Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999992 (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) chr19:51170706A>GN/A show variant in all transcripts   IGV
HGNC symbol SHANK1
Ensembl transcript ID ENST00000293441
Genbank transcript ID NM_016148
UniProt peptide Q9Y566
alteration type single base exchange
alteration region CDS
DNA changes c.4511T>C
cDNA.4530T>C
g.52002T>C
AA changes V1504A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1504
frameshift no
known variant Reference ID: rs3745521
databasehomozygous (G/G)heterozygousallele carriers
1000G13818332214
ExAC7702610213804
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.2460
0.0820
(flanking)-0.1440
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 increased52002wt: 0.2747 / mu: 0.2802 (marginal change - not scored)wt: CTGCCAGCCCCGGGCCCCTGTGACGAGCGGAAGGGGTCCCC
mu: CTGCCAGCCCCGGGCCCCTGCGACGAGCGGAAGGGGTCCCC		 ctgt|GACG
Donor increased52007wt: 0.72 / mu: 0.83wt: TGACGAGCGGAAGGG
mu: CGACGAGCGGAAGGG		 ACGA|gcgg
Donor marginally increased52002wt: 0.9240 / mu: 0.9771 (marginal change - not scored)wt: CCCTGTGACGAGCGG
mu: CCCTGCGACGAGCGG		 CTGT|gacg
Donor marginally increased52000wt: 0.9904 / mu: 0.9907 (marginal change - not scored)wt: GCCCCTGTGACGAGC
mu: GCCCCTGCGACGAGC		 CCCT|gtga
distance from splice site 1258
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1504RFLENCQPRAPVTSGRGPPSEDGP
mutated  not conserved    1504RAPATSGRGPPSEDG
Ptroglodytes  no homologue    
Mmulatta  not conserved  ENSMMUG00000009357  1493RFLENCQPRAPATSGRGPPSEDG
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000038738  1510RFLENCQARPPPAGTRGSSTEDG
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000006583  1419RDKEGYMSRVEQTAS
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0040752  n/a
Celegans  no alignment  C33B4.3  n/a
Xtropicalis  not conserved  ENSXETG00000000210  1355RFMENSTHKEEEEQSKVAMVKVK
protein features
start (aa)end (aa)featuredetails 
17091717COMPBIASPoly-Gly.might get lost (downstream of altered splice site)
18321832CONFLICTS -> C (in Ref. 1; AAD45121/AAF35887).might get lost (downstream of altered splice site)
18441854COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
18961902COMPBIASPoly-Gly.might get lost (downstream of altered splice site)
19701979COMPBIASPoly-Ser.might get lost (downstream of altered splice site)
20982161DOMAINSAM.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 6486 / 6486
position (AA) of stopcodon in wt / mu AA sequence 2162 / 2162
position of stopcodon in wt / mu cDNA 6505 / 6505
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 20 / 20
chromosome 19
strand -1
last intron/exon boundary 5788
theoretical NMD boundary in CDS 5718
length of CDS 6486
coding sequence (CDS) position 4511
cDNA position
(for ins/del: last normal base / first normal base)		 4530
gDNA position
(for ins/del: last normal base / first normal base)		 52002
chromosomal position
(for ins/del: last normal base / first normal base)		 51170706
original gDNA sequence snippet CTGCCAGCCCCGGGCCCCTGTGACGAGCGGAAGGGGTCCCC
altered gDNA sequence snippet CTGCCAGCCCCGGGCCCCTGCGACGAGCGGAAGGGGTCCCC
original cDNA sequence snippet CTGCCAGCCCCGGGCCCCTGTGACGAGCGGAAGGGGTCCCC
altered cDNA sequence snippet CTGCCAGCCCCGGGCCCCTGCGACGAGCGGAAGGGGTCCCC
wildtype AA sequence MTHSPATSED EERHSASECP EGGSESDSSP DGPGRGPRGT RGQGSGAPGS LASVRGLQGR
SMSVPDDAHF SMMVFRIGIP DLHQTKCLRF NPDATIWTAK QQVLCALSES LQDVLNYGLF
QPATSGRDAN FLEEERLLRE YPQSFEKGVP YLEFRYKTRV YKQTNLDEKQ LAKLHTKTGL
KKFLEYVQLG TSDKVARLLD KGLDPNYHDS DSGETPLTLA AQTEGSVEVI RTLCLGGAHI
DFRARDGMTA LHKAACARHC LALTALLDLG GSPNYKDRRG LTPLFHTAMV GGDPRCCELL
LFNRAQLGIA DENGWQEIHQ ACQRGHSQHL EHLLFYGAEP GAQNASGNTA LHICALYNKE
TCARILLYRG ADKDVKNNNG QTPFQVAVIA GNFELGELIR NHREQDVVPF QESPKYAARR
RGPPGTGLTV PPALLRANSD TSMALPDWMV FSAPGAASSG APGPTSGSQG QSQPSAPTTK
LSSGTLRSAS SPRGARARSP SRGRHPEDAK RQPRGRPSSS GTPREGPAGG TGGSGGPGGS
LGSRGRRRKL YSAVPGRSFM AVKSYQAQAE GEISLSKGEK IKVLSIGEGG FWEGQVKGRV
GWFPSDCLEE VANRSQESKQ ESRSDKAKRL FRHYTVGSYD SFDAPSLMDG IGPGSDYIIK
EKTVLLQKKD SEGFGFVLRG AKAQTPIEEF TPTPAFPALQ YLESVDEGGV AWRAGLRMGD
FLIEVNGQNV VKVGHRQVVN MIRQGGNTLM VKVVMVTRHP DMDEAVHKKA PQQAKRLPPP
TISLRSKSMT SELEEMEYEQ QPAPVPSMEK KRTVYQMALN KLDEILAAAQ QTISASESPG
PGGLASLGKH RPKGFFATES SFDPHHRAQP SYERPSFLPP GPGLMLRQKS IGAAEDDRPY
LAPPAMKFSR SLSVPGSEDI PPPPTTSPPE PPYSTPPVPS SSGRLTPSPR GGPFNPGSGG
PLPASSPASF DGPSPPDTRV GSREKSLYHS GPLPPAHHHP PHHHHHHAPP PQPHHHHAHP
PHPPEMETGG SPDDPPPRLA LGPQPSLRGW RGGGPSPTPG APSPSHHGSA GGGGGSSQGP
ALRYFQLPPR AASAAMYVPA RSGRGRKGPL VKQTKVEGEP QKGGGLPPAP SPTSPASPQP
PPAVAAPSEK NSIPIPTIII KAPSTSSSGR SSQGSSTEAE PPTQPEPTGG GGGGGSSPSP
APAMSPVPPS PSPVPTPASP SGPATLDFTS QFGAALVGAA RREGGWQNEA RRRSTLFLST
DAGDEDGGDG GLGTGAAPGP RLRHSKSIDE GMFSAEPYLR LESAGSGAGY GGYGAGSRAY
GGGGGSSAFT SFLPPRPLVH PLTGKALDPA SPLGLALAAR ERALKESSEG GGAPQPPPRP
PSPRYEAPPP TPHHHSPHAH HEPVLRLWGA SPPDPARREL GYRAGLGSQE KSLPASPPAA
RRSLLHRLPP TAPGVGPLLL QLGTEPPAPH PGVSKPWRSA APEEPERLPL HVRFLENCQP
RAPVTSGRGP PSEDGPGVPP PSPRRSVPPS PTSPRASEEN GLPLLVLPPP APSVDVEDGE
FLFVEPLPPP LEFSNSFEKP ESPLTPGPPH PLPDTPAPAT PLPPVPPPAV AAAPPTLDST
ASSLTSYDSE VATLTQGASA APGDPHPPGP PAPAAPAPAA PQPGPDPPPG TDSGIEEVDS
RSSSDHPLET ISSASTLSSL SAEGGGSAGG GGGAGAGVAS GPELLDTYVA YLDGQAFGGS
STPGPPYPPQ LMTPSKLRGR ALGASGGLRP GPSGGLRDPV TPTSPTVSVT GAGTDGLLAL
RACSGPPTAG VAGGPVAVEP EVPPVPLPTA SSLPRKLLPW EEGPGPPPPP LPGPLAQPQA
SALATVKASI ISELSSKLQQ FGGSSAAGGA LPWARGGSGG GGDSHHGGAS YVPERTSSLQ
RQRLSDDSQS SLLSKPVSSL FQNWPKPPLP PLPTGTGVSP TAAAAPGATS PSASSSSTST
RHLQGVEFEM RPPLLRRAPS PSLLPASEHK VSPAPRPSSL PILPSGPLYP GLFDIRGSPT
GGAGGSADPF APVFVPPHPG ISGGLGGALS GASRSLSPTR LLSLPPDKPF GAKPLGFWTK
FDVADWLEWL GLAEHRAQFL DHEIDGSHLP ALTKEDYVDL GVTRVGHRMN IDRALKFFLE
R*
mutated AA sequence MTHSPATSED EERHSASECP EGGSESDSSP DGPGRGPRGT RGQGSGAPGS LASVRGLQGR
SMSVPDDAHF SMMVFRIGIP DLHQTKCLRF NPDATIWTAK QQVLCALSES LQDVLNYGLF
QPATSGRDAN FLEEERLLRE YPQSFEKGVP YLEFRYKTRV YKQTNLDEKQ LAKLHTKTGL
KKFLEYVQLG TSDKVARLLD KGLDPNYHDS DSGETPLTLA AQTEGSVEVI RTLCLGGAHI
DFRARDGMTA LHKAACARHC LALTALLDLG GSPNYKDRRG LTPLFHTAMV GGDPRCCELL
LFNRAQLGIA DENGWQEIHQ ACQRGHSQHL EHLLFYGAEP GAQNASGNTA LHICALYNKE
TCARILLYRG ADKDVKNNNG QTPFQVAVIA GNFELGELIR NHREQDVVPF QESPKYAARR
RGPPGTGLTV PPALLRANSD TSMALPDWMV FSAPGAASSG APGPTSGSQG QSQPSAPTTK
LSSGTLRSAS SPRGARARSP SRGRHPEDAK RQPRGRPSSS GTPREGPAGG TGGSGGPGGS
LGSRGRRRKL YSAVPGRSFM AVKSYQAQAE GEISLSKGEK IKVLSIGEGG FWEGQVKGRV
GWFPSDCLEE VANRSQESKQ ESRSDKAKRL FRHYTVGSYD SFDAPSLMDG IGPGSDYIIK
EKTVLLQKKD SEGFGFVLRG AKAQTPIEEF TPTPAFPALQ YLESVDEGGV AWRAGLRMGD
FLIEVNGQNV VKVGHRQVVN MIRQGGNTLM VKVVMVTRHP DMDEAVHKKA PQQAKRLPPP
TISLRSKSMT SELEEMEYEQ QPAPVPSMEK KRTVYQMALN KLDEILAAAQ QTISASESPG
PGGLASLGKH RPKGFFATES SFDPHHRAQP SYERPSFLPP GPGLMLRQKS IGAAEDDRPY
LAPPAMKFSR SLSVPGSEDI PPPPTTSPPE PPYSTPPVPS SSGRLTPSPR GGPFNPGSGG
PLPASSPASF DGPSPPDTRV GSREKSLYHS GPLPPAHHHP PHHHHHHAPP PQPHHHHAHP
PHPPEMETGG SPDDPPPRLA LGPQPSLRGW RGGGPSPTPG APSPSHHGSA GGGGGSSQGP
ALRYFQLPPR AASAAMYVPA RSGRGRKGPL VKQTKVEGEP QKGGGLPPAP SPTSPASPQP
PPAVAAPSEK NSIPIPTIII KAPSTSSSGR SSQGSSTEAE PPTQPEPTGG GGGGGSSPSP
APAMSPVPPS PSPVPTPASP SGPATLDFTS QFGAALVGAA RREGGWQNEA RRRSTLFLST
DAGDEDGGDG GLGTGAAPGP RLRHSKSIDE GMFSAEPYLR LESAGSGAGY GGYGAGSRAY
GGGGGSSAFT SFLPPRPLVH PLTGKALDPA SPLGLALAAR ERALKESSEG GGAPQPPPRP
PSPRYEAPPP TPHHHSPHAH HEPVLRLWGA SPPDPARREL GYRAGLGSQE KSLPASPPAA
RRSLLHRLPP TAPGVGPLLL QLGTEPPAPH PGVSKPWRSA APEEPERLPL HVRFLENCQP
RAPATSGRGP PSEDGPGVPP PSPRRSVPPS PTSPRASEEN GLPLLVLPPP APSVDVEDGE
FLFVEPLPPP LEFSNSFEKP ESPLTPGPPH PLPDTPAPAT PLPPVPPPAV AAAPPTLDST
ASSLTSYDSE VATLTQGASA APGDPHPPGP PAPAAPAPAA PQPGPDPPPG TDSGIEEVDS
RSSSDHPLET ISSASTLSSL SAEGGGSAGG GGGAGAGVAS GPELLDTYVA YLDGQAFGGS
STPGPPYPPQ LMTPSKLRGR ALGASGGLRP GPSGGLRDPV TPTSPTVSVT GAGTDGLLAL
RACSGPPTAG VAGGPVAVEP EVPPVPLPTA SSLPRKLLPW EEGPGPPPPP LPGPLAQPQA
SALATVKASI ISELSSKLQQ FGGSSAAGGA LPWARGGSGG GGDSHHGGAS YVPERTSSLQ
RQRLSDDSQS SLLSKPVSSL FQNWPKPPLP PLPTGTGVSP TAAAAPGATS PSASSSSTST
RHLQGVEFEM RPPLLRRAPS PSLLPASEHK VSPAPRPSSL PILPSGPLYP GLFDIRGSPT
GGAGGSADPF APVFVPPHPG ISGGLGGALS GASRSLSPTR LLSLPPDKPF GAKPLGFWTK
FDVADWLEWL GLAEHRAQFL DHEIDGSHLP ALTKEDYVDL GVTRVGHRMN IDRALKFFLE
R*
speed 1.40 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