Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 5 transcript(s)...
Querying Taster for transcript #1: ENST00000544769
Querying Taster for transcript #2: ENST00000293441
Querying Taster for transcript #3: ENST00000391813
Querying Taster for transcript #4: ENST00000391814
Querying Taster for transcript #5: ENST00000359082
MT speed 0 s - this script 4.987587 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
SHANK1polymorphism_automatic7.99360577730113e-15simple_aaeaffectedV1504Asingle base exchangers3745521show file
SHANK1polymorphism_automatic7.99360577730113e-15simple_aaeaffectedV1512Asingle base exchangers3745521show file
SHANK1polymorphism_automatic7.99360577730113e-15simple_aaeaffectedV1495Asingle base exchangers3745521show file
SHANK1polymorphism_automatic1.79856129989275e-14simple_aaeaffectedV891Asingle base exchangers3745521show file
SYT3polymorphism_automatic1.554566829709e-07without_aaeaffectedsingle base exchangers3745521show file

Taster files

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 marginally increased52000wt: 0.9904 / mu: 0.9907 (marginal change - not scored)wt: GCCCCTGTGACGAGC
mu: GCCCCTGCGACGAGC		 CCCT|gtga
Donor marginally increased52002wt: 0.9240 / mu: 0.9771 (marginal change - not scored)wt: CCCTGTGACGAGCGG
mu: CCCTGCGACGAGCGG		 CTGT|gacg
Donor increased52007wt: 0.72 / mu: 0.83wt: TGACGAGCGGAAGGG
mu: CGACGAGCGGAAGGG		 ACGA|gcgg
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 0.48 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
back to results table
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 ENST00000391814
Genbank transcript ID N/A
UniProt peptide Q9Y566
alteration type single base exchange
alteration region CDS
DNA changes c.4535T>C
cDNA.4623T>C
g.52002T>C
AA changes V1512A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1512
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 marginally increased52000wt: 0.9904 / mu: 0.9907 (marginal change - not scored)wt: GCCCCTGTGACGAGC
mu: GCCCCTGCGACGAGC		 CCCT|gtga
Donor marginally increased52002wt: 0.9240 / mu: 0.9771 (marginal change - not scored)wt: CCCTGTGACGAGCGG
mu: CCCTGCGACGAGCGG		 CTGT|gacg
Donor increased52007wt: 0.72 / mu: 0.83wt: TGACGAGCGGAAGGG
mu: CGACGAGCGGAAGGG		 ACGA|gcgg
distance from splice site 1258
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1512RFLENCQPRAPVTSGRGPPSEDGP
mutated  not conserved    1512RFLENCQPRAPATSGRGPPSEDG
Ptroglodytes  no homologue    
Mmulatta  not conserved  ENSMMUG00000009357  1493RFLENCQPRAPATSGRGPPSEDG
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000038738  1510RFLENCQARPPPAGTRGSSTEDG
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000006583  1419RDKEGYMSRVEQTAS-DSLSQRG
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0040752  n/a
Celegans  no alignment  C33B4.3  n/a
Xtropicalis  not conserved  ENSXETG00000000210  1361RFMENSTHKEEEEQSKVAMVKVK
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 6510 / 6510
position (AA) of stopcodon in wt / mu AA sequence 2170 / 2170
position of stopcodon in wt / mu cDNA 6598 / 6598
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 89 / 89
chromosome 19
strand -1
last intron/exon boundary 5881
theoretical NMD boundary in CDS 5742
length of CDS 6510
coding sequence (CDS) position 4535
cDNA position
(for ins/del: last normal base / first normal base)		 4623
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 SELEEMVSPW KKKSEYEQQP APVPSMEKKR TVYQMALNKL DEILAAAQQT
ISASESPGPG GLASLGKHRP KGFFATESSF DPHHRAQPSY ERPSFLPPGP GLMLRQKSIG
AAEDDRPYLA PPAMKFSRSL SVPGSEDIPP PPTTSPPEPP YSTPPVPSSS GRLTPSPRGG
PFNPGSGGPL PASSPASFDG PSPPDTRVGS REKSLYHSGP LPPAHHHPPH HHHHHAPPPQ
PHHHHAHPPH PPEMETGGSP DDPPPRLALG PQPSLRGWRG GGPSPTPGAP SPSHHGSAGG
GGGSSQGPAL RYFQLPPRAA SAAMYVPARS GRGRKGPLVK QTKVEGEPQK GGGLPPAPSP
TSPASPQPPP AVAAPSEKNS IPIPTIIIKA PSTSSSGRSS QGSSTEAEPP TQPEPTGGGG
GGGSSPSPAP AMSPVPPSPS PVPTPASPSG PATLDFTSQF GAALVGAARR EGGWQNEARR
RSTLFLSTDA GDEDGGDGGL GTGAAPGPRL RHSKSIDEGM FSAEPYLRLE SAGSGAGYGG
YGAGSRAYGG GGGSSAFTSF LPPRPLVHPL TGKALDPASP LGLALAARER ALKESSEGGG
APQPPPRPPS PRYEAPPPTP HHHSPHAHHE PVLRLWGASP PDPARRELGY RAGLGSQEKS
LPASPPAARR SLLHRLPPTA PGVGPLLLQL GTEPPAPHPG VSKPWRSAAP EEPERLPLHV
RFLENCQPRA PVTSGRGPPS EDGPGVPPPS PRRSVPPSPT SPRASEENGL PLLVLPPPAP
SVDVEDGEFL FVEPLPPPLE FSNSFEKPES PLTPGPPHPL PDTPAPATPL PPVPPPAVAA
APPTLDSTAS SLTSYDSEVA TLTQGASAAP GDPHPPGPPA PAAPAPAAPQ PGPDPPPGTD
SGIEEVDSRS SSDHPLETIS SASTLSSLSA EGGGSAGGGG GAGAGVASGP ELLDTYVAYL
DGQAFGGSST PGPPYPPQLM TPSKLRGRAL GASGGLRPGP SGGLRDPVTP TSPTVSVTGA
GTDGLLALRA CSGPPTAGVA GGPVAVEPEV PPVPLPTASS LPRKLLPWEE GPGPPPPPLP
GPLAQPQASA LATVKASIIS ELSSKLQQFG GSSAAGGALP WARGGSGGGG DSHHGGASYV
PERTSSLQRQ RLSDDSQSSL LSKPVSSLFQ NWPKPPLPPL PTGTGVSPTA AAAPGATSPS
ASSSSTSTRH LQGVEFEMRP PLLRRAPSPS LLPASEHKVS PAPRPSSLPI LPSGPLYPGL
FDIRGSPTGG AGGSADPFAP VFVPPHPGIS GGLGGALSGA SRSLSPTRLL SLPPDKPFGA
KPLGFWTKFD VADWLEWLGL AEHRAQFLDH EIDGSHLPAL TKEDYVDLGV TRVGHRMNID
RALKFFLER*
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 SELEEMVSPW KKKSEYEQQP APVPSMEKKR TVYQMALNKL DEILAAAQQT
ISASESPGPG GLASLGKHRP KGFFATESSF DPHHRAQPSY ERPSFLPPGP GLMLRQKSIG
AAEDDRPYLA PPAMKFSRSL SVPGSEDIPP PPTTSPPEPP YSTPPVPSSS GRLTPSPRGG
PFNPGSGGPL PASSPASFDG PSPPDTRVGS REKSLYHSGP LPPAHHHPPH HHHHHAPPPQ
PHHHHAHPPH PPEMETGGSP DDPPPRLALG PQPSLRGWRG GGPSPTPGAP SPSHHGSAGG
GGGSSQGPAL RYFQLPPRAA SAAMYVPARS GRGRKGPLVK QTKVEGEPQK GGGLPPAPSP
TSPASPQPPP AVAAPSEKNS IPIPTIIIKA PSTSSSGRSS QGSSTEAEPP TQPEPTGGGG
GGGSSPSPAP AMSPVPPSPS PVPTPASPSG PATLDFTSQF GAALVGAARR EGGWQNEARR
RSTLFLSTDA GDEDGGDGGL GTGAAPGPRL RHSKSIDEGM FSAEPYLRLE SAGSGAGYGG
YGAGSRAYGG GGGSSAFTSF LPPRPLVHPL TGKALDPASP LGLALAARER ALKESSEGGG
APQPPPRPPS PRYEAPPPTP HHHSPHAHHE PVLRLWGASP PDPARRELGY RAGLGSQEKS
LPASPPAARR SLLHRLPPTA PGVGPLLLQL GTEPPAPHPG VSKPWRSAAP EEPERLPLHV
RFLENCQPRA PATSGRGPPS EDGPGVPPPS PRRSVPPSPT SPRASEENGL PLLVLPPPAP
SVDVEDGEFL FVEPLPPPLE FSNSFEKPES PLTPGPPHPL PDTPAPATPL PPVPPPAVAA
APPTLDSTAS SLTSYDSEVA TLTQGASAAP GDPHPPGPPA PAAPAPAAPQ PGPDPPPGTD
SGIEEVDSRS SSDHPLETIS SASTLSSLSA EGGGSAGGGG GAGAGVASGP ELLDTYVAYL
DGQAFGGSST PGPPYPPQLM TPSKLRGRAL GASGGLRPGP SGGLRDPVTP TSPTVSVTGA
GTDGLLALRA CSGPPTAGVA GGPVAVEPEV PPVPLPTASS LPRKLLPWEE GPGPPPPPLP
GPLAQPQASA LATVKASIIS ELSSKLQQFG GSSAAGGALP WARGGSGGGG DSHHGGASYV
PERTSSLQRQ RLSDDSQSSL LSKPVSSLFQ NWPKPPLPPL PTGTGVSPTA AAAPGATSPS
ASSSSTSTRH LQGVEFEMRP PLLRRAPSPS LLPASEHKVS PAPRPSSLPI LPSGPLYPGL
FDIRGSPTGG AGGSADPFAP VFVPPHPGIS GGLGGALSGA SRSLSPTRLL SLPPDKPFGA
KPLGFWTKFD VADWLEWLGL AEHRAQFLDH EIDGSHLPAL TKEDYVDLGV TRVGHRMNID
RALKFFLER*
speed 1.42 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
back to results table
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 ENST00000359082
Genbank transcript ID N/A
UniProt peptide Q9Y566
alteration type single base exchange
alteration region CDS
DNA changes c.4484T>C
cDNA.4503T>C
g.52002T>C
AA changes V1495A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1495
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 marginally increased52000wt: 0.9904 / mu: 0.9907 (marginal change - not scored)wt: GCCCCTGTGACGAGC
mu: GCCCCTGCGACGAGC		 CCCT|gtga
Donor marginally increased52002wt: 0.9240 / mu: 0.9771 (marginal change - not scored)wt: CCCTGTGACGAGCGG
mu: CCCTGCGACGAGCGG		 CTGT|gacg
Donor increased52007wt: 0.72 / mu: 0.83wt: TGACGAGCGGAAGGG
mu: CGACGAGCGGAAGGG		 ACGA|gcgg
distance from splice site 1258
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1495RFLENCQPRAPVTSGRGPPSEDGP
mutated  not conserved    1495RFLENCQPRAPATSGRG
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 6459 / 6459
position (AA) of stopcodon in wt / mu AA sequence 2153 / 2153
position of stopcodon in wt / mu cDNA 6478 / 6478
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 5761
theoretical NMD boundary in CDS 5691
length of CDS 6459
coding sequence (CDS) position 4484
cDNA position
(for ins/del: last normal base / first normal base)		 4503
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 SFDAPSDYII KEKTVLLQKK
DSEGFGFVLR GAKAQTPIEE FTPTPAFPAL QYLESVDEGG VAWRAGLRMG DFLIEVNGQN
VVKVGHRQVV NMIRQGGNTL MVKVVMVTRH PDMDEAVHKK APQQAKRLPP PTISLRSKSM
TSELEEMEYE QQPAPVPSME KKRTVYQMAL NKLDEILAAA QQTISASESP GPGGLASLGK
HRPKGFFATE SSFDPHHRAQ PSYERPSFLP PGPGLMLRQK SIGAAEDDRP YLAPPAMKFS
RSLSVPGSED IPPPPTTSPP EPPYSTPPVP SSSGRLTPSP RGGPFNPGSG GPLPASSPAS
FDGPSPPDTR VGSREKSLYH SGPLPPAHHH PPHHHHHHAP PPQPHHHHAH PPHPPEMETG
GSPDDPPPRL ALGPQPSLRG WRGGGPSPTP GAPSPSHHGS AGGGGGSSQG PALRYFQLPP
RAASAAMYVP ARSGRGRKGP LVKQTKVEGE PQKGGGLPPA PSPTSPASPQ PPPAVAAPSE
KNSIPIPTII IKAPSTSSSG RSSQGSSTEA EPPTQPEPTG GGGGGGSSPS PAPAMSPVPP
SPSPVPTPAS PSGPATLDFT SQFGAALVGA ARREGGWQNE ARRRSTLFLS TDAGDEDGGD
GGLGTGAAPG PRLRHSKSID EGMFSAEPYL RLESAGSGAG YGGYGAGSRA YGGGGGSSAF
TSFLPPRPLV HPLTGKALDP ASPLGLALAA RERALKESSE GGGAPQPPPR PPSPRYEAPP
PTPHHHSPHA HHEPVLRLWG ASPPDPARRE LGYRAGLGSQ EKSLPASPPA ARRSLLHRLP
PTAPGVGPLL LQLGTEPPAP HPGVSKPWRS AAPEEPERLP LHVRFLENCQ PRAPVTSGRG
PPSEDGPGVP PPSPRRSVPP SPTSPRASEE NGLPLLVLPP PAPSVDVEDG EFLFVEPLPP
PLEFSNSFEK PESPLTPGPP HPLPDTPAPA TPLPPVPPPA VAAAPPTLDS TASSLTSYDS
EVATLTQGAS AAPGDPHPPG PPAPAAPAPA APQPGPDPPP GTDSGIEEVD SRSSSDHPLE
TISSASTLSS LSAEGGGSAG GGGGAGAGVA SGPELLDTYV AYLDGQAFGG SSTPGPPYPP
QLMTPSKLRG RALGASGGLR PGPSGGLRDP VTPTSPTVSV TGAGTDGLLA LRACSGPPTA
GVAGGPVAVE PEVPPVPLPT ASSLPRKLLP WEEGPGPPPP PLPGPLAQPQ ASALATVKAS
IISELSSKLQ QFGGSSAAGG ALPWARGGSG GGGDSHHGGA SYVPERTSSL QRQRLSDDSQ
SSLLSKPVSS LFQNWPKPPL PPLPTGTGVS PTAAAAPGAT SPSASSSSTS TRHLQGVEFE
MRPPLLRRAP SPSLLPASEH KVSPAPRPSS LPILPSGPLY PGLFDIRGSP TGGAGGSADP
FAPVFVPPHP GISGGLGGAL SGASRSLSPT RLLSLPPDKP FGAKPLGFWT KFDVADWLEW
LGLAEHRAQF LDHEIDGSHL PALTKEDYVD LGVTRVGHRM NIDRALKFFL ER*
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 SFDAPSDYII KEKTVLLQKK
DSEGFGFVLR GAKAQTPIEE FTPTPAFPAL QYLESVDEGG VAWRAGLRMG DFLIEVNGQN
VVKVGHRQVV NMIRQGGNTL MVKVVMVTRH PDMDEAVHKK APQQAKRLPP PTISLRSKSM
TSELEEMEYE QQPAPVPSME KKRTVYQMAL NKLDEILAAA QQTISASESP GPGGLASLGK
HRPKGFFATE SSFDPHHRAQ PSYERPSFLP PGPGLMLRQK SIGAAEDDRP YLAPPAMKFS
RSLSVPGSED IPPPPTTSPP EPPYSTPPVP SSSGRLTPSP RGGPFNPGSG GPLPASSPAS
FDGPSPPDTR VGSREKSLYH SGPLPPAHHH PPHHHHHHAP PPQPHHHHAH PPHPPEMETG
GSPDDPPPRL ALGPQPSLRG WRGGGPSPTP GAPSPSHHGS AGGGGGSSQG PALRYFQLPP
RAASAAMYVP ARSGRGRKGP LVKQTKVEGE PQKGGGLPPA PSPTSPASPQ PPPAVAAPSE
KNSIPIPTII IKAPSTSSSG RSSQGSSTEA EPPTQPEPTG GGGGGGSSPS PAPAMSPVPP
SPSPVPTPAS PSGPATLDFT SQFGAALVGA ARREGGWQNE ARRRSTLFLS TDAGDEDGGD
GGLGTGAAPG PRLRHSKSID EGMFSAEPYL RLESAGSGAG YGGYGAGSRA YGGGGGSSAF
TSFLPPRPLV HPLTGKALDP ASPLGLALAA RERALKESSE GGGAPQPPPR PPSPRYEAPP
PTPHHHSPHA HHEPVLRLWG ASPPDPARRE LGYRAGLGSQ EKSLPASPPA ARRSLLHRLP
PTAPGVGPLL LQLGTEPPAP HPGVSKPWRS AAPEEPERLP LHVRFLENCQ PRAPATSGRG
PPSEDGPGVP PPSPRRSVPP SPTSPRASEE NGLPLLVLPP PAPSVDVEDG EFLFVEPLPP
PLEFSNSFEK PESPLTPGPP HPLPDTPAPA TPLPPVPPPA VAAAPPTLDS TASSLTSYDS
EVATLTQGAS AAPGDPHPPG PPAPAAPAPA APQPGPDPPP GTDSGIEEVD SRSSSDHPLE
TISSASTLSS LSAEGGGSAG GGGGAGAGVA SGPELLDTYV AYLDGQAFGG SSTPGPPYPP
QLMTPSKLRG RALGASGGLR PGPSGGLRDP VTPTSPTVSV TGAGTDGLLA LRACSGPPTA
GVAGGPVAVE PEVPPVPLPT ASSLPRKLLP WEEGPGPPPP PLPGPLAQPQ ASALATVKAS
IISELSSKLQ QFGGSSAAGG ALPWARGGSG GGGDSHHGGA SYVPERTSSL QRQRLSDDSQ
SSLLSKPVSS LFQNWPKPPL PPLPTGTGVS PTAAAAPGAT SPSASSSSTS TRHLQGVEFE
MRPPLLRRAP SPSLLPASEH KVSPAPRPSS LPILPSGPLY PGLFDIRGSP TGGAGGSADP
FAPVFVPPHP GISGGLGGAL SGASRSLSPT RLLSLPPDKP FGAKPLGFWT KFDVADWLEW
LGLAEHRAQF LDHEIDGSHL PALTKEDYVD LGVTRVGHRM NIDRALKFFL ER*
speed 0.91 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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999982 (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 ENST00000391813
Genbank transcript ID N/A
UniProt peptide Q9Y566
alteration type single base exchange
alteration region CDS
DNA changes c.2672T>C
cDNA.2672T>C
g.52002T>C
AA changes V891A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 891
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 marginally increased52000wt: 0.9904 / mu: 0.9907 (marginal change - not scored)wt: GCCCCTGTGACGAGC
mu: GCCCCTGCGACGAGC		 CCCT|gtga
Donor marginally increased52002wt: 0.9240 / mu: 0.9771 (marginal change - not scored)wt: CCCTGTGACGAGCGG
mu: CCCTGCGACGAGCGG		 CTGT|gacg
Donor increased52007wt: 0.72 / mu: 0.83wt: TGACGAGCGGAAGGG
mu: CGACGAGCGGAAGGG		 ACGA|gcgg
distance from splice site 1258
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      891RFLENCQPRAPVTSGRGPPSEDGP
mutated  not conserved    891RFLENCQPRAPATSGRGPPSE
Ptroglodytes  no homologue    
Mmulatta  not conserved  ENSMMUG00000009357  1493RFLENCQPRAPATSGRGPPSEDG
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000038738  1510RFLENCQARPPPAGTRGSSTEDG
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000006583  1413EQTAS-DSLSQRG
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0040752  1283---PAQNGNGNGSTSG
Celegans  no alignment  C33B4.3  n/a
Xtropicalis  not conserved  ENSXETG00000000210  1355RFMENSTHKEEEEQSKVAMVKVK
protein features
start (aa)end (aa)featuredetails 
927927CONFLICTS -> Y (in Ref. 1; AAD45121/AAF35887).might get lost (downstream of altered splice site)
937937CONFLICTP -> T (in Ref. 1; AAD45121/AAF35887).might get lost (downstream of altered splice site)
969969CONFLICTS -> T (in Ref. 1; AAD45121/AAF35887).might get lost (downstream of altered splice site)
10021007COMPBIASPoly-His.might get lost (downstream of altered splice site)
10141019COMPBIASPoly-His.might get lost (downstream of altered splice site)
10851085CONFLICTF -> I (in Ref. 1; AAD45121/AAF35887).might get lost (downstream of altered splice site)
11331133CONFLICTT -> S (in Ref. 1; AAD45121/AAF35887).might get lost (downstream of altered splice site)
11891195COMPBIASPoly-Gly.might get lost (downstream of altered splice site)
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 4647 / 4647
position (AA) of stopcodon in wt / mu AA sequence 1549 / 1549
position of stopcodon in wt / mu cDNA 4647 / 4647
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 1 / 1
chromosome 19
strand -1
last intron/exon boundary 3930
theoretical NMD boundary in CDS 3879
length of CDS 4647
coding sequence (CDS) position 2672
cDNA position
(for ins/del: last normal base / first normal base)		 2672
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 MQLMALEQRF GSGLPGGGQP LCLMMSSPLP PPPPHFSCLP ASDYIIKEKT VLLQKKDSEG
FGFVLRGAKA QTPIEEFTPT PAFPALQYLE SVDEGGVAWR AGLRMGDFLI EVNGQNVVKV
GHRQVVNMIR QGGNTLMVKV VMVTRHPDMD EAVHKKAPQQ AKRLPPPTIS LRSKSMTSEL
EEMEYEQQPA PVPSMEKKRT VYQMALNKLD EILAAAQQTI SASESPGPGG LASLGKHRPK
GFFATESSFD PHHRAQPSYE RPSFLPPGPG LMLRQKSIGA AEDDRPYLAP PAMKFSRSLS
VPGSEDIPPP PTTSPPEPPY STPPVPSSSG RLTPSPRGGP FNPGSGGPLP ASSPASFDGP
SPPDTRVGSR EKSLYHSGPL PPAHHHPPHH HHHHAPPPQP HHHHAHPPHP PEMETGGSPD
DPPPRLALGP QPSLRGWRGG GPSPTPGAPS PSHHGSAGGG GGSSQGPALR YFQLPPRAAS
AAMYVPARSG RGRKGPLVKQ TKVEGEPQKG GGLPPAPSPT SPASPQPPPA VAAPSEKNSI
PIPTIIIKAP STSSSGRSSQ GSSTEAEPPT QPEPTGGGGG GGSSPSPAPA MSPVPPSPSP
VPTPASPSGP ATLDFTSQFG AALVGAARRE GGWQNEARRR STLFLSTDAG DEDGGDGGLG
TGAAPGPRLR HSKSIDEGMF SAEPYLRLES AGSGAGYGGY GAGSRAYGGG GGSSAFTSFL
PPRPLVHPLT GKALDPASPL GLALAARERA LKESSEGGGA PQPPPRPPSP RYEAPPPTPH
HHSPHAHHEP VLRLWGASPP DPARRELGYR AGLGSQEKSL PASPPAARRS LLHRLPPTAP
GVGPLLLQLG TEPPAPHPGV SKPWRSAAPE EPERLPLHVR FLENCQPRAP VTSGRGPPSE
DGPGVPPPSP RRSVPPSPTS PRASEENGLP LLVLPPPAPS VDVEDGEFLF VEPLPPPLEF
SNSFEKPESP LTPGPPHPLP DTPAPATPLP PVPPPAVAAA PPTLDSTASS LTSYDSEVAT
LTQGASAAPG DPHPPGPPAP AAPAPAAPQP GPDPPPGTDS GIEEVDSRSS SDHPLETISS
ASTLSSLSAE GGGSAGGGGG AGAGVASGPE LLDTYVAYLD GQAFGGSSTP GPPYPPQLMT
PSKLRGRALG ASGGLRPGPS GGLRDPVTPT SPTVSVTGAG TDGLLALRAC SGPPTAGVAG
GPVAVEPEVP PVPLPTASSL PRKLLPWEEG PGPPPPPLPG PLAQPQASAL ATVKASIISE
LSSKLQQFGG SSAAGGALPW ARGGSGGGGD SHHGGASYVP ERTSSLQRQR LSDDSQSSLL
SKPVSSLFQN WPKPPLPPLP TGTGVSPTAA AAPGATSPSA SSSSTSTRHL QGVEFEMRPP
LLRRAPSPSL LPASEHKVSP APRPSSLPIL PSGPLYPGLF DIRGSPTGGA GGSADPFAPV
FVPPHPGISG GLGGALSGAS RSLSPTRLLS LPPDKPFGAK PLGFWTKFDV ADWLEWLGLA
EHRAQFLDHE IDGSHLPALT KEDYVDLGVT RVGHRMNIDR ALKFFLER*
mutated AA sequence MQLMALEQRF GSGLPGGGQP LCLMMSSPLP PPPPHFSCLP ASDYIIKEKT VLLQKKDSEG
FGFVLRGAKA QTPIEEFTPT PAFPALQYLE SVDEGGVAWR AGLRMGDFLI EVNGQNVVKV
GHRQVVNMIR QGGNTLMVKV VMVTRHPDMD EAVHKKAPQQ AKRLPPPTIS LRSKSMTSEL
EEMEYEQQPA PVPSMEKKRT VYQMALNKLD EILAAAQQTI SASESPGPGG LASLGKHRPK
GFFATESSFD PHHRAQPSYE RPSFLPPGPG LMLRQKSIGA AEDDRPYLAP PAMKFSRSLS
VPGSEDIPPP PTTSPPEPPY STPPVPSSSG RLTPSPRGGP FNPGSGGPLP ASSPASFDGP
SPPDTRVGSR EKSLYHSGPL PPAHHHPPHH HHHHAPPPQP HHHHAHPPHP PEMETGGSPD
DPPPRLALGP QPSLRGWRGG GPSPTPGAPS PSHHGSAGGG GGSSQGPALR YFQLPPRAAS
AAMYVPARSG RGRKGPLVKQ TKVEGEPQKG GGLPPAPSPT SPASPQPPPA VAAPSEKNSI
PIPTIIIKAP STSSSGRSSQ GSSTEAEPPT QPEPTGGGGG GGSSPSPAPA MSPVPPSPSP
VPTPASPSGP ATLDFTSQFG AALVGAARRE GGWQNEARRR STLFLSTDAG DEDGGDGGLG
TGAAPGPRLR HSKSIDEGMF SAEPYLRLES AGSGAGYGGY GAGSRAYGGG GGSSAFTSFL
PPRPLVHPLT GKALDPASPL GLALAARERA LKESSEGGGA PQPPPRPPSP RYEAPPPTPH
HHSPHAHHEP VLRLWGASPP DPARRELGYR AGLGSQEKSL PASPPAARRS LLHRLPPTAP
GVGPLLLQLG TEPPAPHPGV SKPWRSAAPE EPERLPLHVR FLENCQPRAP ATSGRGPPSE
DGPGVPPPSP RRSVPPSPTS PRASEENGLP LLVLPPPAPS VDVEDGEFLF VEPLPPPLEF
SNSFEKPESP LTPGPPHPLP DTPAPATPLP PVPPPAVAAA PPTLDSTASS LTSYDSEVAT
LTQGASAAPG DPHPPGPPAP AAPAPAAPQP GPDPPPGTDS GIEEVDSRSS SDHPLETISS
ASTLSSLSAE GGGSAGGGGG AGAGVASGPE LLDTYVAYLD GQAFGGSSTP GPPYPPQLMT
PSKLRGRALG ASGGLRPGPS GGLRDPVTPT SPTVSVTGAG TDGLLALRAC SGPPTAGVAG
GPVAVEPEVP PVPLPTASSL PRKLLPWEEG PGPPPPPLPG PLAQPQASAL ATVKASIISE
LSSKLQQFGG SSAAGGALPW ARGGSGGGGD SHHGGASYVP ERTSSLQRQR LSDDSQSSLL
SKPVSSLFQN WPKPPLPPLP TGTGVSPTAA AAPGATSPSA SSSSTSTRHL QGVEFEMRPP
LLRRAPSPSL LPASEHKVSP APRPSSLPIL PSGPLYPGLF DIRGSPTGGA GGSADPFAPV
FVPPHPGISG GLGGALSGAS RSLSPTRLLS LPPDKPFGAK PLGFWTKFDV ADWLEWLGLA
EHRAQFLDHE IDGSHLPALT KEDYVDLGVT RVGHRMNIDR ALKFFLER*
speed 0.87 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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Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999844543317 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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 SYT3
Ensembl transcript ID ENST00000544769
Genbank transcript ID N/A
UniProt peptide Q9BQG1
alteration type single base exchange
alteration region intron
DNA changes g.946T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
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 splice site change before start ATG (at aa -171) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc marginally increased946wt: 0.2747 / mu: 0.2802 (marginal change - not scored)wt: CTGCCAGCCCCGGGCCCCTGTGACGAGCGGAAGGGGTCCCC
mu: CTGCCAGCCCCGGGCCCCTGCGACGAGCGGAAGGGGTCCCC		 ctgt|GACG
Donor increased951wt: 0.72 / mu: 0.83wt: TGACGAGCGGAAGGG
mu: CGACGAGCGGAAGGG		 ACGA|gcgg
Donor marginally increased944wt: 0.9904 / mu: 0.9907 (marginal change - not scored)wt: GCCCCTGTGACGAGC
mu: GCCCCTGCGACGAGC		 CCCT|gtga
Donor marginally increased946wt: 0.9240 / mu: 0.9771 (marginal change - not scored)wt: CCCTGTGACGAGCGG
mu: CCCTGCGACGAGCGG		 CTGT|gacg
distance from splice site 904
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
154TOPO_DOMVesicular (Potential).might get lost (downstream of altered splice site)
5575TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
76590TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
8282CONFLICTP -> H (in Ref. 2; AAH31067).might get lost (downstream of altered splice site)
301402DOMAINC2 1.might get lost (downstream of altered splice site)
324324CONFLICTL -> M (in Ref. 2; AAH28379).might get lost (downstream of altered splice site)
330330METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
330330METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
336336METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
388388METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
388388METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
389389METALCalcium 1; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
390390METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
390390METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
390390METALCalcium 3 (By similarity).might get lost (downstream of altered splice site)
393393METALCalcium 3 (By similarity).might get lost (downstream of altered splice site)
396396METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
396396METALCalcium 3 (By similarity).might get lost (downstream of altered splice site)
433536DOMAINC2 2.might get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 560 / 560
chromosome 19
strand -1
last intron/exon boundary 2336
theoretical NMD boundary in CDS 1726
length of CDS 1773
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 946
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 N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MSGDYEDDLC RRALILVSDL CARVRDADTN DRCQEFNDRI RGYPRGPDAD ISVSLLSVIV
TFCGIVLLGV SLFVSWKLCW VPWRDKGGSA VGGGPLRKDL GPGVGLAGLV GGGGHHLAAG
LGGHPLLGGP HHHAHAAHHP PFAELLEPGS LGGSDTPEPS YLDMDSYPEA AAAAVAAGVK
PSQTSPELPS EGGAGSGLLL LPPSGGGLPS AQSHQQVTSL APTTRYPALP RPLTQQTLTS
QPDPSSEERP PALPLPLPGG EEKAKLIGQI KPELYQGTGP GGRRSGGGPG SGEAGTGAPC
GRISFALRYL YGSDQLVVRI LQALDLPAKD SNGFSDPYVK IYLLPDRKKK FQTKVHRKTL
NPVFNETFQF SVPLAELAQR KLHFSVYDFD RFSRHDLIGQ VVLDNLLELA EQPPDRPLWR
DIVEGGSEKA DLGELNFSLC YLPTAGRLTV TIIKASNLKA MDLTGFSDPY VKASLISEGR
RLKKRKTSIK KNTLNPTYNE ALVFDVAPES VENVGLSIAV VDYDCIGHNE VIGVCRVGPD
AADPHGREHW AEMLANPRKP VEHWHQLVEE KTVTSFTKGS KGLSEKENSE *
mutated AA sequence N/A
speed 0.69 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