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MutationTaster - study a chromosomal position

 MTQE documentation
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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: ENST00000083182
MT speed 0 s - this script 2.174344 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
APPBP2polymorphism_automatic0.000428549002192025simple_aaeaffectedS561Nsingle base exchangers34146848show file

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 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999571450997808 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:58525018C>TN/A show variant in all transcripts   IGV
HGNC symbol APPBP2
Ensembl transcript ID ENST00000083182
Genbank transcript ID NM_006380
UniProt peptide Q92624
alteration type single base exchange
alteration region CDS
DNA changes c.1682G>A
cDNA.1970G>A
g.78563G>A
AA changes S561N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 561
frameshift no
known variant Reference ID: rs34146848
databasehomozygous (T/T)heterozygousallele carriers
1000G164361525
ExAC96428763840
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.1951
1.0381
(flanking)4.8091
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained785580.94mu: GAAGATGTCAACACC AGAT|gtca
Donor gained785630.64mu: TGTCAACACCAGCCC TCAA|cacc
distance from splice site 178
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      561QYSVTDALEDVSTSPQSTEEVVQS
mutated  all conserved    561QYSVTDALEDVNTSPQSTEEVVQ
Ptroglodytes  all conserved  ENSPTRG00000009486  561QYSVTDALEDVNTSPQSTEEVVQ
Mmulatta  all conserved  ENSMMUG00000016566  561QYSVTDALEDVNTSPQSTEEVVQ
Fcatus  all conserved  ENSFCAG00000007028  337QYSVTDALEDVNTSPQSTEEVVQ
Mmusculus  all identical  ENSMUSG00000018481  561QYSVTDALEDVSSSPQSTEEVVQ
Ggallus  all identical  ENSGALG00000005314  562QFSVTDALEDVSSSPQSTEEVVQ
Trubripes  all conserved  ENSTRUG00000007402  561QFAVADALEDVNTTPQKTQEVVQ
Drerio  all conserved  ENSDARG00000007566  561QFAVADALEDVNTTPQSTEQVVQ
Dmelanogaster  not conserved  FBgn0029878  650NLTQNKSSYPAIEVDYSIEEV
Celegans  no homologue    
Xtropicalis  all conserved  ENSXETG00000013509  566QFSVTDALEDVNTSPLSTEEVVQ
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1758 / 1758
position (AA) of stopcodon in wt / mu AA sequence 586 / 586
position of stopcodon in wt / mu cDNA 2046 / 2046
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 289 / 289
chromosome 17
strand -1
last intron/exon boundary 1793
theoretical NMD boundary in CDS 1454
length of CDS 1758
coding sequence (CDS) position 1682
cDNA position
(for ins/del: last normal base / first normal base)		 1970
gDNA position
(for ins/del: last normal base / first normal base)		 78563
chromosomal position
(for ins/del: last normal base / first normal base)		 58525018
original gDNA sequence snippet AGATGCTCTTGAAGATGTCAGCACCAGCCCCCAGTCCACTG
altered gDNA sequence snippet AGATGCTCTTGAAGATGTCAACACCAGCCCCCAGTCCACTG
original cDNA sequence snippet AGATGCTCTTGAAGATGTCAGCACCAGCCCCCAGTCCACTG
altered cDNA sequence snippet AGATGCTCTTGAAGATGTCAACACCAGCCCCCAGTCCACTG
wildtype AA sequence MAAVELEWIP ETLYNTAISA VVDNYIRSRR DIRSLPENIQ FDVYYKLYQQ GRLCQLGSEF
CELEVFAKVL RALDKRHLLH HCFQALMDHG VKVASVLAYS FSRRCSYIAE SDAAVKEKAI
QVGFVLGGFL SDAGWYSDAE KVFLSCLQLC TLHDEMLHWF RAVECCVRLL HVRNGNCKYH
LGEETFKLAQ TYMDKLSKHG QQANKAALYG ELCALLFAKS HYDEAYKWCI EAMKEITAGL
PVKVVVDVLR QASKACVVKR EFKKAEQLIK HAVYLARDHF GSKHPKYSDT LLDYGFYLLN
VDNICQSVAI YQAALDIRQS VFGGKNIHVA TAHEDLAYSS YVHQYSSGKF DNALFHAERA
IGIITHILPE DHLLLASSKR VKALILEEIA IDCHNKETEQ RLLQEAHDLH LSSLQLAKKA
FGEFNVQTAK HYGNLGRLYQ SMRKFKEAEE MHIKAIQIKE QLLGQEDYEV ALSVGHLASL
YNYDMNQYEN AEKLYLRSIA IGKKLFGEGY SGLEYDYRGL IKLYNSIGNY EKVFEYHNVL
SNWNRLRDRQ YSVTDALEDV STSPQSTEEV VQSFLISQNV EGPSC*
mutated AA sequence MAAVELEWIP ETLYNTAISA VVDNYIRSRR DIRSLPENIQ FDVYYKLYQQ GRLCQLGSEF
CELEVFAKVL RALDKRHLLH HCFQALMDHG VKVASVLAYS FSRRCSYIAE SDAAVKEKAI
QVGFVLGGFL SDAGWYSDAE KVFLSCLQLC TLHDEMLHWF RAVECCVRLL HVRNGNCKYH
LGEETFKLAQ TYMDKLSKHG QQANKAALYG ELCALLFAKS HYDEAYKWCI EAMKEITAGL
PVKVVVDVLR QASKACVVKR EFKKAEQLIK HAVYLARDHF GSKHPKYSDT LLDYGFYLLN
VDNICQSVAI YQAALDIRQS VFGGKNIHVA TAHEDLAYSS YVHQYSSGKF DNALFHAERA
IGIITHILPE DHLLLASSKR VKALILEEIA IDCHNKETEQ RLLQEAHDLH LSSLQLAKKA
FGEFNVQTAK HYGNLGRLYQ SMRKFKEAEE MHIKAIQIKE QLLGQEDYEV ALSVGHLASL
YNYDMNQYEN AEKLYLRSIA IGKKLFGEGY SGLEYDYRGL IKLYNSIGNY EKVFEYHNVL
SNWNRLRDRQ YSVTDALEDV NTSPQSTEEV VQSFLISQNV EGPSC*
speed 0.16 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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Problems