Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999995417174 (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) chr1:236706862G>CN/A show variant in all transcripts   IGV
HGNC symbol LGALS8
Ensembl transcript ID ENST00000527974
Genbank transcript ID N/A
UniProt peptide O00214
alteration type single base exchange
alteration region CDS
DNA changes c.678G>C
cDNA.827G>C
g.25563G>C
AA changes R226S Score: 110 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 226
frameshift no
known variant Reference ID: rs2243525
databasehomozygous (C/C)heterozygousallele carriers
1000G116910562225
ExAC31626-304851141
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1170.201
-1.3010.105
(flanking)1.3270.886
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost25560sequence motif lost- wt: tcag|AGGC
 mu: tcag.AGCC
Acc increased25572wt: 0.42 / mu: 0.70wt: TCTTTTCAGAGGCTGCCATTCGCTGCAAGGTTGAACACCCC
mu: TCTTTTCAGAGCCTGCCATTCGCTGCAAGGTTGAACACCCC		 attc|GCTG
Acc gained255650.35mu: TGTGGCTTCTTTTCAGAGCCTGCCATTCGCTGCAAGGTTGA gcct|GCCA
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      226TKIPPMNYVSKRLPFAARLNTPMG
mutated  not conserved    226TKIPPMNYVSKSLPFAARLNTPM
Ptroglodytes  not conserved  ENSPTRG00000002140  226TKIPPMNCVSKSLPFAARLNTPM
Mmulatta  not conserved  ENSMMUG00000015132  226TKIPPMNYVSKSLPFAARLNTPM
Fcatus  not conserved  ENSFCAG00000003385  226AKILPTNCLSKTLPFVARLNSSM
Mmusculus  not conserved  ENSMUSG00000057554  234-----------SLPFEAR
Ggallus  not conserved  ENSGALG00000014371  222---PGMYF--EGVPYVGKLVSAL
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000037066  165NQLQFHLPFRSKLAKGL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000009015  211-----EKLLTFSVPYTGCLPSAL
protein features
start (aa)end (aa)featuredetails 
187317DOMAINGalectin 2.lost
225225CONFLICTD -> H (in Ref. 8; AAL77076).might get lost (downstream of altered splice site)
225233STRANDlost
234237TURNmight get lost (downstream of altered splice site)
238244STRANDmight get lost (downstream of altered splice site)
246249STRANDmight get lost (downstream of altered splice site)
249255REGIONBeta-galactoside binding (By similarity).might get lost (downstream of altered splice site)
256258STRANDmight get lost (downstream of altered splice site)
259259CONFLICTF -> L (in Ref. 7; AAK16736).might get lost (downstream of altered splice site)
266273STRANDmight get lost (downstream of altered splice site)
275282STRANDmight get lost (downstream of altered splice site)
285291STRANDmight get lost (downstream of altered splice site)
297299HELIXmight get lost (downstream of altered splice site)
302315STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1080 / 1080
position (AA) of stopcodon in wt / mu AA sequence 360 / 360
position of stopcodon in wt / mu cDNA 1229 / 1229
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 150 / 150
chromosome 1
strand 1
last intron/exon boundary 1080
theoretical NMD boundary in CDS 880
length of CDS 1080
coding sequence (CDS) position 678
cDNA position
(for ins/del: last normal base / first normal base)		 827
gDNA position
(for ins/del: last normal base / first normal base)		 25563
chromosomal position
(for ins/del: last normal base / first normal base)		 236706862
original gDNA sequence snippet ACTGTGGCTTCTTTTCAGAGGCTGCCATTCGCTGCAAGGTT
altered gDNA sequence snippet ACTGTGGCTTCTTTTCAGAGCCTGCCATTCGCTGCAAGGTT
original cDNA sequence snippet ATGAACTATGTGTCAAAGAGGCTGCCATTCGCTGCAAGGTT
altered cDNA sequence snippet ATGAACTATGTGTCAAAGAGCCTGCCATTCGCTGCAAGGTT
wildtype AA sequence MMLSLNNLQN IIYNPVIPFV GTIPDQLDPG TLIVIRGHVP SDADRFQVDL QNGSSMKPRA
DVAFHFNPRF KRAGCIVCNT LINEKWGREE ITYDTPFKRE KSFEIVIMVL KDKFQVAVNG
KHTLLYGHRI GPEKIDTLGI YGKVNIHSIG FSFSSDLQST QASSLELTEI SRENVPKSGT
PQLPSNRGGD ISKIAPRTVY TKSKDSTVNH TLTCTKIPPM NYVSKRLPFA ARLNTPMGPG
RTVVVKGEVN ANAKSFNVDL LAGKSKDIAL HLNPRLNIKA FVRNSFLQES WGEEERNITS
FPFSPGMYFE MIIYCDVREF KVAVNGVHSL EYKHRFKELS SIDTLEINGD IHLLEVRSW*
mutated AA sequence MMLSLNNLQN IIYNPVIPFV GTIPDQLDPG TLIVIRGHVP SDADRFQVDL QNGSSMKPRA
DVAFHFNPRF KRAGCIVCNT LINEKWGREE ITYDTPFKRE KSFEIVIMVL KDKFQVAVNG
KHTLLYGHRI GPEKIDTLGI YGKVNIHSIG FSFSSDLQST QASSLELTEI SRENVPKSGT
PQLPSNRGGD ISKIAPRTVY TKSKDSTVNH TLTCTKIPPM NYVSKSLPFA ARLNTPMGPG
RTVVVKGEVN ANAKSFNVDL LAGKSKDIAL HLNPRLNIKA FVRNSFLQES WGEEERNITS
FPFSPGMYFE MIIYCDVREF KVAVNGVHSL EYKHRFKELS SIDTLEINGD IHLLEVRSW*
speed 0.65 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