Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.0184864105525594 (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) chr17:2266799G>AN/A show variant in all transcripts   IGV
HGNC symbol SGSM2
Ensembl transcript ID ENST00000426855
Genbank transcript ID NM_001098509
UniProt peptide O43147
alteration type single base exchange
alteration region CDS
DNA changes c.713G>A
cDNA.888G>A
g.26008G>A
AA changes R238K Score: 26 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 238
frameshift no
known variant Reference ID: rs745400
databasehomozygous (A/A)heterozygousallele carriers
1000G82411171941
ExAC15038269117729
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6671
1.5990.999
(flanking)0.090.994
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased26003wt: 0.58 / mu: 1.00wt: TCGGAGGACAGGCTG
mu: TCGGAGGACAAGCTG		 GGAG|gaca
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      238KRHSSGSASEDRLAACARECVESL
mutated  all conserved    238KRHSSGSASEDKLA
Ptroglodytes  all identical  ENSPTRG00000008548  238KRHSSGSASEDRLA
Mmulatta  all identical  ENSMMUG00000022002  238KRHSSGSASEDRLA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000038351  238KRHSSGSASEDRLA
Ggallus  all identical  ENSGALG00000005737  259KRHSSGSTSEDRFA
Trubripes  all identical  ENSTRUG00000005388  384MSEDRFASSAREYVES
Drerio  all conserved  ENSDARG00000063307  243EDKFAASAREYVES
Dmelanogaster  not conserved  FBgn0031116  245SEDTSSGSFKACSPASVAKDYVES
Celegans  all identical  C38H2.1  277RQVSSIAASVERNGSVSRDY
Xtropicalis  all conserved  ENSXETG00000019436  194KRHSSGSMSEDKFAASAREYVES
protein features
start (aa)end (aa)featuredetails 
566939DOMAINRab-GAP TBC.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3021 / 3021
position (AA) of stopcodon in wt / mu AA sequence 1007 / 1007
position of stopcodon in wt / mu cDNA 3196 / 3196
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 176 / 176
chromosome 17
strand 1
last intron/exon boundary 3108
theoretical NMD boundary in CDS 2882
length of CDS 3021
coding sequence (CDS) position 713
cDNA position
(for ins/del: last normal base / first normal base)		 888
gDNA position
(for ins/del: last normal base / first normal base)		 26008
chromosomal position
(for ins/del: last normal base / first normal base)		 2266799
original gDNA sequence snippet CGGCAGCGCGTCGGAGGACAGGCTGGCTGCCTGTGCCCGCG
altered gDNA sequence snippet CGGCAGCGCGTCGGAGGACAAGCTGGCTGCCTGTGCCCGCG
original cDNA sequence snippet CGGCAGCGCGTCGGAGGACAGGCTGGCTGCCTGTGCCCGCG
altered cDNA sequence snippet CGGCAGCGCGTCGGAGGACAAGCTGGCTGCCTGTGCCCGCG
wildtype AA sequence MGSAEDAVKE KLLWNVKKEV KQIMEEAVTR KFVHEDSSHI IALCGAVEAC LLHQLRRRAA
GFLRSDKMAA LFTKVGKTCP VAGEICHKVQ ELQQQAEGRK PSGVSQEALR RQGSASGKAP
ALSPQALKHV WVRTALIEKV LDKVVQYLAE NCSKYYEKEA LLADPVFGPI LASLLVGPCA
LEYTKLKTAD HYWTDPSADE LVQRHRIRGP PTRQDSPAKR PALGIRKRHS SGSASEDRLA
ACARECVESL HQNSRTRLLY GKNHVLVQPK EDMEAVPGYL SLHQSAESLT LKWTPNQLMN
GTLGDSELEK SVYWDYALVV PFSQVVCIHC HQQKSGGTLV LVSQDGIQRP PLHFPQGGHL
LSFLSCLENG LLPRGQLEPP LWTQQGKGKV FPKLRKRSSI RSVDMEEMGT GRATDYVFRI
IYPGHRHEHN AGDMIEMQGF GPSLPAWHLE PLCSQGSSCL SCSSSSSPHA TPSHCSCIPD
RLPLRLLCES MKRQIVSRAF YGWLAHCRHL STVRTHLSAL VHHSVIPPDR PPGASAGLTK
DVWSKYQKDK KNYKELELLR QVYYGGIEHE IRKDVWPFLL GHYKFGMSKK EMEQVDAVVA
ARYQQVLAEW KACEVVVRQR EREAHPATRT KFSSGSSIDS HVQRLIHRDS TISNDVFISV
DDLEPPEPQD PEDSRPKPEQ EAGPGTPGTA VVEQQHSVEF DSPDSGLPSS RNYSVASGIQ
SSLDEGQSVG FEEEDGGGEE GSSGPGPAAH TLREPQDPSQ EKPQAGELEA GEELAAVCAA
AYTIELLDTV ALNLHRIDKD VQRCDRNYWY FTPPNLERLR DVMCSYVWEH LDVGYVQGMC
DLLAPLLVTL DNDQLAYSCF SHLMKRMSQN FPNGGAMDTH FANMRSLIQI LDSELFELMH
QNGDYTHFYF CYRWFLLDFK RELLYEDVFA VWEVIWAARH ISSEHFVLFI ALALVEAYRE
IIRDNNMDFT DIIKFFNERA EHHDAQEILR IARDLVHKVQ MLIENK*
mutated AA sequence MGSAEDAVKE KLLWNVKKEV KQIMEEAVTR KFVHEDSSHI IALCGAVEAC LLHQLRRRAA
GFLRSDKMAA LFTKVGKTCP VAGEICHKVQ ELQQQAEGRK PSGVSQEALR RQGSASGKAP
ALSPQALKHV WVRTALIEKV LDKVVQYLAE NCSKYYEKEA LLADPVFGPI LASLLVGPCA
LEYTKLKTAD HYWTDPSADE LVQRHRIRGP PTRQDSPAKR PALGIRKRHS SGSASEDKLA
ACARECVESL HQNSRTRLLY GKNHVLVQPK EDMEAVPGYL SLHQSAESLT LKWTPNQLMN
GTLGDSELEK SVYWDYALVV PFSQVVCIHC HQQKSGGTLV LVSQDGIQRP PLHFPQGGHL
LSFLSCLENG LLPRGQLEPP LWTQQGKGKV FPKLRKRSSI RSVDMEEMGT GRATDYVFRI
IYPGHRHEHN AGDMIEMQGF GPSLPAWHLE PLCSQGSSCL SCSSSSSPHA TPSHCSCIPD
RLPLRLLCES MKRQIVSRAF YGWLAHCRHL STVRTHLSAL VHHSVIPPDR PPGASAGLTK
DVWSKYQKDK KNYKELELLR QVYYGGIEHE IRKDVWPFLL GHYKFGMSKK EMEQVDAVVA
ARYQQVLAEW KACEVVVRQR EREAHPATRT KFSSGSSIDS HVQRLIHRDS TISNDVFISV
DDLEPPEPQD PEDSRPKPEQ EAGPGTPGTA VVEQQHSVEF DSPDSGLPSS RNYSVASGIQ
SSLDEGQSVG FEEEDGGGEE GSSGPGPAAH TLREPQDPSQ EKPQAGELEA GEELAAVCAA
AYTIELLDTV ALNLHRIDKD VQRCDRNYWY FTPPNLERLR DVMCSYVWEH LDVGYVQGMC
DLLAPLLVTL DNDQLAYSCF SHLMKRMSQN FPNGGAMDTH FANMRSLIQI LDSELFELMH
QNGDYTHFYF CYRWFLLDFK RELLYEDVFA VWEVIWAARH ISSEHFVLFI ALALVEAYRE
IIRDNNMDFT DIIKFFNERA EHHDAQEILR IARDLVHKVQ MLIENK*
speed 1.09 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