Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 8.41879599711805e-06 (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 CM051556)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:33951693C>GN/A show variant in all transcripts   IGV
HGNC symbol SLC45A2
Ensembl transcript ID ENST00000382102
Genbank transcript ID NM_001012509
UniProt peptide Q9UMX9
alteration type single base exchange
alteration region CDS
DNA changes c.1122G>C
cDNA.1180G>C
g.33143G>C
AA changes L374F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 374
frameshift no
known variant Reference ID: rs16891982
databasehomozygous (G/G)heterozygousallele carriers
1000G549279828
ExAC---

known disease mutation at this position, please check HGMD for details (HGMD ID CM051556)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2651
2.1511
(flanking)5.2651
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 increased33146wt: 0.4623 / mu: 0.5224 (marginal change - not scored)wt: TTGTGCATCAACTCC
mu: TTCTGCATCAACTCC		 GTGC|atca
Acc gained331500.49mu: GATGTTGGGGCTTCTGCATCAACTCCGTGTTTTCCTCACTT atca|ACTC
distance from splice site 35
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      374YERGVEVGCWGLCINSVFSSLYSY
mutated  not conserved    374YERGVEVGCWGFCINSVFSSLYS
Ptroglodytes  all identical  ENSPTRG00000016778  374YERGVEVGCWGLCINSVFSSLYS
Mmulatta  all identical  ENSMMUG00000009574  374YERGVEVGCWGLCINSVFSSLYS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000022243  374YERGVEVGCWGLCINSVFSSVYS
Ggallus  all identical  ENSGALG00000003310  334YRRGVEVGCWGLCINAIASSAYS
Trubripes  all identical  ENSTRUG00000014435  416YERGVEVGCWGLCINAVSSALYS
Drerio  all identical  ENSDARG00000002593  403VGCWGLCINAVSSALYS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000002556  393YERGVEVGCWGMCINAISSALYS
protein features
start (aa)end (aa)featuredetails 
367387TRANSMEMHelical; Name=8; (Potential).lost
388398TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
399419TRANSMEMHelical; Name=9; (Potential).might get lost (downstream of altered splice site)
420425TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
426446TRANSMEMHelical; Name=10; (Potential).might get lost (downstream of altered splice site)
447477TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
478498TRANSMEMHelical; Name=11; (Potential).might get lost (downstream of altered splice site)
499504TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
505525TRANSMEMHelical; Name=12; (Potential).might get lost (downstream of altered splice site)
526530TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1383 / 1383
position (AA) of stopcodon in wt / mu AA sequence 461 / 461
position of stopcodon in wt / mu cDNA 1441 / 1441
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 59 / 59
chromosome 5
strand -1
last intron/exon boundary 1215
theoretical NMD boundary in CDS 1106
length of CDS 1383
coding sequence (CDS) position 1122
cDNA position
(for ins/del: last normal base / first normal base)		 1180
gDNA position
(for ins/del: last normal base / first normal base)		 33143
chromosomal position
(for ins/del: last normal base / first normal base)		 33951693
original gDNA sequence snippet GAGGTTGGATGTTGGGGCTTGTGCATCAACTCCGTGTTTTC
altered gDNA sequence snippet GAGGTTGGATGTTGGGGCTTCTGCATCAACTCCGTGTTTTC
original cDNA sequence snippet GAGGTTGGATGTTGGGGCTTGTGCATCAACTCCGTGTTTTC
altered cDNA sequence snippet GAGGTTGGATGTTGGGGCTTCTGCATCAACTCCGTGTTTTC
wildtype AA sequence MGSNSGQAGR HIYKSLADDG PFDSVEPPKR PTSRLIMHSM AMFGREFCYA VEAAYVTPVL
LSVGLPSSLY SIVWFLSPIL GFLLQPVVGS ASDHCRSRWG RRRPYILTLG VMMLVGMALY
LNGATVVAAL IANPRRKLVW AISVTMIGVV LFDFAADFID GPIKAYLFDV CSHQDKEKGL
HYHALFTGFG GALGYLLGAI DWAHLELGRL LGTEFQVMFF FSALVLTLCF TVHLCSISEA
PLTEVAKGIP PQQTPQDPPL SSDGMYEYGS IEKVKNGYVN PELAMQGAKN KNHAEQTRRA
MTLKSLLRAL VNMPPHYRYL CISHLIGWTA FLSNMLFFTD FMGQIVYRGD PYSAHNSTEF
LIYERGVEVG CWGLCINSVF SSLYSYFQKV LVSYIGLKGL YFTGYLLFGL GTGFIGLFPN
VYSTLVLCSL FGVMSSTLYT VPFNLITEYH REEEKEVCCH *
mutated AA sequence MGSNSGQAGR HIYKSLADDG PFDSVEPPKR PTSRLIMHSM AMFGREFCYA VEAAYVTPVL
LSVGLPSSLY SIVWFLSPIL GFLLQPVVGS ASDHCRSRWG RRRPYILTLG VMMLVGMALY
LNGATVVAAL IANPRRKLVW AISVTMIGVV LFDFAADFID GPIKAYLFDV CSHQDKEKGL
HYHALFTGFG GALGYLLGAI DWAHLELGRL LGTEFQVMFF FSALVLTLCF TVHLCSISEA
PLTEVAKGIP PQQTPQDPPL SSDGMYEYGS IEKVKNGYVN PELAMQGAKN KNHAEQTRRA
MTLKSLLRAL VNMPPHYRYL CISHLIGWTA FLSNMLFFTD FMGQIVYRGD PYSAHNSTEF
LIYERGVEVG CWGFCINSVF SSLYSYFQKV LVSYIGLKGL YFTGYLLFGL GTGFIGLFPN
VYSTLVLCSL FGVMSSTLYT VPFNLITEYH REEEKEVCCH *
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