Yum, tasty mutations...

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: ENST00000210444
MT speed 0.92 s - this script 3.013063 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
NANSpolymorphism_automatic0.998772418529044simple_aaeaffectedE68Dsingle base exchangers1058446show file

Taster files

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.00122758147095631 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:100823135G>CN/A show variant in all transcripts   IGV
HGNC symbol NANS
Ensembl transcript ID ENST00000210444
Genbank transcript ID NM_018946
UniProt peptide Q9NR45
alteration type single base exchange
alteration region CDS
DNA changes c.204G>C
cDNA.274G>C
g.4115G>C
AA changes E68D Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 68
frameshift no
known variant Reference ID: rs1058446
databasehomozygous (C/C)heterozygousallele carriers
1000G106751857
ExAC26361885621492
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.5911
1.7531
(flanking)0.3561
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased4106wt: 0.72 / mu: 0.84wt: CGGAAAGCCTTGGAG
mu: CGGAAAGCCTTGGAC		 GAAA|gcct
Donor gained41170.40mu: GGACAGGCCATACAC ACAG|gcca
distance from splice site 72
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      68ELEFKFNRKALERPYTSKHSWGKT
mutated  all conserved    68KFNRKALDRPYTSKHSWGK
Ptroglodytes  all identical  ENSPTRG00000021173  68KFNRKALERPYTSKHSWGK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000028334  68KFNRKALERPYTSKHSWGK
Ggallus  all identical  ENSGALG00000015320  69YKFNKKALERPYTSKHSWGK
Trubripes  all identical  ENSTRUG00000015552  68KFNKRALERPYTSKHSWGK
Drerio  all identical  ENSDARG00000045620  68KFNKKALERPYTSKHSWGK
Dmelanogaster  all conserved  FBgn0038045  64DLPAKFTRSALDREYISDHAWGK
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000006558  68KFNKKALERPYNSPHSWGK
protein features
start (aa)end (aa)featuredetails 
7979MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
232232CONFLICTA -> T (in Ref. 2; BAA91818).might get lost (downstream of altered splice site)
294299STRANDmight get lost (downstream of altered splice site)
294353DOMAINAFP-like.might get lost (downstream of altered splice site)
309311HELIXmight get lost (downstream of altered splice site)
312315STRANDmight get lost (downstream of altered splice site)
321321CONFLICTG -> A (in Ref. 1; AAF75261).might get lost (downstream of altered splice site)
324326STRANDmight get lost (downstream of altered splice site)
327330HELIXmight get lost (downstream of altered splice site)
334337STRANDmight get lost (downstream of altered splice site)
347349HELIXmight get lost (downstream of altered splice site)
356358STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1080 / 1080
position (AA) of stopcodon in wt / mu AA sequence 360 / 360
position of stopcodon in wt / mu cDNA 1150 / 1150
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 71 / 71
chromosome 9
strand 1
last intron/exon boundary 941
theoretical NMD boundary in CDS 820
length of CDS 1080
coding sequence (CDS) position 204
cDNA position
(for ins/del: last normal base / first normal base)		 274
gDNA position
(for ins/del: last normal base / first normal base)		 4115
chromosomal position
(for ins/del: last normal base / first normal base)		 100823135
original gDNA sequence snippet TTTAATCGGAAAGCCTTGGAGAGGCCATACACCTCGAAGCA
altered gDNA sequence snippet TTTAATCGGAAAGCCTTGGACAGGCCATACACCTCGAAGCA
original cDNA sequence snippet TTTAATCGGAAAGCCTTGGAGAGGCCATACACCTCGAAGCA
altered cDNA sequence snippet TTTAATCGGAAAGCCTTGGACAGGCCATACACCTCGAAGCA
wildtype AA sequence MPLELELCPG RWVGGQHPCF IIAEIGQNHQ GDLDVAKRMI RMAKECGADC AKFQKSELEF
KFNRKALERP YTSKHSWGKT YGEHKRHLEF SHDQYRELQR YAEEVGIFFT ASGMDEMAVE
FLHELNVPFF KVGSGDTNNF PYLEKTAKKG RPMVISSGMQ SMDTMKQVYQ IVKPLNPNFC
FLQCTSAYPL QPEDVNLRVI SEYQKLFPDI PIGYSGHETG IAISVAAVAL GAKVLERHIT
LDKTWKGSDH SASLEPGELA ELVRSVRLVE RALGSPTKQL LPCEMACNEK LGKSVVAKVK
IPEGTILTMD MLTVKVGEPK GYPPEDIFNL VGKKVLVTVE EDDTIMEELV DNHGKKIKS*
mutated AA sequence MPLELELCPG RWVGGQHPCF IIAEIGQNHQ GDLDVAKRMI RMAKECGADC AKFQKSELEF
KFNRKALDRP YTSKHSWGKT YGEHKRHLEF SHDQYRELQR YAEEVGIFFT ASGMDEMAVE
FLHELNVPFF KVGSGDTNNF PYLEKTAKKG RPMVISSGMQ SMDTMKQVYQ IVKPLNPNFC
FLQCTSAYPL QPEDVNLRVI SEYQKLFPDI PIGYSGHETG IAISVAAVAL GAKVLERHIT
LDKTWKGSDH SASLEPGELA ELVRSVRLVE RALGSPTKQL LPCEMACNEK LGKSVVAKVK
IPEGTILTMD MLTVKVGEPK GYPPEDIFNL VGKKVLVTVE EDDTIMEELV DNHGKKIKS*
speed 0.92 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