Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999971 (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) chr1:232574921T>CN/A show variant in all transcripts   IGV
HGNC symbol SIPA1L2
Ensembl transcript ID ENST00000308942
Genbank transcript ID N/A
UniProt peptide Q9P2F8
alteration type single base exchange
alteration region CDS
DNA changes c.1186A>G
cDNA.1369A>G
g.122384A>G
AA changes T396A Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 396
frameshift no
known variant Reference ID: rs2275307
databasehomozygous (C/C)heterozygousallele carriers
1000G34810681416
ExAC52302230727537
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.020.097
0.180.005
(flanking)-0.9560
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased122394wt: 0.44 / mu: 0.51wt: CTACGCGTCCACCATCTCCGCCGGCAGTGCTGCGGAAGGCA
mu: CTACGCGTCCGCCATCTCCGCCGGCAGTGCTGCGGAAGGCA		 ccgc|CGGC
Acc increased122392wt: 0.42 / mu: 0.55wt: GGCTACGCGTCCACCATCTCCGCCGGCAGTGCTGCGGAAGG
mu: GGCTACGCGTCCGCCATCTCCGCCGGCAGTGCTGCGGAAGG		 ctcc|GCCG
Donor gained1223830.59mu: GCGTCCGCCATCTCC GTCC|gcca
distance from splice site 68
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      396AKLYSVHGYASTISAGSAAEGSMG
mutated  not conserved    396AKLYSVHGYASAISAGSAAEGSM
Ptroglodytes  not conserved  ENSPTRG00000002114  1322AKLYSVHGYASAISAGSAAEGSM
Mmulatta  not conserved  ENSMMUG00000012068  395AKLYSVHGYASAISAGSAAEGSM
Fcatus  no alignment  ENSFCAG00000007249  n/a
Mmusculus  not conserved  ENSMUSG00000001995  1323AKMYALHGYASAISS-SAADGSM
Ggallus  not conserved  ENSGALG00000011025  1317AKMYAVHSYASAISASHMAEGSM
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000088396  n/a
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000033496  1273-------------SSETIVHGSM
protein features
start (aa)end (aa)featuredetails 
595812DOMAINRap-GAP.might get lost (downstream of altered splice site)
9501026DOMAINPDZ.might get lost (downstream of altered splice site)
10291029MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
11251128COMPBIASPoly-Ser.might get lost (downstream of altered splice site)
12441244MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
12881288CONFLICTS -> P (in Ref. 2; BAB14273).might get lost (downstream of altered splice site)
13081308CONFLICTD -> V (in Ref. 2; BAB14273).might get lost (downstream of altered splice site)
13211384COMPBIASSer-rich.might get lost (downstream of altered splice site)
14061406MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
14611461MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
14781478MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
14881488MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15491549MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
15521552MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
16541712COILEDPotential.might get lost (downstream of altered splice site)
17021702CONFLICTT -> I (in Ref. 2; BAB14273).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2337 / 2337
position (AA) of stopcodon in wt / mu AA sequence 779 / 779
position of stopcodon in wt / mu cDNA 2520 / 2520
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 184 / 184
chromosome 1
strand -1
last intron/exon boundary 2374
theoretical NMD boundary in CDS 2140
length of CDS 2337
coding sequence (CDS) position 1186
cDNA position
(for ins/del: last normal base / first normal base)		 1369
gDNA position
(for ins/del: last normal base / first normal base)		 122384
chromosomal position
(for ins/del: last normal base / first normal base)		 232574921
original gDNA sequence snippet CTGTGCATGGCTACGCGTCCACCATCTCCGCCGGCAGTGCT
altered gDNA sequence snippet CTGTGCATGGCTACGCGTCCGCCATCTCCGCCGGCAGTGCT
original cDNA sequence snippet CTGTGCATGGCTACGCGTCCACCATCTCCGCCGGCAGTGCT
altered cDNA sequence snippet CTGTGCATGGCTACGCGTCCGCCATCTCCGCCGGCAGTGCT
wildtype AA sequence MSPCFSFIGC KLCSIVTRGC ETVEMTLRRN GLGQLGFHVN FEGIVADVEP FGFAWKAGLR
QGSRLVEICK VAVATLTHEQ MIDLLRTSVT VKVVIIQPHD DGSPRRGCSE LCRIPMVEYK
LDSEGTPCEY KTPFRRNTTW HRVPTPALQP LSRASPIPGT PDRLPCQQLL QQAQAAIPRS
TSFDRKLPDG TRSSPSNQSS SSDPGPGGSG PWRPQVGYDG CQSPLLLEHQ GSGPLECDGA
REREDTMEAS RHPETKWHGP PSKVLGSYKE RALQKDGSCK DSPNKLSHIG DKSCSSHSSS
NTLSSNTSSN SDDKHFGSGD LMDPELLGLT YIKGASTDSG IDTAPCMPAT ILGPVHLAGS
RSLIHSRAEQ WADAADVSGP DDEPAKLYSV HGYASTISAG SAAEGSMGDL SEISSHSSGS
HHSGSPSAHC SKSSGSLDSS KVYIVSHSSG QQVPGSMSKP YHRQGAVNKY VIGWKKSEGS
PPPEEPEVTE CPGMYSEMDV MSTATQHQTV VGDAVAETQH VLSKEDFLKL MLPDSPLVEE
GRRKFSFYGN LSPRRSLYRT LSDESICSNR RGSSFGSSRS SVLDQALPND ILFSTTPPYH
STLPPRAHPA PSMGSLRNEF WFSDGSLSDK SKCADPGLMP LPDTATGLDW THLVDAARAF
EDQRVASFCT LTDMQHGQDL EGAQELPLCV DPGSGKEFMD TTGERSPSPL TGKVNQLELI
LRQLQTDLRK EKQDKAVLQA EVQHLRQDNM RLQEESQTAT AQLRKFTEWF FTTIDKKS*
mutated AA sequence MSPCFSFIGC KLCSIVTRGC ETVEMTLRRN GLGQLGFHVN FEGIVADVEP FGFAWKAGLR
QGSRLVEICK VAVATLTHEQ MIDLLRTSVT VKVVIIQPHD DGSPRRGCSE LCRIPMVEYK
LDSEGTPCEY KTPFRRNTTW HRVPTPALQP LSRASPIPGT PDRLPCQQLL QQAQAAIPRS
TSFDRKLPDG TRSSPSNQSS SSDPGPGGSG PWRPQVGYDG CQSPLLLEHQ GSGPLECDGA
REREDTMEAS RHPETKWHGP PSKVLGSYKE RALQKDGSCK DSPNKLSHIG DKSCSSHSSS
NTLSSNTSSN SDDKHFGSGD LMDPELLGLT YIKGASTDSG IDTAPCMPAT ILGPVHLAGS
RSLIHSRAEQ WADAADVSGP DDEPAKLYSV HGYASAISAG SAAEGSMGDL SEISSHSSGS
HHSGSPSAHC SKSSGSLDSS KVYIVSHSSG QQVPGSMSKP YHRQGAVNKY VIGWKKSEGS
PPPEEPEVTE CPGMYSEMDV MSTATQHQTV VGDAVAETQH VLSKEDFLKL MLPDSPLVEE
GRRKFSFYGN LSPRRSLYRT LSDESICSNR RGSSFGSSRS SVLDQALPND ILFSTTPPYH
STLPPRAHPA PSMGSLRNEF WFSDGSLSDK SKCADPGLMP LPDTATGLDW THLVDAARAF
EDQRVASFCT LTDMQHGQDL EGAQELPLCV DPGSGKEFMD TTGERSPSPL TGKVNQLELI
LRQLQTDLRK EKQDKAVLQA EVQHLRQDNM RLQEESQTAT AQLRKFTEWF FTTIDKKS*
speed 1.33 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