Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999944408 (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
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:46501268C>TN/A show variant in all transcripts   IGV
HGNC symbol LTF
Ensembl transcript ID ENST00000231751
Genbank transcript ID NM_002343
UniProt peptide P02788
alteration type single base exchange
alteration region CDS
DNA changes c.85G>A
cDNA.381G>A
g.25457G>A
AA changes A29T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs1126477
databasehomozygous (T/T)heterozygousallele carriers
1000G64810561704
ExAC75291770925238
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6930.001
-1.4560
(flanking)-0.8940.004
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased25449wt: 0.9866 / mu: 0.9957 (marginal change - not scored)wt: TGTTCAGTGGTGCGC
mu: TGTTCAGTGGTGCAC		 TTCA|gtgg
distance from splice site 42
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29LAGRRRSVQWCAVSQPEATKCFQW
mutated  not conserved    29LAGRRRSVQWCTVSQPEATKCFQ
Ptroglodytes  not conserved  ENSPTRG00000014850  29LAGPRRRSVQWCTVSQPEATKCFR
Mmulatta  all identical  ENSMMUG00000014261  29LAARRRSVRWCAVSKPEATKCSQ
Fcatus  not conserved  ENSFCAG00000014504  29LGTPGRRVRWCTISQAEETKCTK
Mmusculus  all identical  ENSMUSG00000032496  29LA-KATTVQWCAVSNSEEEKCLR
Ggallus  not conserved  ENSGALG00000006453  29FAAPPKSVIRWCTISSPEEKKCNN
Trubripes  not conserved  ENSTRUG00000005493  27IRWCLKSEAEYLKCKR
Drerio  not conserved  ENSDARG00000016771  29SASAQKKVKWCVTTQNEQSKC--
Dmelanogaster  not conserved  FBgn0036299  454CVTSENELDKCIK
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000011814  31MPPKEKQVRWCAKSKSEFSKCRD
protein features
start (aa)end (aa)featuredetails 
2431STRANDlost
25352DOMAINTransferrin-like 1.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2133 / 2133
position (AA) of stopcodon in wt / mu AA sequence 711 / 711
position of stopcodon in wt / mu cDNA 2429 / 2429
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 297 / 297
chromosome 3
strand -1
last intron/exon boundary 2395
theoretical NMD boundary in CDS 2048
length of CDS 2133
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 381
gDNA position
(for ins/del: last normal base / first normal base)		 25457
chromosomal position
(for ins/del: last normal base / first normal base)		 46501268
original gDNA sequence snippet GGAGGAGTGTTCAGTGGTGCGCCGTATCCCAACCCGAGGCC
altered gDNA sequence snippet GGAGGAGTGTTCAGTGGTGCACCGTATCCCAACCCGAGGCC
original cDNA sequence snippet GGAGGAGTGTTCAGTGGTGCGCCGTATCCCAACCCGAGGCC
altered cDNA sequence snippet GGAGGAGTGTTCAGTGGTGCACCGTATCCCAACCCGAGGCC
wildtype AA sequence MKLVFLVLLF LGALGLCLAG RRRSVQWCAV SQPEATKCFQ WQRNMRKVRG PPVSCIKRDS
PIQCIQAIAE NRADAVTLDG GFIYEAGLAP YKLRPVAAEV YGTERQPRTH YYAVAVVKKG
GSFQLNELQG LKSCHTGLRR TAGWNVPIGT LRPFLNWTGP PEPIEAAVAR FFSASCVPGA
DKGQFPNLCR LCAGTGENKC AFSSQEPYFS YSGAFKCLRD GAGDVAFIRE STVFEDLSDE
AERDEYELLC PDNTRKPVDK FKDCHLARVP SHAVVARSVN GKEDAIWNLL RQAQEKFGKD
KSPKFQLFGS PSGQKDLLFK DSAIGFSRVP PRIDSGLYLG SGYFTAIQNL RKSEEEVAAR
RARVVWCAVG EQELRKCNQW SGLSEGSVTC SSASTTEDCI ALVLKGEADA MSLDGGYVYT
AGKCGLVPVL AENYKSQQSS DPDPNCVDRP VEGYLAVAVV RRSDTSLTWN SVKGKKSCHT
AVDRTAGWNI PMGLLFNQTG SCKFDEYFSQ SCAPGSDPRS NLCALCIGDE QGENKCVPNS
NERYYGYTGA FRCLAENAGD VAFVKDVTVL QNTDGNNNEA WAKDLKLADF ALLCLDGKRK
PVTEARSCHL AMAPNHAVVS RMDKVERLKQ VLLHQQAKFG RNGSDCPDKF CLFQSETKNL
LFNDNTECLA RLHGKTTYEK YLGPQYVAGI TNLKKCSTSP LLEACEFLRK *
mutated AA sequence MKLVFLVLLF LGALGLCLAG RRRSVQWCTV SQPEATKCFQ WQRNMRKVRG PPVSCIKRDS
PIQCIQAIAE NRADAVTLDG GFIYEAGLAP YKLRPVAAEV YGTERQPRTH YYAVAVVKKG
GSFQLNELQG LKSCHTGLRR TAGWNVPIGT LRPFLNWTGP PEPIEAAVAR FFSASCVPGA
DKGQFPNLCR LCAGTGENKC AFSSQEPYFS YSGAFKCLRD GAGDVAFIRE STVFEDLSDE
AERDEYELLC PDNTRKPVDK FKDCHLARVP SHAVVARSVN GKEDAIWNLL RQAQEKFGKD
KSPKFQLFGS PSGQKDLLFK DSAIGFSRVP PRIDSGLYLG SGYFTAIQNL RKSEEEVAAR
RARVVWCAVG EQELRKCNQW SGLSEGSVTC SSASTTEDCI ALVLKGEADA MSLDGGYVYT
AGKCGLVPVL AENYKSQQSS DPDPNCVDRP VEGYLAVAVV RRSDTSLTWN SVKGKKSCHT
AVDRTAGWNI PMGLLFNQTG SCKFDEYFSQ SCAPGSDPRS NLCALCIGDE QGENKCVPNS
NERYYGYTGA FRCLAENAGD VAFVKDVTVL QNTDGNNNEA WAKDLKLADF ALLCLDGKRK
PVTEARSCHL AMAPNHAVVS RMDKVERLKQ VLLHQQAKFG RNGSDCPDKF CLFQSETKNL
LFNDNTECLA RLHGKTTYEK YLGPQYVAGI TNLKKCSTSP LLEACEFLRK *
speed 0.88 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