Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999335304109446 (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 CM176738)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:91007360T>GN/A show variant in all transcripts   IGV
HGNC symbol LIPA
Ensembl transcript ID ENST00000371829
Genbank transcript ID N/A
UniProt peptide P38571
alteration type single base exchange
alteration region CDS
DNA changes c.46A>C
cDNA.720A>C
g.167023A>C
AA changes T16P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 16
frameshift no
known variant Reference ID: rs1051338
databasehomozygous (G/G)heterozygousallele carriers
1000G2469411187
ExAC64891978926278

known disease mutation at this position, please check HGMD for details (HGMD ID CM176738)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8610.901
1.1950.98
(flanking)0.8830.995
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased167029wt: 0.44 / mu: 0.82wt: GTTTGGTTCTCTGGACCCTGCATTCTGAGGGGTCTGGAGGG
mu: GTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAGGG		 ctgc|ATTC
Acc increased167027wt: 0.76 / mu: 0.88wt: CTGTTTGGTTCTCTGGACCCTGCATTCTGAGGGGTCTGGAG
mu: CTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAG		 ccct|GCAT
Acc increased167031wt: 0.65 / mu: 0.91wt: TTGGTTCTCTGGACCCTGCATTCTGAGGGGTCTGGAGGGAA
mu: TTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAGGGAA		 gcat|TCTG
Acc marginally increased167013wt: 0.2716 / mu: 0.2933 (marginal change - not scored)wt: TTGGGGTTGGTGGTCTGTTTGGTTCTCTGGACCCTGCATTC
mu: TTGGGGTTGGTGGTCTGTTTGGTTCTCTGGCCCCTGCATTC		 tttg|GTTC
Acc marginally increased167014wt: 0.2238 / mu: 0.2331 (marginal change - not scored)wt: TGGGGTTGGTGGTCTGTTTGGTTCTCTGGACCCTGCATTCT
mu: TGGGGTTGGTGGTCTGTTTGGTTCTCTGGCCCCTGCATTCT		 ttgg|TTCT
Acc marginally increased167021wt: 0.9597 / mu: 0.9663 (marginal change - not scored)wt: GGTGGTCTGTTTGGTTCTCTGGACCCTGCATTCTGAGGGGT
mu: GGTGGTCTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGT		 tctg|GACC
Acc gained1670330.43mu: GGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAGGGAAAC attc|TGAG
Acc gained1670250.61mu: GTCTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCTGG gccc|CTGC
Acc gained1670340.42mu: GTTCTCTGGCCCCTGCATTCTGAGGGGTCTGGAGGGAAACT ttct|GAGG
distance from splice site 47
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      16FLGLVVCLVLWTLHSEGSGGKLTA
mutated  not conserved    16FLGLVVCLVLWPLHSEGSGGKLT
Ptroglodytes  all identical  ENSPTRG00000002732  16FLGLVVCLVLWTLHSEGSGGKLT
Mmulatta  all identical  ENSMMUG00000022551  16FLGLVVCLVLWTLHSEASGGKLT
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000024781  14LQGLVFVFTIGILLSRVPTGTVS
Ggallus  no alignment  ENSGALG00000006378  n/a
Trubripes  no alignment  ENSTRUG00000002726  n/a
Drerio  no alignment  ENSDARG00000018529  n/a
Dmelanogaster  no alignment  FBgn0023495  n/a
Celegans  all conserved  F46B6.8  14FLAQITCLICTSFLLLQTINAHP
Xtropicalis  no alignment  ENSXETG00000009273  n/a
protein features
start (aa)end (aa)featuredetails 
121SIGNALPotential.lost
3636CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
7272CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
101101CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
161161CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
174174ACT_SITECharge relay system (By similarity).might get lost (downstream of altered splice site)
273273CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
321321CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
374374ACT_SITECharge relay system (By similarity).might get lost (downstream of altered splice site)
397397CONFLICTK -> R (in Ref. 5; BAD96480).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1200 / 1200
position (AA) of stopcodon in wt / mu AA sequence 400 / 400
position of stopcodon in wt / mu cDNA 1874 / 1874
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 675 / 675
chromosome 10
strand -1
last intron/exon boundary 1641
theoretical NMD boundary in CDS 916
length of CDS 1200
coding sequence (CDS) position 46
cDNA position
(for ins/del: last normal base / first normal base)		 720
gDNA position
(for ins/del: last normal base / first normal base)		 167023
chromosomal position
(for ins/del: last normal base / first normal base)		 91007360
original gDNA sequence snippet TGGTCTGTTTGGTTCTCTGGACCCTGCATTCTGAGGGGTCT
altered gDNA sequence snippet TGGTCTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCT
original cDNA sequence snippet TGGTCTGTTTGGTTCTCTGGACCCTGCATTCTGAGGGGTCT
altered cDNA sequence snippet TGGTCTGTTTGGTTCTCTGGCCCCTGCATTCTGAGGGGTCT
wildtype AA sequence MKMRFLGLVV CLVLWTLHSE GSGGKLTAVD PETNMNVSEI ISYWGFPSEE YLVETEDGYI
LCLNRIPHGR KNHSDKGPKP VVFLQHGLLA DSSNWVTNLA NSSLGFILAD AGFDVWMGNS
RGNTWSRKHK TLSVSQDEFW AFSYDEMAKY DLPASINFIL NKTGQEQVYY VGHSQGTTIG
FIAFSQIPEL AKRIKMFFAL GPVASVAFCT SPMAKLGRLP DHLIKDLFGD KEFLPQSAFL
KWLGTHVCTH VILKELCGNL CFLLCGFNER NLNMSRVDVY TTHSPAGTSV QNMLHWSQAV
KFQKFQAFDW GSSAKNYFHY NQSYPPTYNV KDMLVPTAVW SGGHDWLADV YDVNILLTQI
TNLVFHESIP EWEHLDFIWG LDAPWRLYNK IINLMRKYQ*
mutated AA sequence MKMRFLGLVV CLVLWPLHSE GSGGKLTAVD PETNMNVSEI ISYWGFPSEE YLVETEDGYI
LCLNRIPHGR KNHSDKGPKP VVFLQHGLLA DSSNWVTNLA NSSLGFILAD AGFDVWMGNS
RGNTWSRKHK TLSVSQDEFW AFSYDEMAKY DLPASINFIL NKTGQEQVYY VGHSQGTTIG
FIAFSQIPEL AKRIKMFFAL GPVASVAFCT SPMAKLGRLP DHLIKDLFGD KEFLPQSAFL
KWLGTHVCTH VILKELCGNL CFLLCGFNER NLNMSRVDVY TTHSPAGTSV QNMLHWSQAV
KFQKFQAFDW GSSAKNYFHY NQSYPPTYNV KDMLVPTAVW SGGHDWLADV YDVNILLTQI
TNLVFHESIP EWEHLDFIWG LDAPWRLYNK IINLMRKYQ*
speed 0.61 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