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 ENST00000395871
Genbank transcript ID NM_001199082
UniProt peptide Q7Z5L7
alteration type single base exchange
alteration region CDS
DNA changes c.1133T>C
cDNA.1171T>C
g.16744T>C
AA changes V378A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 378
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      378NELAALARGALVGMAQLRELYLTS
mutated  not conserved    378NELAALARGALAGMAQLRELYLT
Ptroglodytes  not conserved  ENSPTRG00000000749  520GALAGMAQLRELYLT
Mmulatta  not conserved  ENSMMUG00000007604  521GALAGMAQLRELYLT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000028600  473GALAGMAQLRELYLT
Ggallus  not conserved  ENSGALG00000021869  87NEISDIPKGTLSGMTKLRELYLS
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000019025  454GALLGMTSLRELYLT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
360380REPEATLRR 12.lost
381402REPEATLRR 13.might get lost (downstream of altered splice site)
405426REPEATLRR 14.might get lost (downstream of altered splice site)
410410CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
431452REPEATLRR 15.might get lost (downstream of altered splice site)
476489REPEATLRR 16.might get lost (downstream of altered splice site)
502522REPEATLRR 17.might get lost (downstream of altered splice site)
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 1560 / 1560
position (AA) of stopcodon in wt / mu AA sequence 520 / 520
position of stopcodon in wt / mu cDNA 1598 / 1598
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 39 / 39
chromosome 1
strand 1
last intron/exon boundary 1626
theoretical NMD boundary in CDS 1537
length of CDS 1560
coding sequence (CDS) position 1133
cDNA position
(for ins/del: last normal base / first normal base)		 1171
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 LQNNKLEKIP PGAFSELSSL RELYLQNNYL
TDEGLDNETF WKLSSLEYLD LSSNNLSRVP AGLPRSLVLL HLEKNAIRSV DANVLTPIRS
LEYLLLHSNQ LREQGIHPLA FQGLKRLHTV HLYNNALERV PSGLPRRVRT LMILHNQITG
IGREDFATTY FLEELNLSYN RITSPQVHRD AFRKLRLLRS LDLSGNRLHT LPPGLPRNVH
VLKVKRNELA ALARGALVGM AQLRELYLTS NRLRSRALGP RAWVDLAHLQ LLDIAGNQLT
EIPEGLPESL EYLYLQNNKI SAVPANAFDS TPNLKGIFLR FNKLAVGSVV DSAFRRLKHL
QVLDIEGNLE FGDISKDRGR LGKEKEEEEE EEEEEEETR*
mutated AA sequence MEGARARGAQ LRLGERVRPV GRRSAPGRSR FRQPWRPGAS DSAPPAGTMA QSRVLLLLLL
LPPQLHLGPV LAVRAPGFGR SGGHSLSPEE NEFAEEEPVL VLSPEEPGPG PAAVSCPRDC
ACSQEGVVDC GGIDLREFPG DLPEHTNHLS LQNNKLEKIP PGAFSELSSL RELYLQNNYL
TDEGLDNETF WKLSSLEYLD LSSNNLSRVP AGLPRSLVLL HLEKNAIRSV DANVLTPIRS
LEYLLLHSNQ LREQGIHPLA FQGLKRLHTV HLYNNALERV PSGLPRRVRT LMILHNQITG
IGREDFATTY FLEELNLSYN RITSPQVHRD AFRKLRLLRS LDLSGNRLHT LPPGLPRNVH
VLKVKRNELA ALARGALAGM AQLRELYLTS NRLRSRALGP RAWVDLAHLQ LLDIAGNQLT
EIPEGLPESL EYLYLQNNKI SAVPANAFDS TPNLKGIFLR FNKLAVGSVV DSAFRRLKHL
QVLDIEGNLE FGDISKDRGR LGKEKEEEEE EEEEEEETR*
speed 1.26 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