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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: ENST00000339480
MT speed 1.24 s - this script 3.962041 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJB4disease_causing_automatic0.999991077872513simple_aaeaffected0G12Dsingle base exchangers80358211show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999991077872513 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM035046)
  • known disease mutation: rs5007 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:35226890G>AN/A show variant in all transcripts   IGV
HGNC symbol GJB4
Ensembl transcript ID ENST00000339480
Genbank transcript ID NM_153212
UniProt peptide Q9NTQ9
alteration type single base exchange
alteration region CDS
DNA changes c.35G>A
cDNA.405G>A
g.1549G>A
AA changes G12D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS
12
frameshift no
known variant Reference ID: rs80358211
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5007 (pathogenic for Erythrokeratodermia variabilis et progressiva 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM035046)

known disease mutation at this position, please check HGMD for details (HGMD ID CM035046)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035046)
regulatory features E2F6, Transcription Factor, E2F6 Transcription Factor Binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.3641
6.0011
(flanking)-2.3430.028
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1550wt: 0.86 / mu: 0.97wt: AGTGGCGTGAACAAG
mu: AGTGACGTGAACAAG
 TGGC|gtga
Donor marginally increased1545wt: 0.9934 / mu: 0.9986 (marginal change - not scored)wt: TGCTGAGTGGCGTGA
mu: TGCTGAGTGACGTGA
 CTGA|gtgg
Donor marginally increased1553wt: 0.9566 / mu: 0.9780 (marginal change - not scored)wt: GGCGTGAACAAGTAC
mu: GACGTGAACAAGTAC
 CGTG|aaca
Donor marginally increased1540wt: 0.9245 / mu: 0.9598 (marginal change - not scored)wt: GGGCCTGCTGAGTGG
mu: GGGCCTGCTGAGTGA
 GCCT|gctg
Donor gained15470.46mu: CTGAGTGACGTGAAC GAGT|gacg
distance from splice site 357
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      12MNWAFLQGLLSGVNKYSTVLSRIW
mutated  not conserved    12MNWAFLQGLLSDVNKYSTVLSRI
Ptroglodytes  all identical  ENSPTRG00000022950  12MNWAFLQGLLSGVNKYSTALSRI
Mmulatta  all identical  ENSMMUG00000001860  12MNWAFLQGLLSGVNKYSTALSRI
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000046623  12MNWGFLQGILSGVNKYSTALGRI
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
120TOPO_DOMCytoplasmic (Potential).lost
2140TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
4175TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
7698TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
99126TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
127149TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
150187TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
188210TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
211266TOPO_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 801 / 801
position (AA) of stopcodon in wt / mu AA sequence 267 / 267
position of stopcodon in wt / mu cDNA 1171 / 1171
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 371 / 371
chromosome 1
strand 1
last intron/exon boundary 49
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 801
coding sequence (CDS) position 35
cDNA position
(for ins/del: last normal base / first normal base)
405
gDNA position
(for ins/del: last normal base / first normal base)
1549
chromosomal position
(for ins/del: last normal base / first normal base)
35226890
original gDNA sequence snippet TCTGCAGGGCCTGCTGAGTGGCGTGAACAAGTACTCCACAG
altered gDNA sequence snippet TCTGCAGGGCCTGCTGAGTGACGTGAACAAGTACTCCACAG
original cDNA sequence snippet TCTGCAGGGCCTGCTGAGTGGCGTGAACAAGTACTCCACAG
altered cDNA sequence snippet TCTGCAGGGCCTGCTGAGTGACGTGAACAAGTACTCCACAG
wildtype AA sequence MNWAFLQGLL SGVNKYSTVL SRIWLSVVFI FRVLVYVVAA EEVWDDEQKD FVCNTKQPGC
PNVCYDEFFP VSHVRLWALQ LILVTCPSLL VVMHVAYREE RERKHHLKHG PNAPSLYDNL
SKKRGGLWWT YLLSLIFKAA VDAGFLYIFH RLYKDYDMPR VVACSVEPCP HTVDCYISRP
TEKKVFTYFM VTTAAICILL NLSEVFYLVG KRCMEIFGPR HRRPRCRECL PDTCPPYVLS
QGGHPEDGNS VLMKAGSAPV DAGGYP*
mutated AA sequence MNWAFLQGLL SDVNKYSTVL SRIWLSVVFI FRVLVYVVAA EEVWDDEQKD FVCNTKQPGC
PNVCYDEFFP VSHVRLWALQ LILVTCPSLL VVMHVAYREE RERKHHLKHG PNAPSLYDNL
SKKRGGLWWT YLLSLIFKAA VDAGFLYIFH RLYKDYDMPR VVACSVEPCP HTVDCYISRP
TEKKVFTYFM VTTAAICILL NLSEVFYLVG KRCMEIFGPR HRRPRCRECL PDTCPPYVLS
QGGHPEDGNS VLMKAGSAPV DAGGYP*
speed 1.24 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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