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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: ENST00000284268
MT speed 0.38 s - this script 2.418238 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ANKHdisease_causing_automatic0.999999998386815simple_aaeaffected0M48Tsingle base exchangers121908407show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999998386815 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM022762)
  • known disease mutation: rs5195 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:14769254A>GN/A show variant in all transcripts   IGV
HGNC symbol ANKH
Ensembl transcript ID ENST00000284268
Genbank transcript ID NM_054027
UniProt peptide Q9HCJ1
alteration type single base exchange
alteration region CDS
DNA changes c.143T>C
cDNA.474T>C
g.102634T>C
AA changes M48T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 48
frameshift no
known variant Reference ID: rs121908407
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5195 (pathogenic for Familial calcium pyrophosphate deposition) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM022762)

known disease mutation at this position, please check HGMD for details (HGMD ID CM022762)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022762)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.931
4.9011
(flanking)4.9011
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased102629wt: 0.79 / mu: 0.91wt: GCAGTCGAGATGCTG
mu: GCAGTCGAGACGCTG		 AGTC|gaga
Donor marginally increased102626wt: 0.9728 / mu: 0.9942 (marginal change - not scored)wt: GATGCAGTCGAGATG
mu: GATGCAGTCGAGACG		 TGCA|gtcg
distance from splice site 47
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      48GIAAVKEDAVEMLASYGLAYSLMK
mutated  not conserved    48GIAAVKEDAVETLASYGLAYSLM
Ptroglodytes  all identical  ENSPTRG00000016739  48GIAAVKEDAVEMLASYGLAYSLM
Mmulatta  all identical  ENSMMUG00000021942  48GIAAVKEDAVEMLASYGLAYSLM
Fcatus  all identical  ENSFCAG00000012251  16GIAAVKEDAVEMLASYGLAYSLM
Mmusculus  all identical  ENSMUSG00000022265  48GIAAVKEDAVEMLASYGLAYSLM
Ggallus  all identical  ENSGALG00000012964  48GIAAVKEDAVEMLASYGLAYSLM
Trubripes  all identical  ENSTRUG00000008542  48GIATVKEDAVEMLASYGLAYSLM
Drerio  all identical  ENSDARG00000014969  48GIAAVKEDAVEMLASYGLAYSLM
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000001724  20GIAAVKEDAIEMLASYGLAYSLM
protein features
start (aa)end (aa)featuredetails 
185TOPO_DOMCytoplasmic (Potential).lost
7878CONFLICTN -> S (in Ref. 1; AAF88039).might get lost (downstream of altered splice site)
86106TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
107131TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
132152TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
153158TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
159179TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
180189TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
190210TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
211326TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
327347TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
348350TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
351371TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
372403TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
404426TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
427429TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
430452TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
453492TOPO_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 1479 / 1479
position (AA) of stopcodon in wt / mu AA sequence 493 / 493
position of stopcodon in wt / mu cDNA 1810 / 1810
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 332 / 332
chromosome 5
strand -1
last intron/exon boundary 1697
theoretical NMD boundary in CDS 1315
length of CDS 1479
coding sequence (CDS) position 143
cDNA position
(for ins/del: last normal base / first normal base)		 474
gDNA position
(for ins/del: last normal base / first normal base)		 102634
chromosomal position
(for ins/del: last normal base / first normal base)		 14769254
original gDNA sequence snippet CAAGGAGGATGCAGTCGAGATGCTGGCCAGCTACGGGCTGG
altered gDNA sequence snippet CAAGGAGGATGCAGTCGAGACGCTGGCCAGCTACGGGCTGG
original cDNA sequence snippet CAAGGAGGATGCAGTCGAGATGCTGGCCAGCTACGGGCTGG
altered cDNA sequence snippet CAAGGAGGATGCAGTCGAGACGCTGGCCAGCTACGGGCTGG
wildtype AA sequence MVKFPALTHY WPLIRFLVPL GITNIAIDFG EQALNRGIAA VKEDAVEMLA SYGLAYSLMK
FFTGPMSDFK NVGLVFVNSK RDRTKAVLCM VVAGAIAAVF HTLIAYSDLG YYIINKLHHV
DESVGSKTRR AFLYLAAFPF MDAMAWTHAG ILLKHKYSFL VGCASISDVI AQVVFVAILL
HSHLECREPL LIPILSLYMG ALVRCTTLCL GYYKNIHDII PDRSGPELGG DATIRKMLSF
WWPLALILAT QRISRPIVNL FVSRDLGGSS AATEAVAILT ATYPVGHMPY GWLTEIRAVY
PAFDKNNPSN KLVSTSNTVT AAHIKKFTFV CMALSLTLCF VMFWTPNVSE KILIDIIGVD
FAFAELCVVP LRIFSFFPVP VTVRAHLTGW LMTLKKTFVL APSSVLRIIV LIASLVVLPY
LGVHGATLGV GSLLAGFVGE STMVAIAACY VYRKQKKKME NESATEGEDS AMTDMPPTEE
VTDIVEMREE NE*
mutated AA sequence MVKFPALTHY WPLIRFLVPL GITNIAIDFG EQALNRGIAA VKEDAVETLA SYGLAYSLMK
FFTGPMSDFK NVGLVFVNSK RDRTKAVLCM VVAGAIAAVF HTLIAYSDLG YYIINKLHHV
DESVGSKTRR AFLYLAAFPF MDAMAWTHAG ILLKHKYSFL VGCASISDVI AQVVFVAILL
HSHLECREPL LIPILSLYMG ALVRCTTLCL GYYKNIHDII PDRSGPELGG DATIRKMLSF
WWPLALILAT QRISRPIVNL FVSRDLGGSS AATEAVAILT ATYPVGHMPY GWLTEIRAVY
PAFDKNNPSN KLVSTSNTVT AAHIKKFTFV CMALSLTLCF VMFWTPNVSE KILIDIIGVD
FAFAELCVVP LRIFSFFPVP VTVRAHLTGW LMTLKKTFVL APSSVLRIIV LIASLVVLPY
LGVHGATLGV GSLLAGFVGE STMVAIAACY VYRKQKKKME NESATEGEDS AMTDMPPTEE
VTDIVEMREE NE*
speed 0.38 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