Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000272286
MT speed 1.54 s - this script 5.321637 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABCG8disease_causing_automatic0.999999999807452simple_aaeaffected0P231Tsingle base exchangers137852993show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999807452 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM012313)
  • known disease mutation: rs4974 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:44079622C>AN/A show variant in all transcripts   IGV
HGNC symbol ABCG8
Ensembl transcript ID ENST00000272286
Genbank transcript ID NM_022437
UniProt peptide Q9H221
alteration type single base exchange
alteration region CDS
DNA changes c.691C>A
cDNA.781C>A
g.13520C>A
AA changes P231T Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS
231
frameshift no
known variant Reference ID: rs137852993
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs4974 (pathogenic for Sitosterolemia 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM012313)

known disease mutation at this position, please check HGMD for details (HGMD ID CM012313)
known disease mutation at this position, please check HGMD for details (HGMD ID CM012313)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9371
5.3391
(flanking)5.3391
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost13522sequence motif lost- wt: CCAG|gtga
 mu: ACAG.gtga
Donor marginally decreased13522wt: 0.9929 / mu: 0.9846 (marginal change - not scored)wt: AACCCAGGTGAGGGC
mu: AACACAGGTGAGGGC
 CCCA|ggtg
Donor marginally increased13523wt: 0.9878 / mu: 0.9893 (marginal change - not scored)wt: ACCCAGGTGAGGGCC
mu: ACACAGGTGAGGGCC
 CCAG|gtga
Donor increased13512wt: 0.53 / mu: 0.60wt: GCTCCTGTGGAACCC
mu: GCTCCTGTGGAACAC
 TCCT|gtgg
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      231RVSIGVQLLWNPGILILDEPTSGL
mutated  not conserved    231RVSIGVQLLWNTGILILDEPT
Ptroglodytes  all identical  ENSPTRG00000011879  231RVSIGVQLLWNPGILILDEPT
Mmulatta  all identical  ENSMMUG00000008081  231RVSIGVQLLWNPGILILDEPT
Fcatus  all identical  ENSFCAG00000013467  229RVSIAVQLLWNPGILILDEPT
Mmusculus  all identical  ENSMUSG00000024254  232RVSIGVQLLWNPGILILDEP
Ggallus  all identical  ENSGALG00000009958  208RVSIAVQLLWNPGILILDEPTSG
Trubripes  all identical  ENSTRUG00000009126  202RVSIAVQLLWNPGILILDEPTSG
Drerio  all identical  ENSDARG00000063059  206RVSIAVQLLWNPGILILDEPTSG
Dmelanogaster  not conserved  FBgn0051121  459RLSVACQLLAQSSLLILDQVTSN
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000009293  214RVSIGVQLLWNPGILILDEPTSG
protein features
start (aa)end (aa)featuredetails 
1416TOPO_DOMCytoplasmic (Potential).lost
47313DOMAINABC transporter.lost
411665DOMAINABC transmembrane type-2.might get lost (downstream of altered splice site)
417437TRANSMEMHelical; Name=1; (Potential).might get lost (downstream of altered splice site)
438447TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
448468TRANSMEMHelical; Name=2; (Potential).might get lost (downstream of altered splice site)
469492TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
493513TRANSMEMHelical; Name=3; (Potential).might get lost (downstream of altered splice site)
514531TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
532552TRANSMEMHelical; Name=4; (Potential).might get lost (downstream of altered splice site)
553569TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
570590TRANSMEMHelical; Name=5; (Potential).might get lost (downstream of altered splice site)
591639TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
619619CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
640660TRANSMEMHelical; Name=6; (Potential).might get lost (downstream of altered splice site)
661673TOPO_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 2022 / 2022
position (AA) of stopcodon in wt / mu AA sequence 674 / 674
position of stopcodon in wt / mu cDNA 2112 / 2112
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 91 / 91
chromosome 2
strand 1
last intron/exon boundary 1975
theoretical NMD boundary in CDS 1834
length of CDS 2022
coding sequence (CDS) position 691
cDNA position
(for ins/del: last normal base / first normal base)
781
gDNA position
(for ins/del: last normal base / first normal base)
13520
chromosomal position
(for ins/del: last normal base / first normal base)
44079622
original gDNA sequence snippet GGGTGCAGCTCCTGTGGAACCCAGGTGAGGGCCTGGGGGGC
altered gDNA sequence snippet GGGTGCAGCTCCTGTGGAACACAGGTGAGGGCCTGGGGGGC
original cDNA sequence snippet GGGTGCAGCTCCTGTGGAACCCAGGAATCCTTATTCTCGAC
altered cDNA sequence snippet GGGTGCAGCTCCTGTGGAACACAGGAATCCTTATTCTCGAC
wildtype AA sequence MAGKAAEERG LPKGATPQDT SGLQDRLFSS ESDNSLYFTY SGQPNTLEVR DLNYQVDLAS
QVPWFEQLAQ FKMPWTSPSC QNSCELGIQN LSFKVRSGQM LAIIGSSGCG RASLLDVITG
RGHGGKIKSG QIWINGQPSS PQLVRKCVAH VRQHNQLLPN LTVRETLAFI AQMRLPRTFS
QAQRDKRVED VIAELRLRQC ADTRVGNMYV RGLSGGERRR VSIGVQLLWN PGILILDEPT
SGLDSFTAHN LVKTLSRLAK GNRLVLISLH QPRSDIFRLF DLVLLMTSGT PIYLGAAQHM
VQYFTAIGYP CPRYSNPADF YVDLTSIDRR SREQELATRE KAQSLAALFL EKVRDLDDFL
WKAETKDLDE DTCVESSVTP LDTNCLPSPT KMPGAVQQFT TLIRRQISND FRDLPTLLIH
GAEACLMSMT IGFLYFGHGS IQLSFMDTAA LLFMIGALIP FNVILDVISK CYSERAMLYY
ELEDGLYTTG PYFFAKILGE LPEHCAYIII YGMPTYWLAN LRPGLQPFLL HFLLVWLVVF
CCRIMALAAA ALLPTFHMAS FFSNALYNSF YLAGGFMINL SSLWTVPAWI SKVSFLRWCF
EGLMKIQFSR RTYKMPLGNL TIAVSGDKIL SVMELDSYPL YAIYLIVIGL SGGFMVLYYV
SLRFIKQKPS QDW*
mutated AA sequence MAGKAAEERG LPKGATPQDT SGLQDRLFSS ESDNSLYFTY SGQPNTLEVR DLNYQVDLAS
QVPWFEQLAQ FKMPWTSPSC QNSCELGIQN LSFKVRSGQM LAIIGSSGCG RASLLDVITG
RGHGGKIKSG QIWINGQPSS PQLVRKCVAH VRQHNQLLPN LTVRETLAFI AQMRLPRTFS
QAQRDKRVED VIAELRLRQC ADTRVGNMYV RGLSGGERRR VSIGVQLLWN TGILILDEPT
SGLDSFTAHN LVKTLSRLAK GNRLVLISLH QPRSDIFRLF DLVLLMTSGT PIYLGAAQHM
VQYFTAIGYP CPRYSNPADF YVDLTSIDRR SREQELATRE KAQSLAALFL EKVRDLDDFL
WKAETKDLDE DTCVESSVTP LDTNCLPSPT KMPGAVQQFT TLIRRQISND FRDLPTLLIH
GAEACLMSMT IGFLYFGHGS IQLSFMDTAA LLFMIGALIP FNVILDVISK CYSERAMLYY
ELEDGLYTTG PYFFAKILGE LPEHCAYIII YGMPTYWLAN LRPGLQPFLL HFLLVWLVVF
CCRIMALAAA ALLPTFHMAS FFSNALYNSF YLAGGFMINL SSLWTVPAWI SKVSFLRWCF
EGLMKIQFSR RTYKMPLGNL TIAVSGDKIL SVMELDSYPL YAIYLIVIGL SGGFMVLYYV
SLRFIKQKPS QDW*
speed 1.54 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
back to results table

Problems