Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999996702986922 (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 CM054062)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:17409560C>TN/A show variant in all transcripts   IGV
HGNC symbol PEMT
Ensembl transcript ID ENST00000395782
Genbank transcript ID NM_148173
UniProt peptide Q9UBM1
alteration type single base exchange
alteration region CDS
DNA changes c.523G>A
cDNA.590G>A
g.85463G>A
AA changes V175M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 175
frameshift no
known variant Reference ID: rs7946
databasehomozygous (T/T)heterozygousallele carriers
1000G55510161571
ExAC106361149522131

known disease mutation at this position, please check HGMD for details (HGMD ID CM054062)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.0510.067
0.3310.052
(flanking)0.4050.048
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased85473wt: 0.7180 / mu: 0.7283 (marginal change - not scored)wt: CACCTACATAGTGGCTCTCCTATACGAAGAGTGAGTAGGGG
mu: CACCTACATAATGGCTCTCCTATACGAAGAGTGAGTAGGGG		 tcct|ATAC
Acc marginally increased85457wt: 0.5630 / mu: 0.6371 (marginal change - not scored)wt: CGGTGCTGGTGGCCCTCACCTACATAGTGGCTCTCCTATAC
mu: CGGTGCTGGTGGCCCTCACCTACATAATGGCTCTCCTATAC		 acct|ACAT
Acc marginally increased85463wt: 0.2357 / mu: 0.2523 (marginal change - not scored)wt: TGGTGGCCCTCACCTACATAGTGGCTCTCCTATACGAAGAG
mu: TGGTGGCCCTCACCTACATAATGGCTCTCCTATACGAAGAG		 atag|TGGC
Donor gained854540.35mu: CCCTCACCTACATAA CTCA|ccta
Donor gained854590.34mu: ACCTACATAATGGCT CTAC|ataa
distance from splice site 20
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      175LLTVLVALTYIVALLYEEPFTAEI
mutated  all conserved    175LLTVLVALTYIMALLYE
Ptroglodytes  all identical  ENSPTRG00000008832  212LLTVLVALTYIVALLYE
Mmulatta  all identical  ENSMMUG00000006495  212LLTVLVALTYMVALLYE
Fcatus  all identical  ENSFCAG00000005701  212LLTVVVALIYMVAIQYE
Mmusculus  all identical  ENSMUSG00000000301  212LLTVLVAIVYVVALLYE
Ggallus  all conserved  ENSGALG00000004875  220LLTAVVAISYTIAVLYE
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000040450  206VLTAVVALSYKVAIAYEGPF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005734  175LLTALVALCYKVAILYE
protein features
start (aa)end (aa)featuredetails 
158178TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 600 / 600
position (AA) of stopcodon in wt / mu AA sequence 200 / 200
position of stopcodon in wt / mu cDNA 667 / 667
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 68 / 68
chromosome 17
strand -1
last intron/exon boundary 610
theoretical NMD boundary in CDS 492
length of CDS 600
coding sequence (CDS) position 523
cDNA position
(for ins/del: last normal base / first normal base)		 590
gDNA position
(for ins/del: last normal base / first normal base)		 85463
chromosomal position
(for ins/del: last normal base / first normal base)		 17409560
original gDNA sequence snippet TGGTGGCCCTCACCTACATAGTGGCTCTCCTATACGAAGAG
altered gDNA sequence snippet TGGTGGCCCTCACCTACATAATGGCTCTCCTATACGAAGAG
original cDNA sequence snippet TGGTGGCCCTCACCTACATAGTGGCTCTCCTATACGAAGAG
altered cDNA sequence snippet TGGTGGCCCTCACCTACATAATGGCTCTCCTATACGAAGAG
wildtype AA sequence MTRLLGYVDP LDPSFVAAVI TITFNPLYWN VVARWEHKTR KLSRAFGSPY LACYSLSVTI
LLLNFLRSHC FTQAMLSQPR MESLDTPAAY SLGLALLGLG VVLVLSSFFA LGFAGTFLGD
YFGILKEARV TVFPFNILDN PMYWGSTANY LGWAIMHASP TGLLLTVLVA LTYIVALLYE
EPFTAEIYRQ KASGSHKRS*
mutated AA sequence MTRLLGYVDP LDPSFVAAVI TITFNPLYWN VVARWEHKTR KLSRAFGSPY LACYSLSVTI
LLLNFLRSHC FTQAMLSQPR MESLDTPAAY SLGLALLGLG VVLVLSSFFA LGFAGTFLGD
YFGILKEARV TVFPFNILDN PMYWGSTANY LGWAIMHASP TGLLLTVLVA LTYIMALLYE
EPFTAEIYRQ KASGSHKRS*
speed 1.04 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