Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999481 (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 CI128391)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:6411935T>CN/A show variant in all transcripts   IGV
HGNC symbol SMPD1
Ensembl transcript ID ENST00000356761
Genbank transcript ID N/A
UniProt peptide P17405
alteration type single base exchange
alteration region CDS
DNA changes c.107T>C
cDNA.281T>C
g.281T>C
AA changes V36A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 36
frameshift no
known variant Reference ID: rs1050228
databasehomozygous (C/C)heterozygousallele carriers
1000G9219691890
ExAC18416-406514351

known disease mutation at this position, please check HGMD for details (HGMD ID CI128391)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.0290.014
-0.0270.001
(flanking)-0.2930.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 212
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      36AGAPGLLWMGLVLALALALALALA
mutated  not conserved    36AGAPGLLWMGLALALALALALAL
Ptroglodytes  all identical  ENSPTRG00000003285  36ARAPGLLWMGLVLALALALAL--
Mmulatta  all identical  ENSMMUG00000007717  36FGAPRLLWMGLVLVLALALALAL
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000037049  36LPAPRVGLLWMGL------GLALVL
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000076121  n/a
Dmelanogaster  no alignment  FBgn0034997  n/a
Celegans  no alignment  ZK455.4  n/a
Xtropicalis  no alignment  ENSXETG00000030479  n/a
protein features
start (aa)end (aa)featuredetails 
146SIGNALlost
3536CONFLICTMissing (in Ref. 4; CAA42584).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1728 / 1728
position (AA) of stopcodon in wt / mu AA sequence 576 / 576
position of stopcodon in wt / mu cDNA 1902 / 1902
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 175 / 175
chromosome 11
strand 1
last intron/exon boundary 1493
theoretical NMD boundary in CDS 1268
length of CDS 1728
coding sequence (CDS) position 107
cDNA position
(for ins/del: last normal base / first normal base)		 281
gDNA position
(for ins/del: last normal base / first normal base)		 281
chromosomal position
(for ins/del: last normal base / first normal base)		 6411935
original gDNA sequence snippet ACTCCTTTGGATGGGCCTGGTGCTGGCGCTGGCGCTGGCGC
altered gDNA sequence snippet ACTCCTTTGGATGGGCCTGGCGCTGGCGCTGGCGCTGGCGC
original cDNA sequence snippet ACTCCTTTGGATGGGCCTGGTGCTGGCGCTGGCGCTGGCGC
altered cDNA sequence snippet ACTCCTTTGGATGGGCCTGGCGCTGGCGCTGGCGCTGGCGC
wildtype AA sequence MPRYGASLRQ SCPRSGREQG QDGTAGAPGL LWMGLVLALA LALALALALS DSRVLWAPAE
AHPLSPQGHP ARLHRIVPRL RDVFGWGNLT CPICKGLFTA INLGLKKEPN VARVGSVAIK
LCNLLKIAPP AVCQSIVHLF EDDMVEVWRR SVLSPSEACG LLLGSTCGHW DIFSSWNISL
PTVPKPPPKP PSPPAPGAPV SRILFLTDLH WDHDYLEGTD PDCADPLCCR RGSGLPPASR
PGAGYWGEYS KCDLPLRTLE SLLSGLGPAG PFDMVYWTGD IPAHDVWHQT RQDQLRALTT
VTALVRKFLG PVPVYPAVGN HESTPVNSFP PPFIEGNHSS RWLYEAMAKA WEPWLPAEAL
RTLRKVHIIG HIPPGHCLKS WSWNYYRIVA RYENTLAAQF FGHTHVDEFE VFYDEETLSR
PLAVAFLAPS ATTYIGLNPG YRVYQIDGNY SGSSHVVLDH ETYILNLTQA NIPGAIPHWQ
LLYRARETYG LPNTLPTAWH NLVYRMRGDM QLFQTFWFLY HKGHPPSEPC GTPCRLATLC
AQLSARADSP ALCRHLMPDG SLPEAQSLWP RPLFC*
mutated AA sequence MPRYGASLRQ SCPRSGREQG QDGTAGAPGL LWMGLALALA LALALALALS DSRVLWAPAE
AHPLSPQGHP ARLHRIVPRL RDVFGWGNLT CPICKGLFTA INLGLKKEPN VARVGSVAIK
LCNLLKIAPP AVCQSIVHLF EDDMVEVWRR SVLSPSEACG LLLGSTCGHW DIFSSWNISL
PTVPKPPPKP PSPPAPGAPV SRILFLTDLH WDHDYLEGTD PDCADPLCCR RGSGLPPASR
PGAGYWGEYS KCDLPLRTLE SLLSGLGPAG PFDMVYWTGD IPAHDVWHQT RQDQLRALTT
VTALVRKFLG PVPVYPAVGN HESTPVNSFP PPFIEGNHSS RWLYEAMAKA WEPWLPAEAL
RTLRKVHIIG HIPPGHCLKS WSWNYYRIVA RYENTLAAQF FGHTHVDEFE VFYDEETLSR
PLAVAFLAPS ATTYIGLNPG YRVYQIDGNY SGSSHVVLDH ETYILNLTQA NIPGAIPHWQ
LLYRARETYG LPNTLPTAWH NLVYRMRGDM QLFQTFWFLY HKGHPPSEPC GTPCRLATLC
AQLSARADSP ALCRHLMPDG SLPEAQSLWP RPLFC*
speed 1.12 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