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: ENST00000381486
Querying Taster for transcript #2: ENST00000263834
Querying Taster for transcript #3: ENST00000389825
Querying Taster for transcript #4: ENST00000381483
Querying Taster for transcript #5: ENST00000234142
MT speed 6.44 s - this script 5.902293 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GREB1polymorphism_automatic8.43543013218095e-10simple_aaeaffectedN77Tsingle base exchangers10929757show file
GREB1polymorphism_automatic8.43543013218095e-10simple_aaeaffectedN77Tsingle base exchangers10929757show file
GREB1polymorphism_automatic8.43543013218095e-10simple_aaeaffectedN77Tsingle base exchangers10929757show file
GREB1polymorphism_automatic8.43543013218095e-10simple_aaeaffectedN77Tsingle base exchangers10929757show file
GREB1polymorphism_automatic3.59237415760161e-05without_aaeaffectedsingle base exchangers10929757show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999156457 (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) chr2:11702661A>CN/A show variant in all transcripts   IGV
HGNC symbol GREB1
Ensembl transcript ID ENST00000263834
Genbank transcript ID NM_148903
UniProt peptide Q4ZG55
alteration type single base exchange
alteration region CDS
DNA changes c.230A>C
cDNA.657A>C
g.28420A>C
AA changes N77T Score: 65 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 77
frameshift no
known variant Reference ID: rs10929757
databasehomozygous (C/C)heterozygousallele carriers
1000G5709421512
ExAC18162-355714605
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4620.009
0.6010.007
(flanking)-0.5460.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased28429wt: 0.74 / mu: 0.93wt: TGGCCCCCCAAACCCTTTCCAGCTGCACCCTCTGCCTGAAG
mu: TGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAG		 tcca|GCTG
Acc gained284300.37mu: GGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAGG ccag|CTGC
Acc gained284280.45mu: ATGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAA ttcc|AGCT
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      77GEGGLETNGPPNPFQLHPLPEGCC
mutated  not conserved    77GEGGLETNGPPTPFQLHPLPEGC
Ptroglodytes  all identical  ENSPTRG00000022786  77GEGGLETNGPPNPFQLHPLPEGC
Mmulatta  all identical  ENSMMUG00000020249  77GEGGLETNSPPNPFQLHPPPEGC
Fcatus  all identical  ENSFCAG00000008510  77GEGALEPSGPPNPYQMHPPPEGC
Mmusculus  all identical  ENSMUSG00000036523  77GEGGLEPSSPPNAYQLPPPPEGC
Ggallus  not conserved  ENSGALG00000016455  77EEEEGSESSSPVSYQMKPPPEGC
Trubripes  not conserved  ENSTRUG00000000142  75DEDASEDTSPHIPYQMKPPPEGC
Drerio  not conserved  ENSDARG00000070794  75GS---DSNSPPIPYQMKSPPEGS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000023793  77FTGGGRGSSSPPLSYQSKPPPEGC
protein features
start (aa)end (aa)featuredetails 
829829CONFLICTI -> S (in Ref. 1; AAG39036).might get lost (downstream of altered splice site)
11091232COMPBIASSer-rich.might get lost (downstream of altered splice site)
18681888TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1230 / 1230
position (AA) of stopcodon in wt / mu AA sequence 410 / 410
position of stopcodon in wt / mu cDNA 1657 / 1657
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 428 / 428
chromosome 2
strand 1
last intron/exon boundary 1587
theoretical NMD boundary in CDS 1109
length of CDS 1230
coding sequence (CDS) position 230
cDNA position
(for ins/del: last normal base / first normal base)		 657
gDNA position
(for ins/del: last normal base / first normal base)		 28420
chromosomal position
(for ins/del: last normal base / first normal base)		 11702661
original gDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered gDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
original cDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered cDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
wildtype AA sequence MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPNPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKVFVN GATQMVALGP AEPASPRSL*
mutated AA sequence MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPTPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKVFVN GATQMVALGP AEPASPRSL*
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
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999156457 (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) chr2:11702661A>CN/A show variant in all transcripts   IGV
HGNC symbol GREB1
Ensembl transcript ID ENST00000381483
Genbank transcript ID NM_033090
UniProt peptide Q4ZG55
alteration type single base exchange
alteration region CDS
DNA changes c.230A>C
cDNA.481A>C
g.28420A>C
AA changes N77T Score: 65 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 77
frameshift no
known variant Reference ID: rs10929757
databasehomozygous (C/C)heterozygousallele carriers
1000G5709421512
ExAC18162-355714605
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4620.009
0.6010.007
(flanking)-0.5460.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased28429wt: 0.74 / mu: 0.93wt: TGGCCCCCCAAACCCTTTCCAGCTGCACCCTCTGCCTGAAG
mu: TGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAG		 tcca|GCTG
Acc gained284300.37mu: GGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAGG ccag|CTGC
Acc gained284280.45mu: ATGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAA ttcc|AGCT
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      77GEGGLETNGPPNPFQLHPLPEGCC
mutated  not conserved    77GEGGLETNGPPTPFQLHPLPEGC
Ptroglodytes  all identical  ENSPTRG00000022786  77GEGGLETNGPPNPFQLHPLPEGC
Mmulatta  all identical  ENSMMUG00000020249  77GEGGLETNSPPNPFQLHPPPEGC
Fcatus  all identical  ENSFCAG00000008510  77GEGALEPSGPPNPYQMHPPPEGC
Mmusculus  all identical  ENSMUSG00000036523  77GEGGLEPSSPPNAYQLPPPPEGC
Ggallus  not conserved  ENSGALG00000016455  77EEEEGSESSSPVSYQMKPPPEGC
Trubripes  not conserved  ENSTRUG00000000142  75DEDASEDTSPHIPYQMKPPPEGC
Drerio  not conserved  ENSDARG00000070794  75GS---DSNSPPIPYQMKSPPEGS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000023793  77FTGGGRGSSSPPLSYQSKPPPEGC
protein features
start (aa)end (aa)featuredetails 
829829CONFLICTI -> S (in Ref. 1; AAG39036).might get lost (downstream of altered splice site)
11091232COMPBIASSer-rich.might get lost (downstream of altered splice site)
18681888TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1374 / 1374
position (AA) of stopcodon in wt / mu AA sequence 458 / 458
position of stopcodon in wt / mu cDNA 1625 / 1625
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 252 / 252
chromosome 2
strand 1
last intron/exon boundary 1597
theoretical NMD boundary in CDS 1295
length of CDS 1374
coding sequence (CDS) position 230
cDNA position
(for ins/del: last normal base / first normal base)		 481
gDNA position
(for ins/del: last normal base / first normal base)		 28420
chromosomal position
(for ins/del: last normal base / first normal base)		 11702661
original gDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered gDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
original cDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered cDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
wildtype AA sequence MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPNPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKGHGN FPYLCGNLND VVVSPLLYTC YQNSQSVSRA
YEQYGASAIQ PISEEMQLLL TVYYLVQLAH QIRNPDV*
mutated AA sequence MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPTPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKGHGN FPYLCGNLND VVVSPLLYTC YQNSQSVSRA
YEQYGASAIQ PISEEMQLLL TVYYLVQLAH QIRNPDV*
speed 1.31 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: 0.999999999156457 (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) chr2:11702661A>CN/A show variant in all transcripts   IGV
HGNC symbol GREB1
Ensembl transcript ID ENST00000381486
Genbank transcript ID NM_014668
UniProt peptide Q4ZG55
alteration type single base exchange
alteration region CDS
DNA changes c.230A>C
cDNA.530A>C
g.28420A>C
AA changes N77T Score: 65 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 77
frameshift no
known variant Reference ID: rs10929757
databasehomozygous (C/C)heterozygousallele carriers
1000G5709421512
ExAC18162-355714605
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4620.009
0.6010.007
(flanking)-0.5460.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased28429wt: 0.74 / mu: 0.93wt: TGGCCCCCCAAACCCTTTCCAGCTGCACCCTCTGCCTGAAG
mu: TGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAG		 tcca|GCTG
Acc gained284300.37mu: GGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAGG ccag|CTGC
Acc gained284280.45mu: ATGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAA ttcc|AGCT
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      77GEGGLETNGPPNPFQLHPLPEGCC
mutated  not conserved    77GEGGLETNGPPTPFQLHPLPEGC
Ptroglodytes  all identical  ENSPTRG00000022786  77GEGGLETNGPPNPFQLHPLPEGC
Mmulatta  all identical  ENSMMUG00000020249  77GEGGLETNSPPNPFQLHPPPEGC
Fcatus  all identical  ENSFCAG00000008510  77GEGALEPSGPPNPYQMHPPPEGC
Mmusculus  all identical  ENSMUSG00000036523  77GEGGLEPSSPPNAYQLPPPPEGC
Ggallus  not conserved  ENSGALG00000016455  77EEEEGSESSSPVSYQMKPPPEGC
Trubripes  not conserved  ENSTRUG00000000142  75DEDASEDTSPHIPYQMKPPPEGC
Drerio  not conserved  ENSDARG00000070794  75GS---DSNSPPIPYQMKSPPEGS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000023793  77FTGGGRGSSSPPLSYQSKPPPEGC
protein features
start (aa)end (aa)featuredetails 
829829CONFLICTI -> S (in Ref. 1; AAG39036).might get lost (downstream of altered splice site)
11091232COMPBIASSer-rich.might get lost (downstream of altered splice site)
18681888TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5850 / 5850
position (AA) of stopcodon in wt / mu AA sequence 1950 / 1950
position of stopcodon in wt / mu cDNA 6150 / 6150
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 301 / 301
chromosome 2
strand 1
last intron/exon boundary 5987
theoretical NMD boundary in CDS 5636
length of CDS 5850
coding sequence (CDS) position 230
cDNA position
(for ins/del: last normal base / first normal base)		 530
gDNA position
(for ins/del: last normal base / first normal base)		 28420
chromosomal position
(for ins/del: last normal base / first normal base)		 11702661
original gDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered gDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
original cDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered cDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
wildtype AA sequence MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPNPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKGHGN FPYLCGNLND VVVSPLLYTC YQNSQSVSRA
YEQYGASAIQ PISEEMQLLL TVYYLVQLAA DQVPLMEDLE QIFLRSWRES HLTEIRQYQQ
APPQPFPPAP SAAAPVTSAQ LPWLASLAAS SCNDSVHVIE CAYSLAEGLS EMFRLLVEGK
LAKTNYVVII CACRSAAIDS CIAVTGKYQA RILSESLLTP AEYQKEVNYE LVTGKVDSLG
AFFSTLCPEG DIDILLDKFH QENQGHISSS LAASSVTKAA SLDVSGTPVC TSYNLEPHSI
RPFQLAVAQK LLSHVCSIAD SSTQNLDLGS FEKVDFLICI PPSEVTYQQT LLHVWHSGVL
LELGLKKEHM TKQRVEQYVL KLDTEAQTKF KAFLQNSFQN PHTLFVLIHD HAHWDLVSST
VHNLYSQSDP SVGLVDRLLN CREVKEAPNI VTLHVTSFPY ALQTQHTLIS PYNEIHWPAS
CSNGVDLYHE NKKYFGLSEF IESTLSGHSL PLLRYDSSFE AMVTALGKRF PRLHSAVIRT
FVLVQHYAAA LMAVSGLPQM KNYTSVETLE ITQNLLNSPK QCPCGHGLMV LLRVPCSPLA
VVAYERLAHV RARLALEEHF EIILGSPSSG VTVGKHFVKQ LRMWQKIEDV EWRPQTYLEL
EGLPCILIFS GMDPHGESLP RSLRYCDLRL INSSCLVRTA LEQELGLAAY FVSNEVPLEK
GARNEALESD AEKLSSTDNE DEELGTEGST SEKRSPMKRE RSRSHDSASS SLSSKASGSA
LGGESSAQPT ALPQGEHARS PQPRGPAEEG RAPGEKQRPR ASQGPPSAIS RHSPGPTPQP
DCSLRTGQRS VQVSVTSSCS QLSSSSGSSS SSVAPAAGTW VLQASQCSLT KACRQPPIVF
LPKLVYDMVV STDSSGLPKA ASLLPSPSVM WASSFRPLLS KTMTSTEQSL YYRQWTVPRP
SHMDYGNRAE GRVDGFHPRR LLLSGPPQIG KTGAYLQFLS VLSRMLVRLT EVDVYDEEEI
NINLREESDW HYLQLSDPWP DLELFKKLPF DYIIHDPKYE DASLICSHYQ GIKSEDRGMS
RKPEDLYVRR QTARMRLSKY AAYNTYHHCE QCHQYMGFHP RYQLYESTLH AFAFSYSMLG
EEIQLHFIIP KSKEHHFVFS QPGGQLESMR LPLVTDKSHE YIKSPTFTPT TGRHEHGLFN
LYHAMDGASH LHVLVVKEYE MAIYKKYWPN HIMLVLPSIF NSAGVGAAHF LIKELSYHNL
ELERNRQEEL GIKPQDIWPF IVISDDSCVM WNVVDVNSAG ERSREFSWSE RNVSLKHIMQ
HIEAAPDIMH YALLGLRKWS SKTRASEVQE PFSRCHVHNF IILNVDLTQN VQYNQNRFLC
DDVDFNLRVH SAGLLLCRFN RFSVMKKQIV VGGHRSFHIT SKVSDNSAAV VPAQYICAPD
SKHTFLAAPA QLLLEKFLQH HSHLFFPLSL KNHDHPVLSV DCYLNLGSQI SVCYVSSRPH
SLNISCSDLL FSGLLLYLCD SFVGASFLKK FHFLKGATLC VICQDRSSLR QTVVRLELED
EWQFRLRDEF QTANAREDRP LFFLTGRHI*
mutated AA sequence MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPTPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKGHGN FPYLCGNLND VVVSPLLYTC YQNSQSVSRA
YEQYGASAIQ PISEEMQLLL TVYYLVQLAA DQVPLMEDLE QIFLRSWRES HLTEIRQYQQ
APPQPFPPAP SAAAPVTSAQ LPWLASLAAS SCNDSVHVIE CAYSLAEGLS EMFRLLVEGK
LAKTNYVVII CACRSAAIDS CIAVTGKYQA RILSESLLTP AEYQKEVNYE LVTGKVDSLG
AFFSTLCPEG DIDILLDKFH QENQGHISSS LAASSVTKAA SLDVSGTPVC TSYNLEPHSI
RPFQLAVAQK LLSHVCSIAD SSTQNLDLGS FEKVDFLICI PPSEVTYQQT LLHVWHSGVL
LELGLKKEHM TKQRVEQYVL KLDTEAQTKF KAFLQNSFQN PHTLFVLIHD HAHWDLVSST
VHNLYSQSDP SVGLVDRLLN CREVKEAPNI VTLHVTSFPY ALQTQHTLIS PYNEIHWPAS
CSNGVDLYHE NKKYFGLSEF IESTLSGHSL PLLRYDSSFE AMVTALGKRF PRLHSAVIRT
FVLVQHYAAA LMAVSGLPQM KNYTSVETLE ITQNLLNSPK QCPCGHGLMV LLRVPCSPLA
VVAYERLAHV RARLALEEHF EIILGSPSSG VTVGKHFVKQ LRMWQKIEDV EWRPQTYLEL
EGLPCILIFS GMDPHGESLP RSLRYCDLRL INSSCLVRTA LEQELGLAAY FVSNEVPLEK
GARNEALESD AEKLSSTDNE DEELGTEGST SEKRSPMKRE RSRSHDSASS SLSSKASGSA
LGGESSAQPT ALPQGEHARS PQPRGPAEEG RAPGEKQRPR ASQGPPSAIS RHSPGPTPQP
DCSLRTGQRS VQVSVTSSCS QLSSSSGSSS SSVAPAAGTW VLQASQCSLT KACRQPPIVF
LPKLVYDMVV STDSSGLPKA ASLLPSPSVM WASSFRPLLS KTMTSTEQSL YYRQWTVPRP
SHMDYGNRAE GRVDGFHPRR LLLSGPPQIG KTGAYLQFLS VLSRMLVRLT EVDVYDEEEI
NINLREESDW HYLQLSDPWP DLELFKKLPF DYIIHDPKYE DASLICSHYQ GIKSEDRGMS
RKPEDLYVRR QTARMRLSKY AAYNTYHHCE QCHQYMGFHP RYQLYESTLH AFAFSYSMLG
EEIQLHFIIP KSKEHHFVFS QPGGQLESMR LPLVTDKSHE YIKSPTFTPT TGRHEHGLFN
LYHAMDGASH LHVLVVKEYE MAIYKKYWPN HIMLVLPSIF NSAGVGAAHF LIKELSYHNL
ELERNRQEEL GIKPQDIWPF IVISDDSCVM WNVVDVNSAG ERSREFSWSE RNVSLKHIMQ
HIEAAPDIMH YALLGLRKWS SKTRASEVQE PFSRCHVHNF IILNVDLTQN VQYNQNRFLC
DDVDFNLRVH SAGLLLCRFN RFSVMKKQIV VGGHRSFHIT SKVSDNSAAV VPAQYICAPD
SKHTFLAAPA QLLLEKFLQH HSHLFFPLSL KNHDHPVLSV DCYLNLGSQI SVCYVSSRPH
SLNISCSDLL FSGLLLYLCD SFVGASFLKK FHFLKGATLC VICQDRSSLR QTVVRLELED
EWQFRLRDEF QTANAREDRP LFFLTGRHI*
speed 1.35 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: 0.999999999156457 (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) chr2:11702661A>CN/A show variant in all transcripts   IGV
HGNC symbol GREB1
Ensembl transcript ID ENST00000234142
Genbank transcript ID N/A
UniProt peptide Q4ZG55
alteration type single base exchange
alteration region CDS
DNA changes c.230A>C
cDNA.492A>C
g.28420A>C
AA changes N77T Score: 65 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 77
frameshift no
known variant Reference ID: rs10929757
databasehomozygous (C/C)heterozygousallele carriers
1000G5709421512
ExAC18162-355714605
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4620.009
0.6010.007
(flanking)-0.5460.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased28429wt: 0.74 / mu: 0.93wt: TGGCCCCCCAAACCCTTTCCAGCTGCACCCTCTGCCTGAAG
mu: TGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAG		 tcca|GCTG
Acc gained284300.37mu: GGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAGG ccag|CTGC
Acc gained284280.45mu: ATGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAA ttcc|AGCT
distance from splice site 48
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      77GEGGLETNGPPNPFQLHPLPEGCC
mutated  not conserved    77GEGGLETNGPPTPFQLHPLPEGC
Ptroglodytes  all identical  ENSPTRG00000022786  77GEGGLETNGPPNPFQLHPLPEGC
Mmulatta  all identical  ENSMMUG00000020249  77GEGGLETNSPPNPFQLHPPPEGC
Fcatus  all identical  ENSFCAG00000008510  77GEGALEPSGPPNPYQMHPPPEGC
Mmusculus  all identical  ENSMUSG00000036523  77GEGGLEPSSPPNAYQLPPPPEGC
Ggallus  not conserved  ENSGALG00000016455  77EEEEGSESSSPVSYQMKPPPEGC
Trubripes  not conserved  ENSTRUG00000000142  75DEDASEDTSPHIPYQMKPPPEGC
Drerio  not conserved  ENSDARG00000070794  75GS---DSNSPPIPYQMKSPPEGS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000023793  77FTGGGRGSSSPPLSYQSKPPPEGC
protein features
start (aa)end (aa)featuredetails 
829829CONFLICTI -> S (in Ref. 1; AAG39036).might get lost (downstream of altered splice site)
11091232COMPBIASSer-rich.might get lost (downstream of altered splice site)
18681888TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5850 / 5850
position (AA) of stopcodon in wt / mu AA sequence 1950 / 1950
position of stopcodon in wt / mu cDNA 6112 / 6112
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 263 / 263
chromosome 2
strand 1
last intron/exon boundary 5949
theoretical NMD boundary in CDS 5636
length of CDS 5850
coding sequence (CDS) position 230
cDNA position
(for ins/del: last normal base / first normal base)		 492
gDNA position
(for ins/del: last normal base / first normal base)		 28420
chromosomal position
(for ins/del: last normal base / first normal base)		 11702661
original gDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered gDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
original cDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered cDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
wildtype AA sequence MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPNPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKGHGN FPYLCGNLND VVVSPLLYTC YQNSQSVSRA
YEQYGASAIQ PISEEMQLLL TVYYLVQLAA DQVPLMEDLE QIFLRSWRES HLTEIRQYQQ
APPQPFPPAP SAAAPVTSAQ LPWLASLAAS SCNDSVHVIE CAYSLAEGLS EMFRLLVEGK
LAKTNYVVII CACRSAAIDS CIAVTGKYQA RILSESLLTP AEYQKEVNYE LVTGKVDSLG
AFFSTLCPEG DIDILLDKFH QENQGHISSS LAASSVTKAA SLDVSGTPVC TSYNLEPHSI
RPFQLAVAQK LLSHVCSIAD SSTQNLDLGS FEKVDFLICI PPSEVTYQQT LLHVWHSGVL
LELGLKKEHM TKQRVEQYVL KLDTEAQTKF KAFLQNSFQN PHTLFVLIHD HAHWDLVSST
VHNLYSQSDP SVGLVDRLLN CREVKEAPNI VTLHVTSFPY ALQTQHTLIS PYNEIHWPAS
CSNGVDLYHE NKKYFGLSEF IESTLSGHSL PLLRYDSSFE AMVTALGKRF PRLHSAVIRT
FVLVQHYAAA LMAVSGLPQM KNYTSVETLE ITQNLLNSPK QCPCGHGLMV LLRVPCSPLA
VVAYERLAHV RARLALEEHF EIILGSPSSG VTVGKHFVKQ LRMWQKIEDV EWRPQTYLEL
EGLPCILIFS GMDPHGESLP RSLRYCDLRL INSSCLVRTA LEQELGLAAY FVSNEVPLEK
GARNEALESD AEKLSSTDNE DEELGTEGST SEKRSPMKRE RSRSHDSASS SLSSKASGSA
LGGESSAQPT ALPQGEHARS PQPRGPAEEG RAPGEKQRPR ASQGPPSAIS RHSPGPTPQP
DCSLRTGQRS VQVSVTSSCS QLSSSSGSSS SSVAPAAGTW VLQASQCSLT KACRQPPIVF
LPKLVYDMVV STDSSGLPKA ASLLPSPSVM WASSFRPLLS KTMTSTEQSL YYRQWTVPRP
SHMDYGNRAE GRVDGFHPRR LLLSGPPQIG KTGAYLQFLS VLSRMLVRLT EVDVYDEEEI
NINLREESDW HYLQLSDPWP DLELFKKLPF DYIIHDPKYE DASLICSHYQ GIKSEDRGMS
RKPEDLYVRR QTARMRLSKY AAYNTYHHCE QCHQYMGFHP RYQLYESTLH AFAFSYSMLG
EEIQLHFIIP KSKEHHFVFS QPGGQLESMR LPLVTDKSHE YIKSPTFTPT TGRHEHGLFN
LYHAMDGASH LHVLVVKEYE MAIYKKYWPN HIMLVLPSIF NSAGVGAAHF LIKELSYHNL
ELERNRQEEL GIKPQDIWPF IVISDDSCVM WNVVDVNSAG ERSREFSWSE RNVSLKHIMQ
HIEAAPDIMH YALLGLRKWS SKTRASEVQE PFSRCHVHNF IILNVDLTQN VQYNQNRFLC
DDVDFNLRVH SAGLLLCRFN RFSVMKKQIV VGGHRSFHIT SKVSDNSAAV VPAQYICAPD
SKHTFLAAPA QLLLEKFLQH HSHLFFPLSL KNHDHPVLSV DCYLNLGSQI SVCYVSSRPH
SLNISCSDLL FSGLLLYLCD SFVGASFLKK FHFLKGATLC VICQDRSSLR QTVVRLELED
EWQFRLRDEF QTANAREDRP LFFLTGRHI*
mutated AA sequence MGNSYAGQLK TTRFEEVLHN SIEASLRSNN LVPRPIFSQL YLEAEQQLAA LEGGSRVDNE
EEEEEGEGGL ETNGPPTPFQ LHPLPEGCCT TDGFCQAGKD LRLVSISNEP MDVPAGFLLV
GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE FSNHINLKLT
TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP ALESTAAFPS
EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN LLALPRPSAL
GILSNSGPPK KRHKGWSPES PSAPDGGCPQ GGGNRAKYES AGMSCVPQVG LVGPASVTFP
VVASGEPVSV PDNLLKICKA KPVIFKGHGN FPYLCGNLND VVVSPLLYTC YQNSQSVSRA
YEQYGASAIQ PISEEMQLLL TVYYLVQLAA DQVPLMEDLE QIFLRSWRES HLTEIRQYQQ
APPQPFPPAP SAAAPVTSAQ LPWLASLAAS SCNDSVHVIE CAYSLAEGLS EMFRLLVEGK
LAKTNYVVII CACRSAAIDS CIAVTGKYQA RILSESLLTP AEYQKEVNYE LVTGKVDSLG
AFFSTLCPEG DIDILLDKFH QENQGHISSS LAASSVTKAA SLDVSGTPVC TSYNLEPHSI
RPFQLAVAQK LLSHVCSIAD SSTQNLDLGS FEKVDFLICI PPSEVTYQQT LLHVWHSGVL
LELGLKKEHM TKQRVEQYVL KLDTEAQTKF KAFLQNSFQN PHTLFVLIHD HAHWDLVSST
VHNLYSQSDP SVGLVDRLLN CREVKEAPNI VTLHVTSFPY ALQTQHTLIS PYNEIHWPAS
CSNGVDLYHE NKKYFGLSEF IESTLSGHSL PLLRYDSSFE AMVTALGKRF PRLHSAVIRT
FVLVQHYAAA LMAVSGLPQM KNYTSVETLE ITQNLLNSPK QCPCGHGLMV LLRVPCSPLA
VVAYERLAHV RARLALEEHF EIILGSPSSG VTVGKHFVKQ LRMWQKIEDV EWRPQTYLEL
EGLPCILIFS GMDPHGESLP RSLRYCDLRL INSSCLVRTA LEQELGLAAY FVSNEVPLEK
GARNEALESD AEKLSSTDNE DEELGTEGST SEKRSPMKRE RSRSHDSASS SLSSKASGSA
LGGESSAQPT ALPQGEHARS PQPRGPAEEG RAPGEKQRPR ASQGPPSAIS RHSPGPTPQP
DCSLRTGQRS VQVSVTSSCS QLSSSSGSSS SSVAPAAGTW VLQASQCSLT KACRQPPIVF
LPKLVYDMVV STDSSGLPKA ASLLPSPSVM WASSFRPLLS KTMTSTEQSL YYRQWTVPRP
SHMDYGNRAE GRVDGFHPRR LLLSGPPQIG KTGAYLQFLS VLSRMLVRLT EVDVYDEEEI
NINLREESDW HYLQLSDPWP DLELFKKLPF DYIIHDPKYE DASLICSHYQ GIKSEDRGMS
RKPEDLYVRR QTARMRLSKY AAYNTYHHCE QCHQYMGFHP RYQLYESTLH AFAFSYSMLG
EEIQLHFIIP KSKEHHFVFS QPGGQLESMR LPLVTDKSHE YIKSPTFTPT TGRHEHGLFN
LYHAMDGASH LHVLVVKEYE MAIYKKYWPN HIMLVLPSIF NSAGVGAAHF LIKELSYHNL
ELERNRQEEL GIKPQDIWPF IVISDDSCVM WNVVDVNSAG ERSREFSWSE RNVSLKHIMQ
HIEAAPDIMH YALLGLRKWS SKTRASEVQE PFSRCHVHNF IILNVDLTQN VQYNQNRFLC
DDVDFNLRVH SAGLLLCRFN RFSVMKKQIV VGGHRSFHIT SKVSDNSAAV VPAQYICAPD
SKHTFLAAPA QLLLEKFLQH HSHLFFPLSL KNHDHPVLSV DCYLNLGSQI SVCYVSSRPH
SLNISCSDLL FSGLLLYLCD SFVGASFLKK FHFLKGATLC VICQDRSSLR QTVVRLELED
EWQFRLRDEF QTANAREDRP LFFLTGRHI*
speed 1.38 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: without_aae, prob: 0.999964076258424 (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) chr2:11702661A>CN/A show variant in all transcripts   IGV
HGNC symbol GREB1
Ensembl transcript ID ENST00000389825
Genbank transcript ID N/A
UniProt peptide Q4ZG55
alteration type single base exchange
alteration region 5'UTR
DNA changes cDNA.211A>C
g.28420A>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs10929757
databasehomozygous (C/C)heterozygousallele carriers
1000G5709421512
ExAC18162-355714605
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4620.009
0.6010.007
(flanking)-0.5460.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites splice site change before start ATG (at aa -30) |
effectgDNA positionscoredetection sequence  exon-intron border
Acc increased28429wt: 0.74 / mu: 0.93wt: TGGCCCCCCAAACCCTTTCCAGCTGCACCCTCTGCCTGAAG
mu: TGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAG		 tcca|GCTG
Acc gained284300.37mu: GGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAGG ccag|CTGC
Acc gained284280.45mu: ATGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAA ttcc|AGCT
distance from splice site 48
Kozak consensus sequence altered? no
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
829829CONFLICTI -> S (in Ref. 1; AAG39036).might get lost (downstream of altered splice site)
11091232COMPBIASSer-rich.might get lost (downstream of altered splice site)
18681888TRANSMEMHelical; (Potential).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 312 / 312
chromosome 2
strand 1
last intron/exon boundary 754
theoretical NMD boundary in CDS 392
length of CDS 762
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 211
gDNA position
(for ins/del: last normal base / first normal base)		 28420
chromosomal position
(for ins/del: last normal base / first normal base)		 11702661
original gDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered gDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
original cDNA sequence snippet GGAAACAAATGGCCCCCCAAACCCTTTCCAGCTGCACCCTC
altered cDNA sequence snippet GGAAACAAATGGCCCCCCAACCCCTTTCCAGCTGCACCCTC
wildtype AA sequence MDVPAGFLLV GVKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE
FSNHINLKLT TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP
ALESTAAFPS EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN
LLALPRPSAL GSSACPGRPG DPALLWAKAR GGMGAAGLGP LSLLESDVAS MRVRPGPQVP
PESVGLGPGP GAL*
mutated AA sequence N/A
speed 1.00 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

Problems