Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.966507702153947 (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) chr2:11706693T>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 CDS
DNA changes c.35T>C
cDNA.346T>C
g.32452T>C
AA changes V12A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 12
frameshift no
known variant Reference ID: rs4669751
databasehomozygous (C/C)heterozygousallele carriers
1000G4737731246
ExAC37091609619805
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)6.0941
1.2531
(flanking)0.1070.996
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 increased32445wt: 0.6059 / mu: 0.6422 (marginal change - not scored)wt: TCCCTGCGGGCTTTCTCCTCGTGGGGGTCAAGTCCCCCAGC
mu: TCCCTGCGGGCTTTCTCCTCGTGGGGGCCAAGTCCCCCAGC		 ctcg|TGGG
Acc marginally increased32446wt: 0.9828 / mu: 0.9869 (marginal change - not scored)wt: CCCTGCGGGCTTTCTCCTCGTGGGGGTCAAGTCCCCCAGCC
mu: CCCTGCGGGCTTTCTCCTCGTGGGGGCCAAGTCCCCCAGCC		 tcgt|GGGG
Acc marginally increased32448wt: 0.9595 / mu: 0.9642 (marginal change - not scored)wt: CTGCGGGCTTTCTCCTCGTGGGGGTCAAGTCCCCCAGCCTG
mu: CTGCGGGCTTTCTCCTCGTGGGGGCCAAGTCCCCCAGCCTG		 gtgg|GGGT
Acc marginally increased32444wt: 0.9642 / mu: 0.9732 (marginal change - not scored)wt: GTCCCTGCGGGCTTTCTCCTCGTGGGGGTCAAGTCCCCCAG
mu: GTCCCTGCGGGCTTTCTCCTCGTGGGGGCCAAGTCCCCCAG		 cctc|GTGG
Donor increased32444wt: 0.35 / mu: 0.66wt: CTCCTCGTGGGGGTC
mu: CTCCTCGTGGGGGCC		 CCTC|gtgg
distance from splice site 88
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      12MDVPAGFLLVGVKSPSLPDHLLVC
mutated  not conserved    12MDVPAGFLLVGAKSPSLPDHLLV
Ptroglodytes  not conserved  ENSPTRG00000022786  122MDVPAGFLLVGAKSPSLPDHLLV
Mmulatta  not conserved  ENSMMUG00000020249  122IDVPVGFLLVGAKSPSLPDHLLV
Fcatus  no alignment  ENSFCAG00000008510  n/a
Mmusculus  not conserved  ENSMUSG00000036523  122IEVPAGFLLVGAKSPSLPDHLLV
Ggallus  not conserved  ENSGALG00000016455  122IDVPSGFLLVGAKSPNLPDHLLV
Trubripes  all identical  ENSTRUG00000000142  120DVPPGFLLVGVKSHTLPEDLLV
Drerio  not conserved  ENSDARG00000070794  117LEVPPGFLLVGAKSPSVPDHILV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023793  123DVPPGFLLVGVKSPSLPDHILV
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 762 / 762
position (AA) of stopcodon in wt / mu AA sequence 254 / 254
position of stopcodon in wt / mu cDNA 1073 / 1073
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 35
cDNA position
(for ins/del: last normal base / first normal base)		 346
gDNA position
(for ins/del: last normal base / first normal base)		 32452
chromosomal position
(for ins/del: last normal base / first normal base)		 11706693
original gDNA sequence snippet GGGCTTTCTCCTCGTGGGGGTCAAGTCCCCCAGCCTGCCGG
altered gDNA sequence snippet GGGCTTTCTCCTCGTGGGGGCCAAGTCCCCCAGCCTGCCGG
original cDNA sequence snippet GGGCTTTCTCCTCGTGGGGGTCAAGTCCCCCAGCCTGCCGG
altered cDNA sequence snippet GGGCTTTCTCCTCGTGGGGGCCAAGTCCCCCAGCCTGCCGG
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 MDVPAGFLLV GAKSPSLPDH LLVCAVDKRF LPDDNGHNAL LGFSGNCVGC GKKGFCYFTE
FSNHINLKLT TQPKKQKHLK YYLVRNAQGT LTKGPLICWK GSEFRSRQIP ASTCSSSLFP
ALESTAAFPS EPVPGTNPSI LMGAQQAGPA SDHPSLNAAM GPAVFNGKDS PKCQQLAKNN
LLALPRPSAL GSSACPGRPG DPALLWAKAR GGMGAAGLGP LSLLESDVAS MRVRPGPQVP
PESVGLGPGP GAL*
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