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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 s - this script 2.792015 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ANKHdisease_causing_automatic0.999999871688546simple_aaeaffected0P5Lsingle base exchangers121908409show file

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999871688546 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM022761)
  • known disease mutation: rs5198 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:14871543G>AN/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.14C>T
cDNA.345C>T
g.345C>T
AA changes P5L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 5
frameshift no
known variant Reference ID: rs121908409
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5198 (pathogenic for Familial calcium pyrophosphate deposition) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM022761)

known disease mutation at this position, please check HGMD for details (HGMD ID CM022761)
known disease mutation at this position, please check HGMD for details (HGMD ID CM022761)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.3571
2.161
(flanking)3.0671
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased349wt: 0.51 / mu: 0.64wt: CCGGCGCTCACGCAC
mu: CTGGCGCTCACGCAC		 GGCG|ctca
distance from splice site 83
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      5 MVKFPALTHYWPLIRFL
mutated  not conserved    5 MVKFLALTHYWPLIRFLVPLGI
Ptroglodytes  all identical  ENSPTRG00000016739  5 MVKFPALTHYWPLIRFLVPLGI
Mmulatta  all identical  ENSMMUG00000021942  5 MVKFPALTHYWPLIRFLVPLGI
Fcatus  no alignment  ENSFCAG00000012251  n/a
Mmusculus  all identical  ENSMUSG00000022265  5 MVKFPALTHYWPLIRFLVPLGI
Ggallus  all identical  ENSGALG00000012964  5 MVKFPALTNYWPLIRFLVPLGI
Trubripes  all identical  ENSTRUG00000008542  5 MVEFPSLSPYWPLIRFLVPLAI
Drerio  all identical  ENSDARG00000014969  5 MMKFPALTHYWPLIRFLVPLAI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000001724  n/a
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 14
cDNA position
(for ins/del: last normal base / first normal base)		 345
gDNA position
(for ins/del: last normal base / first normal base)		 345
chromosomal position
(for ins/del: last normal base / first normal base)		 14871543
original gDNA sequence snippet GGGGACTATGGTGAAATTCCCGGCGCTCACGCACTACTGGC
altered gDNA sequence snippet GGGGACTATGGTGAAATTCCTGGCGCTCACGCACTACTGGC
original cDNA sequence snippet GGGGACTATGGTGAAATTCCCGGCGCTCACGCACTACTGGC
altered cDNA sequence snippet GGGGACTATGGTGAAATTCCTGGCGCTCACGCACTACTGGC
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 MVKFLALTHY 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*
speed 0.69 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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