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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 1.17 s - this script 5.354642 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJB4disease_causing_automatic0.993797085450051simple_aaeaffected0T85Psingle base exchangers80358210show file

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Prediction

disease causing

Model: simple_aae, prob: 0.993797085450051 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM035048)
  • known disease mutation: rs5006 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:35227108A>CN/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.253A>C
cDNA.623A>C
g.1767A>C
AA changes T85P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS
85
frameshift no
known variant Reference ID: rs80358210
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs5006 (pathogenic for Erythrokeratodermia variabilis et progressiva 2|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM035048)

known disease mutation at this position, please check HGMD for details (HGMD ID CM035048)
known disease mutation at this position, please check HGMD for details (HGMD ID CM035048)
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
Max, Transcription Factor, Max TF binding (-1)
Max, Transcription Factor, Max TF binding
Max, Transcription Factor, Max TF binding (1)
USF1, Transcription Factor, USF1 Transcription Factor Binding (-1)
USF1, Transcription Factor, USF1 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding (1)
mxl-1::mdl-1, Transcription Factor Complex, mxl-1::mdl-1 Binding (-1)
mxl-1::mdl-1, Transcription Factor Complex, mxl-1::mdl-1 Binding (1)
phyloP / phastCons
PhyloPPhastCons
(flanking)1.1041
1.6451
(flanking)6.1171
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased1763wt: 0.2307 / mu: 0.2453 (marginal change - not scored)wt: TGGGCCCTACAGCTCATCCTGGTCACGTGCCCCTCACTGCT
mu: TGGGCCCTACAGCTCATCCTGGTCCCGTGCCCCTCACTGCT
 cctg|GTCA
Acc increased1768wt: 0.43 / mu: 0.48wt: CCTACAGCTCATCCTGGTCACGTGCCCCTCACTGCTCGTGG
mu: CCTACAGCTCATCCTGGTCCCGTGCCCCTCACTGCTCGTGG
 tcac|GTGC
Acc gained17740.78mu: GCTCATCCTGGTCCCGTGCCCCTCACTGCTCGTGGTCATGC gccc|CTCA
Acc gained17770.43mu: CATCCTGGTCCCGTGCCCCTCACTGCTCGTGGTCATGCACG cctc|ACTG
distance from splice site 575
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      85VRLWALQLILVTCPSLLVVMHVAY
mutated  not conserved    85VRLWALQLILVPCPSLLVVMHVA
Ptroglodytes  all identical  ENSPTRG00000022950  85VRLWALQLILVTCPSLLVVMHVA
Mmulatta  all identical  ENSMMUG00000001860  85VRLWALQLILVTCPSLLVVMHVA
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000046623  85VRLWALQLILVTCPSLLVVMHVA
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 
7698TRANSMEMHelical; (Potential).lost
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 253
cDNA position
(for ins/del: last normal base / first normal base)
623
gDNA position
(for ins/del: last normal base / first normal base)
1767
chromosomal position
(for ins/del: last normal base / first normal base)
35227108
original gDNA sequence snippet CCCTACAGCTCATCCTGGTCACGTGCCCCTCACTGCTCGTG
altered gDNA sequence snippet CCCTACAGCTCATCCTGGTCCCGTGCCCCTCACTGCTCGTG
original cDNA sequence snippet CCCTACAGCTCATCCTGGTCACGTGCCCCTCACTGCTCGTG
altered cDNA sequence snippet CCCTACAGCTCATCCTGGTCCCGTGCCCCTCACTGCTCGTG
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 SGVNKYSTVL SRIWLSVVFI FRVLVYVVAA EEVWDDEQKD FVCNTKQPGC
PNVCYDEFFP VSHVRLWALQ LILVPCPSLL VVMHVAYREE RERKHHLKHG PNAPSLYDNL
SKKRGGLWWT YLLSLIFKAA VDAGFLYIFH RLYKDYDMPR VVACSVEPCP HTVDCYISRP
TEKKVFTYFM VTTAAICILL NLSEVFYLVG KRCMEIFGPR HRRPRCRECL PDTCPPYVLS
QGGHPEDGNS VLMKAGSAPV DAGGYP*
speed 1.17 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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