRUG00000010213  278EKITLCISVLLSLTVFLLLITEI
Drerio  all identical  ENSDARG00000070724  278EKITLCISVLLSLTVFLLLITEI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023746  157EKITLCISVLLSLTVFLLLITEI
protein features
start (aa)end (aa)featuredetails 
273295HELIXlost
275293TRANSMEMHelical; (Potential).lost
300302STRANDmight get lost (downstream of altered splice site)
307329HELIXmight get lost (downstream of altered splice site)
309330TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
331600TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
598618HELIXmight get lost (downstream of altered splice site)
601619TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
622624TURNmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1884 / 1884
position (AA) of stopcodon in wt / mu AA sequence 628 / 628
position of stopcodon in wt / mu cDNA 2106 / 2106
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 223 / 223
chromosome 20
strand -1
last intron/exon boundary 1981
theoretical NMD boundary in CDS 1708
length of CDS 1884
coding sequence (CDS) position 851
cDNA position
(for ins/del: last normal base / first normal base)		 1073
gDNA position
(for ins/del: last normal base / first normal base)		 27842
chromosomal position
(for ins/del: last normal base / first normal base)		 61981912
original gDNA sequence snippet GTGCATCTCCGTGCTGCTGTCGCTCACCGTCTTCCTGCTGC
altered gDNA sequence snippet GTGCATCTCCGTGCTGCTGTTGCTCACCGTCTTCCTGCTGC
original cDNA sequence snippet GTGCATCTCCGTGCTGCTGTCGCTCACCGTCTTCCTGCTGC
altered cDNA sequence snippet GTGCATCTCCGTGCTGCTGTTGCTCACCGTCTTCCTGCTGC
wildtype AA sequence MELGGPGAPR LLPPLLLLLG TGLLRASSHV ETRAHAEERL LKKLFSGYNK WSRPVANISD
VVLVRFGLSI AQLIDVDEKN QMMTTNVWVK QEWHDYKLRW DPADYENVTS IRIPSELIWR
PDIVLYNNAD GDFAVTHLTK AHLFHDGRVQ WTPPAIYKSS CSIDVTFFPF DQQNCTMKFG
SWTYDKAKID LVNMHSRVDQ LDFWESGEWV IVDAVGTYNT RKYECCAEIY PDITYAFVIR
RLPLFYTINL IIPCLLISCL TVLVFYLPSE CGEKITLCIS VLLSLTVFLL LITEIIPSTS
LVIPLIGEYL LFTMIFVTLS IVITVFVLNV HHRSPRTHTM PTWVRRVFLD IVPRLLLMKR
PSVVKDNCRR LIESMHKMAS APRFWPEPEG EPPATSGTQS LHPPSPSFCV PLDVPAEPGP
SCKSPSDQLP PQQPLEAEKA SPHPSPGPCR PPHGTQAPGL AKARSLSVQH MSSPGEAVEG
GVRCRSRSIQ YCVPRDDAAP EADGQAAGAL ASRNTHSAEL PPPDQPSPCK CTCKKEPSSV
SPSATVKTRS TKAPPPHLPL SPALTRAVEG VQYIADHLKA EDTDFSVKED WKYVAMVIDR
IFLWMFIIVC LLGTVGLFLP PWLAGMI*
mutated AA sequence MELGGPGAPR LLPPLLLLLG TGLLRASSHV ETRAHAEERL LKKLFSGYNK WSRPVANISD
VVLVRFGLSI AQLIDVDEKN QMMTTNVWVK QEWHDYKLRW DPADYENVTS IRIPSELIWR
PDIVLYNNAD GDFAVTHLTK AHLFHDGRVQ WTPPAIYKSS CSIDVTFFPF DQQNCTMKFG
SWTYDKAKID LVNMHSRVDQ LDFWESGEWV IVDAVGTYNT RKYECCAEIY PDITYAFVIR
RLPLFYTINL IIPCLLISCL TVLVFYLPSE CGEKITLCIS VLLLLTVFLL LITEIIPSTS
LVIPLIGEYL LFTMIFVTLS IVITVFVLNV HHRSPRTHTM PTWVRRVFLD IVPRLLLMKR
PSVVKDNCRR LIESMHKMAS APRFWPEPEG EPPATSGTQS LHPPSPSFCV PLDVPAEPGP
SCKSPSDQLP PQQPLEAEKA SPHPSPGPCR PPHGTQAPGL AKARSLSVQH MSSPGEAVEG
GVRCRSRSIQ YCVPRDDAAP EADGQAAGAL ASRNTHSAEL PPPDQPSPCK CTCKKEPSSV
SPSATVKTRS TKAPPPHLPL SPALTRAVEG VQYIADHLKA EDTDFSVKED WKYVAMVIDR
IFLWMFIIVC LLGTVGLFLP PWLAGMI*
speed 0.81 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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