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 gained284280.45mu: ATGGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAA ttcc|AGCT
Acc gained284300.37mu: GGCCCCCCAACCCCTTTCCAGCTGCACCCTCTGCCTGAAGG ccag|CTGC
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 1.64 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