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MutationTaster - study a chromosomal position

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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 1.71 s - this script 3.801662 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ABCG8disease_causing_automatic6.05628156361474e-06simple_aaeaffected0G574Rsingle base exchangers137852988show file

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Prediction

disease causing

Model: simple_aae, prob: 6.05628156361474e-06 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM003584)
  • known disease mutation: rs4968 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:44102516G>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.1720G>A
cDNA.1810G>A
g.36414G>A
AA changes G574R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS
574
frameshift no
known variant Reference ID: rs137852988
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC077

known disease mutation: rs4968 (pathogenic for Sitosterolemia|Sitosterolemia 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM003584)

known disease mutation at this position, please check HGMD for details (HGMD ID CM003584)
known disease mutation at this position, please check HGMD for details (HGMD ID CM003584)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-3.3650
2.7040.023
(flanking)0.2770.003
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 increased36414wt: 0.9581 / mu: 0.9693 (marginal change - not scored)wt: ACAACTCCTTCTACCTCGCCGGGGGCTTCATGATAAACTTG
mu: ACAACTCCTTCTACCTCGCCAGGGGCTTCATGATAAACTTG
 gccg|GGGG
Acc increased36411wt: 0.43 / mu: 0.51wt: TCTACAACTCCTTCTACCTCGCCGGGGGCTTCATGATAAAC
mu: TCTACAACTCCTTCTACCTCGCCAGGGGCTTCATGATAAAC
 ctcg|CCGG
Acc marginally increased36405wt: 0.6970 / mu: 0.7246 (marginal change - not scored)wt: ATGCCCTCTACAACTCCTTCTACCTCGCCGGGGGCTTCATG
mu: ATGCCCTCTACAACTCCTTCTACCTCGCCAGGGGCTTCATG
 ttct|ACCT
Acc marginally increased36409wt: 0.8979 / mu: 0.9007 (marginal change - not scored)wt: CCTCTACAACTCCTTCTACCTCGCCGGGGGCTTCATGATAA
mu: CCTCTACAACTCCTTCTACCTCGCCAGGGGCTTCATGATAA
 acct|CGCC
Donor increased36410wt: 0.64 / mu: 0.98wt: TACCTCGCCGGGGGC
mu: TACCTCGCCAGGGGC
 CCTC|gccg
Donor gained364140.42mu: TCGCCAGGGGCTTCA GCCA|gggg
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      574SNALYNSFYLAGGFMINLSSLWTV
mutated  not conserved    574SNALYNSFYLARGFMINLSSLWT
Ptroglodytes  all identical  ENSPTRG00000011879  574SNALYNSFYLTGGFMINLSSLWT
Mmulatta  not conserved  ENSMMUG00000008081  574SNALYNSFYLTAGYMINLSSLWT
Fcatus  all identical  ENSFCAG00000013467  573GNALYNSFYLTGGFMISLDNLWI
Mmusculus  not conserved  ENSMUSG00000024254  574CNALYNSFYLTAGFMINLDNLWI
Ggallus  all identical  ENSGALG00000009958  544GNVLFTSFYLSGGFVISLEQLWT
Trubripes  all identical  ENSTRUG00000009126  547GNALFTVFYLTGGFVINIENMWL
Drerio  not conserved  ENSDARG00000063059  553GNALFTVFYLTAGFVISLENMWMAT
Dmelanogaster  all identical  FBgn0051121  783NGLISLAVAAVGGYLVHPQNLAQ
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000009293  560SNAIFTSSYLTGGFIIRLENLWT
protein features
start (aa)end (aa)featuredetails 
411665DOMAINABC transmembrane type-2.lost
570590TRANSMEMHelical; Name=5; (Potential).lost
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 1720
cDNA position
(for ins/del: last normal base / first normal base)
1810
gDNA position
(for ins/del: last normal base / first normal base)
36414
chromosomal position
(for ins/del: last normal base / first normal base)
44102516
original gDNA sequence snippet ACAACTCCTTCTACCTCGCCGGGGGCTTCATGATAAACTTG
altered gDNA sequence snippet ACAACTCCTTCTACCTCGCCAGGGGCTTCATGATAAACTTG
original cDNA sequence snippet ACAACTCCTTCTACCTCGCCGGGGGCTTCATGATAAACTTG
altered cDNA sequence snippet ACAACTCCTTCTACCTCGCCAGGGGCTTCATGATAAACTTG
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 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 YLARGFMINL SSLWTVPAWI SKVSFLRWCF
EGLMKIQFSR RTYKMPLGNL TIAVSGDKIL SVMELDSYPL YAIYLIVIGL SGGFMVLYYV
SLRFIKQKPS QDW*
speed 1.71 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
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