Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.939497795997364 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM166416)
  • protein features (might be) affected
  • splice site changes
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr21:15516948C>TN/A show variant in all transcripts   IGV
HGNC symbol LIPI
Ensembl transcript ID ENST00000344577
Genbank transcript ID NM_198996
UniProt peptide Q6XZB0
alteration type single base exchange
alteration region CDS
DNA changes c.1354G>A
cDNA.1380G>A
g.66219G>A
AA changes E452K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 452
frameshift no
known variant Reference ID: rs2822432
databasehomozygous (T/T)heterozygousallele carriers
1000G3339231256
ExAC68501906725917

known disease mutation at this position, please check HGMD for details (HGMD ID CM166416)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3981
3.2121
(flanking)0.3431
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 increased66222wt: 0.9974 / mu: 0.9982 (marginal change - not scored)wt: CAGAAAGGTAAGAAA
mu: CAAAAAGGTAAGAAA		 GAAA|ggta
Donor marginally increased66216wt: 0.5002 / mu: 0.5344 (marginal change - not scored)wt: CATACCCAGAAAGGT
mu: CATACCCAAAAAGGT		 TACC|caga
Donor marginally increased66217wt: 0.9339 / mu: 0.9556 (marginal change - not scored)wt: ATACCCAGAAAGGTA
mu: ATACCCAAAAAGGTA		 ACCC|agaa
Donor gained662150.33mu: ACATACCCAAAAAGG ATAC|ccaa
distance from splice site 5
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      452QRLMLKSLTYPERPPLCRYNIVLK
mutated  all conserved    452QRLMLKSLTYPKRPPLCRYNIVL
Ptroglodytes  all identical  ENSPTRG00000013785  452QSLMLKSLTYPERPPLCRYNIVL
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016924  425EGRER-PLCRYDVVV
Drerio  not conserved  ENSDARG00000005332  368LRIRISPLEKPYRSLMCRYDI
Dmelanogaster  no alignment  FBgn0034166  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
455455DISULFIDBy similarity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1446 / 1446
position (AA) of stopcodon in wt / mu AA sequence 482 / 482
position of stopcodon in wt / mu cDNA 1472 / 1472
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 27 / 27
chromosome 21
strand -1
last intron/exon boundary 1385
theoretical NMD boundary in CDS 1308
length of CDS 1446
coding sequence (CDS) position 1354
cDNA position
(for ins/del: last normal base / first normal base)		 1380
gDNA position
(for ins/del: last normal base / first normal base)		 66219
chromosomal position
(for ins/del: last normal base / first normal base)		 15516948
original gDNA sequence snippet TAAAATCACTTACATACCCAGAAAGGTAAGAAAATTAAATT
altered gDNA sequence snippet TAAAATCACTTACATACCCAAAAAGGTAAGAAAATTAAATT
original cDNA sequence snippet TAAAATCACTTACATACCCAGAAAGACCACCACTTTGCAGG
altered cDNA sequence snippet TAAAATCACTTACATACCCAAAAAGACCACCACTTTGCAGG
wildtype AA sequence MLLKCLHNNL CQKYSAHAFQ FSPRNVLWLL VVCLRSDNKR PCLEFSQLSV KDSFRDLFIP
RIETILMMYT RNNLNCAEPL FEQNNSLNVN FNTQKKTVWL IHGYRPVGSI PLWLQNFVRI
LLNEEDMNVI VVDWSRGATT FIYNRAVKNT RKVAVSLSVH IKNLLKHGAS LDNFHFIGVS
LGAHISGFVG KIFHGQLGRI TGLDPAGPRF SRKPPYSRLD YTDAKFVDVI HSDSNGLGIQ
EPLGHIDFYP NGGNKQPGCP KSIFSGIQFI KCNHQRAVHL FMASLETNCN FISFPCRSYK
DYKTSLCVDC DCFKEKSCPR LGYQAKLFKG VLKERMEGRP LRTTVFLDTS GTYPFCTYYF
VLSIIVPDKT MMDGSFSFKL LNQLGMIEEP RLYEKNKPFY KLQEVKILAQ FYNDFVNISS
IGLTYFQSSN LQCSTCTYKI QRLMLKSLTY PERPPLCRYN IVLKDREEVF LNPNTCTPKN
T*
mutated AA sequence MLLKCLHNNL CQKYSAHAFQ FSPRNVLWLL VVCLRSDNKR PCLEFSQLSV KDSFRDLFIP
RIETILMMYT RNNLNCAEPL FEQNNSLNVN FNTQKKTVWL IHGYRPVGSI PLWLQNFVRI
LLNEEDMNVI VVDWSRGATT FIYNRAVKNT RKVAVSLSVH IKNLLKHGAS LDNFHFIGVS
LGAHISGFVG KIFHGQLGRI TGLDPAGPRF SRKPPYSRLD YTDAKFVDVI HSDSNGLGIQ
EPLGHIDFYP NGGNKQPGCP KSIFSGIQFI KCNHQRAVHL FMASLETNCN FISFPCRSYK
DYKTSLCVDC DCFKEKSCPR LGYQAKLFKG VLKERMEGRP LRTTVFLDTS GTYPFCTYYF
VLSIIVPDKT MMDGSFSFKL LNQLGMIEEP RLYEKNKPFY KLQEVKILAQ FYNDFVNISS
IGLTYFQSSN LQCSTCTYKI QRLMLKSLTY PKRPPLCRYN IVLKDREEVF LNPNTCTPKN
T*
speed 0.89 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