Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.992404666400992 (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 CM140252)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr14:88407888A>GN/A show variant in all transcripts   IGV
HGNC symbol GALC
Ensembl transcript ID ENST00000393568
Genbank transcript ID NM_001201401
UniProt peptide P54803
alteration type single base exchange
alteration region CDS
DNA changes c.1616T>C
cDNA.1630T>C
g.52122T>C
AA changes I539T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 539
frameshift no
known variant Reference ID: rs398607
databasehomozygous (G/G)heterozygousallele carriers
1000G55311351688
ExAC12358805120409

known disease mutation at this position, please check HGMD for details (HGMD ID CM140252)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8670
5.1250.441
(flanking)0.2830.334
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 increased52112wt: 0.2919 / mu: 0.3121 (marginal change - not scored)wt: CCGTTTTATTTTGCAGGACCAATCTGACTATAAAGTGTGAT
mu: CCGTTTTATTTTGCAGGACCAATCTGACTACAAAGTGTGAT		 acca|ATCT
Donor increased52113wt: 0.24 / mu: 0.26wt: GACCAATCTGACTAT
mu: GACCAATCTGACTAC		 CCAA|tctg
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      539IIGDYNWTNLTIKCDVYIETPDTG
mutated  not conserved    539IIGDYNWTNLTTKCDVYIETPDT
Ptroglodytes  all identical  ENSPTRG00000006602  539IIGDYNWTNLTIKCDVYIETPDT
Mmulatta  all identical  ENSMMUG00000017261  562IIGDYNWTNLTIKCDVYIETPDT
Fcatus  no alignment  ENSFCAG00000003064  n/a
Mmusculus  all conserved  ENSMUSG00000021003  561VIGDHHWTNMTVQCDVYIETPRS
Ggallus  all conserved  ENSGALG00000010593  523IIGNFQWVNLTVTCDIYIEKPID
Trubripes  all conserved  ENSTRUG00000008387  547VIGDYQWQNLTVTCDV
Drerio  all conserved  ENSDARG00000016474  542VIGDYAWHDVMVSCDVYMEAVQT
Dmelanogaster  no homologue    
Celegans  all conserved  C29E4.10  421AVMAYRKKNSILNAEVNIPKHST
Xtropicalis  all conserved  ENSXETG00000016608  553VIGNYQWSNVTVTSDIYIETPDT
protein features
start (aa)end (aa)featuredetails 
556556CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
559559CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
602602CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1989 / 1989
position (AA) of stopcodon in wt / mu AA sequence 663 / 663
position of stopcodon in wt / mu cDNA 2003 / 2003
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 15 / 15
chromosome 14
strand -1
last intron/exon boundary 1857
theoretical NMD boundary in CDS 1792
length of CDS 1989
coding sequence (CDS) position 1616
cDNA position
(for ins/del: last normal base / first normal base)		 1630
gDNA position
(for ins/del: last normal base / first normal base)		 52122
chromosomal position
(for ins/del: last normal base / first normal base)		 88407888
original gDNA sequence snippet TTGCAGGACCAATCTGACTATAAAGTGTGATGTATACATAG
altered gDNA sequence snippet TTGCAGGACCAATCTGACTACAAAGTGTGATGTATACATAG
original cDNA sequence snippet CAACTGGACCAATCTGACTATAAAGTGTGATGTATACATAG
altered cDNA sequence snippet CAACTGGACCAATCTGACTACAAAGTGTGATGTATACATAG
wildtype AA sequence MAEWLLSASW QRRAKAMTAA AGSAGRAAVP LLLCALLAPG GAYVLDDSDG LGREFDGIGA
VSGGGPNFGA SLHILKVEIG GDGQTTDGTE PSHMHYALDE NYFRGYEWWL MKEAKKRNPN
ITLIGLPWSF PGWLGKGFDW PYVNLQLTAY YVVTWIVGAK RYHDLDIDYI GIWNERSYNA
NYIKILRKML NYQGLQRVKI IASDNLWESI SASMLLDAEL FKVVDVIGAH YPGTHSAKDA
KLTGKKLWSS EDFSTLNSDM GAGCWGRILN QNYINGYMTS TIAWNLVASY YEQLPYGRCG
LMTAQEPWSG HYVVESPVWV SAHTTQFTQP GWYYLKTVGH LEKGGSYVAL TDGLGNLTII
IETMSHKHSK CIRPFLPYFN VSQQFATFVL KGSFSEIPEL QVWYTKLGKT SERFLFKQLD
SLWLLDSDGS FTLSLHEDEL FTLTTLTTGR KGSYPLPPKS QPFPSTYKDD FNVDYPFFSE
APNFADQTGV FEYFTNIEDP GEHHFTLRQV LNQRPITWAA DASNTISIIG DYNWTNLTIK
CDVYIETPDT GGVFIAGRVN KGGILIRSAR GIFFWIFANG SYRVTGDLAG WIIYALGRVE
VTAKKWYTLT LTIKGHFTSG MLNDKSLWTD IPVNFPKNGW AAIGTHSFEF AQFDNFLVEA
TR*
mutated AA sequence MAEWLLSASW QRRAKAMTAA AGSAGRAAVP LLLCALLAPG GAYVLDDSDG LGREFDGIGA
VSGGGPNFGA SLHILKVEIG GDGQTTDGTE PSHMHYALDE NYFRGYEWWL MKEAKKRNPN
ITLIGLPWSF PGWLGKGFDW PYVNLQLTAY YVVTWIVGAK RYHDLDIDYI GIWNERSYNA
NYIKILRKML NYQGLQRVKI IASDNLWESI SASMLLDAEL FKVVDVIGAH YPGTHSAKDA
KLTGKKLWSS EDFSTLNSDM GAGCWGRILN QNYINGYMTS TIAWNLVASY YEQLPYGRCG
LMTAQEPWSG HYVVESPVWV SAHTTQFTQP GWYYLKTVGH LEKGGSYVAL TDGLGNLTII
IETMSHKHSK CIRPFLPYFN VSQQFATFVL KGSFSEIPEL QVWYTKLGKT SERFLFKQLD
SLWLLDSDGS FTLSLHEDEL FTLTTLTTGR KGSYPLPPKS QPFPSTYKDD FNVDYPFFSE
APNFADQTGV FEYFTNIEDP GEHHFTLRQV LNQRPITWAA DASNTISIIG DYNWTNLTTK
CDVYIETPDT GGVFIAGRVN KGGILIRSAR GIFFWIFANG SYRVTGDLAG WIIYALGRVE
VTAKKWYTLT LTIKGHFTSG MLNDKSLWTD IPVNFPKNGW AAIGTHSFEF AQFDNFLVEA
TR*
speed 0.99 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