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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: ENST00000236671
MT speed 0 s - this script 2.376663 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CTSDdisease_causing_automatic0.999999998065918simple_aae0F229Isingle base exchangers121912789show file

Taster files

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999998065918 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM061695)
  • known disease mutation: rs17573 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:1778573A>TN/A show variant in all transcripts   IGV
HGNC symbol CTSD
Ensembl transcript ID ENST00000236671
Genbank transcript ID NM_001909
UniProt peptide P07339
alteration type single base exchange
alteration region CDS
DNA changes c.685T>A
cDNA.818T>A
g.6650T>A
AA changes F229I Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 229
frameshift no
known variant Reference ID: rs121912789
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17573 (pathogenic for Neuronal ceroid lipofuscinosis 10) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM061695)

known disease mutation at this position, please check HGMD for details (HGMD ID CM061695)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061695)
regulatory features H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.1461
4.1461
(flanking)-0.0170.994
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 20
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      229LMQQKLVDQNIFSFYLSRDPDAQP
mutated  not conserved    229LMQQKLVDQNIISFYLSRDPDAQ
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000003874  229LMQQKLVDQNIFSFYLNRDPTAQ
Fcatus  all identical  ENSFCAG00000007823  224LMKQKLVEKNIFSFYLNXXXXXX
Mmusculus  all identical  ENSMUSG00000007891  227LMQQKLVDKNIFSFYLNRDPEG
Ggallus  all identical  ENSGALG00000006613  217VMQQKLIEKNIFSFYLNRDPTAQ
Trubripes  all identical  ENSTRUG00000012591  208IMSQKKVEKNVFSFYLNRNPDTQ
Drerio  all identical  ENSDARG00000057698  215MMSQKKVEKNVFSFYLNRNPDTQ
Dmelanogaster  no homologue    
Celegans  all identical  R12H7.2  233LFEQKKVPSNLFSFWLNRNPDSE
Xtropicalis  all identical  ENSXETG00000024954  151IMAQKLVESNIFSFYLNRNPDTQ
protein features
start (aa)end (aa)featuredetails 
224233STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1239 / 1239
position (AA) of stopcodon in wt / mu AA sequence 413 / 413
position of stopcodon in wt / mu cDNA 1372 / 1372
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 134 / 134
chromosome 11
strand -1
last intron/exon boundary 1205
theoretical NMD boundary in CDS 1021
length of CDS 1239
coding sequence (CDS) position 685
cDNA position
(for ins/del: last normal base / first normal base)		 818
gDNA position
(for ins/del: last normal base / first normal base)		 6650
chromosomal position
(for ins/del: last normal base / first normal base)		 1778573
original gDNA sequence snippet AGCTGGTGGACCAGAACATCTTCTCCTTCTACCTGAGCAGG
altered gDNA sequence snippet AGCTGGTGGACCAGAACATCATCTCCTTCTACCTGAGCAGG
original cDNA sequence snippet AGCTGGTGGACCAGAACATCTTCTCCTTCTACCTGAGCAGG
altered cDNA sequence snippet AGCTGGTGGACCAGAACATCATCTCCTTCTACCTGAGCAGG
wildtype AA sequence MQPSSLLPLA LCLLAAPASA LVRIPLHKFT SIRRTMSEVG GSVEDLIAKG PVSKYSQAVP
AVTEGPIPEV LKNYMDAQYY GEIGIGTPPQ CFTVVFDTGS SNLWVPSIHC KLLDIACWIH
HKYNSDKSST YVKNGTSFDI HYGSGSLSGY LSQDTVSVPC QSASSASALG GVKVERQVFG
EATKQPGITF IAAKFDGILG MAYPRISVNN VLPVFDNLMQ QKLVDQNIFS FYLSRDPDAQ
PGGELMLGGT DSKYYKGSLS YLNVTRKAYW QVHLDQVEVA SGLTLCKEGC EAIVDTGTSL
MVGPVDEVRE LQKAIGAVPL IQGEYMIPCE KVSTLPAITL KLGGKGYKLS PEDYTLKVSQ
AGKTLCLSGF MGMDIPPPSG PLWILGDVFI GRYYTVFDRD NNRVGFAEAA RL*
mutated AA sequence MQPSSLLPLA LCLLAAPASA LVRIPLHKFT SIRRTMSEVG GSVEDLIAKG PVSKYSQAVP
AVTEGPIPEV LKNYMDAQYY GEIGIGTPPQ CFTVVFDTGS SNLWVPSIHC KLLDIACWIH
HKYNSDKSST YVKNGTSFDI HYGSGSLSGY LSQDTVSVPC QSASSASALG GVKVERQVFG
EATKQPGITF IAAKFDGILG MAYPRISVNN VLPVFDNLMQ QKLVDQNIIS FYLSRDPDAQ
PGGELMLGGT DSKYYKGSLS YLNVTRKAYW QVHLDQVEVA SGLTLCKEGC EAIVDTGTSL
MVGPVDEVRE LQKAIGAVPL IQGEYMIPCE KVSTLPAITL KLGGKGYKLS PEDYTLKVSQ
AGKTLCLSGF MGMDIPPPSG PLWILGDVFI GRYYTVFDRD NNRVGFAEAA RL*
speed 0.37 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