Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999994286726 (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) chr1:53544597T>CN/A show variant in all transcripts   IGV
HGNC symbol PODN
Ensembl transcript ID ENST00000312553
Genbank transcript ID NM_153703
UniProt peptide Q7Z5L7
alteration type single base exchange
alteration region CDS
DNA changes c.1559T>C
cDNA.1566T>C
g.16744T>C
AA changes V520A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 520
frameshift no
known variant Reference ID: rs1288389
databasehomozygous (C/C)heterozygousallele carriers
1000G9069971903
ExAC25261-177557506
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7810.482
1.7970.464
(flanking)-1.7720.085
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained167450.51mu: CTGGCGGGCATGGCT GGCG|ggca
distance from splice site 98
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      520NELAALARGALVGMAQLRELYLTS
mutated  not conserved    520NELAALARGALAGMAQLRELYLT
Ptroglodytes  not conserved  ENSPTRG00000000749  520NELAALARGALAGMAQLRELYLT
Mmulatta  not conserved  ENSMMUG00000007604  521NELAALARGALAGMAQLRELYLT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000028600  473NELAALARGALAGMAQLR
Ggallus  not conserved  ENSGALG00000021869  87NEISDIPKGTLSGMTKLRELYLS
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000019025  454PEGALLGMTSLRELYLT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
502522REPEATLRR 17.lost
523544REPEATLRR 18.might get lost (downstream of altered splice site)
547568REPEATLRR 19.might get lost (downstream of altered splice site)
573595REPEATLRR 20.might get lost (downstream of altered splice site)
598611COMPBIASGlu-rich.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1986 / 1986
position (AA) of stopcodon in wt / mu AA sequence 662 / 662
position of stopcodon in wt / mu cDNA 1993 / 1993
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 8 / 8
chromosome 1
strand 1
last intron/exon boundary 2021
theoretical NMD boundary in CDS 1963
length of CDS 1986
coding sequence (CDS) position 1559
cDNA position
(for ins/del: last normal base / first normal base)		 1566
gDNA position
(for ins/del: last normal base / first normal base)		 16744
chromosomal position
(for ins/del: last normal base / first normal base)		 53544597
original gDNA sequence snippet CTTGGCACGAGGGGCGCTGGTGGGCATGGCTCAGCTGCGTG
altered gDNA sequence snippet CTTGGCACGAGGGGCGCTGGCGGGCATGGCTCAGCTGCGTG
original cDNA sequence snippet CTTGGCACGAGGGGCGCTGGTGGGCATGGCTCAGCTGCGTG
altered cDNA sequence snippet CTTGGCACGAGGGGCGCTGGCGGGCATGGCTCAGCTGCGTG
wildtype AA sequence MEGARARGAQ LRLGERVRPV GRRSAPGRSR FRQPWRPGAS DSAPPAGTMA QSRVLLLLLL
LPPQLHLGPV LAVRAPGFGR SGGHSLSPEE NEFAEEEPVL VLSPEEPGPG PAAVSCPRDC
ACSQEGVVDC GGIDLREFPG DLPEHTNHLS LQNNQLEKIY PEELSRLHRL ETLNLQNNRL
TSRGLPEKAF EHLTNLNYLY LANNKLTLAP RFLPNALISV DFAANYLTKI YGLTFGQKPN
LRSVYLHNNK LADAGLPDNM FNGSSNVEVL ILSSNFLRHV PKHLPPALYK LHLKNNKLEK
IPPGAFSELS SLRELYLQNN YLTDEGLDNE TFWKLSSLEY LDLSSNNLSR VPAGLPRSLV
LLHLEKNAIR SVDANVLTPI RSLEYLLLHS NQLREQGIHP LAFQGLKRLH TVHLYNNALE
RVPSGLPRRV RTLMILHNQI TGIGREDFAT TYFLEELNLS YNRITSPQVH RDAFRKLRLL
RSLDLSGNRL HTLPPGLPRN VHVLKVKRNE LAALARGALV GMAQLRELYL TSNRLRSRAL
GPRAWVDLAH LQLLDIAGNQ LTEIPEGLPE SLEYLYLQNN KISAVPANAF DSTPNLKGIF
LRFNKLAVGS VVDSAFRRLK HLQVLDIEGN LEFGDISKDR GRLGKEKEEE EEEEEEEEET
R*
mutated AA sequence MEGARARGAQ LRLGERVRPV GRRSAPGRSR FRQPWRPGAS DSAPPAGTMA QSRVLLLLLL
LPPQLHLGPV LAVRAPGFGR SGGHSLSPEE NEFAEEEPVL VLSPEEPGPG PAAVSCPRDC
ACSQEGVVDC GGIDLREFPG DLPEHTNHLS LQNNQLEKIY PEELSRLHRL ETLNLQNNRL
TSRGLPEKAF EHLTNLNYLY LANNKLTLAP RFLPNALISV DFAANYLTKI YGLTFGQKPN
LRSVYLHNNK LADAGLPDNM FNGSSNVEVL ILSSNFLRHV PKHLPPALYK LHLKNNKLEK
IPPGAFSELS SLRELYLQNN YLTDEGLDNE TFWKLSSLEY LDLSSNNLSR VPAGLPRSLV
LLHLEKNAIR SVDANVLTPI RSLEYLLLHS NQLREQGIHP LAFQGLKRLH TVHLYNNALE
RVPSGLPRRV RTLMILHNQI TGIGREDFAT TYFLEELNLS YNRITSPQVH RDAFRKLRLL
RSLDLSGNRL HTLPPGLPRN VHVLKVKRNE LAALARGALA GMAQLRELYL TSNRLRSRAL
GPRAWVDLAH LQLLDIAGNQ LTEIPEGLPE SLEYLYLQNN KISAVPANAF DSTPNLKGIF
LRFNKLAVGS VVDSAFRRLK HLQVLDIEGN LEFGDISKDR GRLGKEKEEE EEEEEEEEET
R*
speed 0.64 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