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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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000373366
Querying Taster for transcript #2: ENST00000373362
MT speed 0 s - this script 3.333314 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJB3disease_causing_automatic0.99962344746187simple_aaeaffected0C86Ssingle base exchangers74315317show file
GJB3disease_causing_automatic0.99962344746187simple_aaeaffected0C86Ssingle base exchangers74315317show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99962344746187 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980933)
  • known disease mutation: rs6484 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:35250619T>AN/A show variant in all transcripts   IGV
HGNC symbol GJB3
Ensembl transcript ID ENST00000373366
Genbank transcript ID NM_024009
UniProt peptide O75712
alteration type single base exchange
alteration region CDS
DNA changes c.256T>A
cDNA.871T>A
g.3830T>A
AA changes C86S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS
86
frameshift no
known variant Reference ID: rs74315317
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs6484 (pathogenic for Erythrokeratodermia variabilis et progressiva 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980933)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980933)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980933)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.7570.005
1.6740.934
(flanking)3.2391
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 increased3827wt: 0.8004 / mu: 0.8255 (marginal change - not scored)wt: CCCTGCAGCTCATCTTCGTCACATGCCCCTCGCTGCTGGTC
mu: CCCTGCAGCTCATCTTCGTCACAAGCCCCTCGCTGCTGGTC
 gtca|CATG
Acc marginally increased3830wt: 0.9518 / mu: 0.9519 (marginal change - not scored)wt: TGCAGCTCATCTTCGTCACATGCCCCTCGCTGCTGGTCATC
mu: TGCAGCTCATCTTCGTCACAAGCCCCTCGCTGCTGGTCATC
 acat|GCCC
Donor increased3825wt: 0.48 / mu: 0.98wt: CTTCGTCACATGCCC
mu: CTTCGTCACAAGCCC
 TCGT|caca
distance from splice site 281
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      86RLWALQLIFVTCPSLLVILHVAYR
mutated  not conserved    86RLWALQLIFVTSPSLLVILHVAY
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000022677  86RLWALQLIFVTCPSLLVILHVAY
Fcatus  all identical  ENSFCAG00000014055  86RLWALQLIFVTCPSLLVILHVAY
Mmusculus  all identical  ENSMUSG00000042367  86RLWALQLIFVTCPSMLVILHVAY
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042866  86RLWALQLIFVTCPSLMVVMHVKY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000016481  86RLWALQLIFVTCPSLLVIMHVSY
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)
211270TOPO_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 813 / 813
position (AA) of stopcodon in wt / mu AA sequence 271 / 271
position of stopcodon in wt / mu cDNA 1428 / 1428
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 616 / 616
chromosome 1
strand 1
last intron/exon boundary 591
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 813
coding sequence (CDS) position 256
cDNA position
(for ins/del: last normal base / first normal base)
871
gDNA position
(for ins/del: last normal base / first normal base)
3830
chromosomal position
(for ins/del: last normal base / first normal base)
35250619
original gDNA sequence snippet TGCAGCTCATCTTCGTCACATGCCCCTCGCTGCTGGTCATC
altered gDNA sequence snippet TGCAGCTCATCTTCGTCACAAGCCCCTCGCTGCTGGTCATC
original cDNA sequence snippet TGCAGCTCATCTTCGTCACATGCCCCTCGCTGCTGGTCATC
altered cDNA sequence snippet TGCAGCTCATCTTCGTCACAAGCCCCTCGCTGCTGGTCATC
wildtype AA sequence MDWKTLQALL SGVNKYSTAF GRIWLSVVFV FRVLVYVVAA ERVWGDEQKD FDCNTKQPGC
TNVCYDNYFP ISNIRLWALQ LIFVTCPSLL VILHVAYREE RERRHRQKHG DQCAKLYDNA
GKKHGGLWWT YLFSLIFKLI IEFLFLYLLH TLWHGFNMPR LVQCANVAPC PNIVDCYIAR
PTEKKIFTYF MVGASAVCIV LTICELCYLI CHRVLRGLHK DKPRGGCSPS SSASRASTCR
CHHKLVEAGE VDPDPGNNKL QASAPNLTPI *
mutated AA sequence MDWKTLQALL SGVNKYSTAF GRIWLSVVFV FRVLVYVVAA ERVWGDEQKD FDCNTKQPGC
TNVCYDNYFP ISNIRLWALQ LIFVTSPSLL VILHVAYREE RERRHRQKHG DQCAKLYDNA
GKKHGGLWWT YLFSLIFKLI IEFLFLYLLH TLWHGFNMPR LVQCANVAPC PNIVDCYIAR
PTEKKIFTYF MVGASAVCIV LTICELCYLI CHRVLRGLHK DKPRGGCSPS SSASRASTCR
CHHKLVEAGE VDPDPGNNKL QASAPNLTPI *
speed 0.84 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
back to results table
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99962344746187 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980933)
  • known disease mutation: rs6484 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:35250619T>AN/A show variant in all transcripts   IGV
HGNC symbol GJB3
Ensembl transcript ID ENST00000373362
Genbank transcript ID NM_001005752
UniProt peptide O75712
alteration type single base exchange
alteration region CDS
DNA changes c.256T>A
cDNA.446T>A
g.3830T>A
AA changes C86S Score: 112 explain score(s)
position(s) of altered AA
if AA alteration in CDS
86
frameshift no
known variant Reference ID: rs74315317
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs6484 (pathogenic for Erythrokeratodermia variabilis et progressiva 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980933)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980933)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980933)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
USF1, Transcription Factor, USF1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.7570.005
1.6740.934
(flanking)3.2391
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 increased3827wt: 0.8004 / mu: 0.8255 (marginal change - not scored)wt: CCCTGCAGCTCATCTTCGTCACATGCCCCTCGCTGCTGGTC
mu: CCCTGCAGCTCATCTTCGTCACAAGCCCCTCGCTGCTGGTC
 gtca|CATG
Acc marginally increased3830wt: 0.9518 / mu: 0.9519 (marginal change - not scored)wt: TGCAGCTCATCTTCGTCACATGCCCCTCGCTGCTGGTCATC
mu: TGCAGCTCATCTTCGTCACAAGCCCCTCGCTGCTGGTCATC
 acat|GCCC
Donor increased3825wt: 0.48 / mu: 0.98wt: CTTCGTCACATGCCC
mu: CTTCGTCACAAGCCC
 TCGT|caca
distance from splice site 281
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      86RLWALQLIFVTCPSLLVILHVAYR
mutated  not conserved    86RLWALQLIFVTSPSLLVILHVAY
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000022677  86RLWALQLIFVTCPSLLVILHVAY
Fcatus  all identical  ENSFCAG00000014055  86RLWALQLIFVTCPSLLVILHVAY
Mmusculus  all identical  ENSMUSG00000042367  86RLWALQLIFVTCPSMLVILHVAY
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042866  86RLWALQLIFVTCPSLMVVMHVKY
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000016481  86RLWALQLIFVTCPSLLVIMHVSY
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)
211270TOPO_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 813 / 813
position (AA) of stopcodon in wt / mu AA sequence 271 / 271
position of stopcodon in wt / mu cDNA 1003 / 1003
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 191 / 191
chromosome 1
strand 1
last intron/exon boundary 166
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 813
coding sequence (CDS) position 256
cDNA position
(for ins/del: last normal base / first normal base)
446
gDNA position
(for ins/del: last normal base / first normal base)
3830
chromosomal position
(for ins/del: last normal base / first normal base)
35250619
original gDNA sequence snippet TGCAGCTCATCTTCGTCACATGCCCCTCGCTGCTGGTCATC
altered gDNA sequence snippet TGCAGCTCATCTTCGTCACAAGCCCCTCGCTGCTGGTCATC
original cDNA sequence snippet TGCAGCTCATCTTCGTCACATGCCCCTCGCTGCTGGTCATC
altered cDNA sequence snippet TGCAGCTCATCTTCGTCACAAGCCCCTCGCTGCTGGTCATC
wildtype AA sequence MDWKTLQALL SGVNKYSTAF GRIWLSVVFV FRVLVYVVAA ERVWGDEQKD FDCNTKQPGC
TNVCYDNYFP ISNIRLWALQ LIFVTCPSLL VILHVAYREE RERRHRQKHG DQCAKLYDNA
GKKHGGLWWT YLFSLIFKLI IEFLFLYLLH TLWHGFNMPR LVQCANVAPC PNIVDCYIAR
PTEKKIFTYF MVGASAVCIV LTICELCYLI CHRVLRGLHK DKPRGGCSPS SSASRASTCR
CHHKLVEAGE VDPDPGNNKL QASAPNLTPI *
mutated AA sequence MDWKTLQALL SGVNKYSTAF GRIWLSVVFV FRVLVYVVAA ERVWGDEQKD FDCNTKQPGC
TNVCYDNYFP ISNIRLWALQ LIFVTSPSLL VILHVAYREE RERRHRQKHG DQCAKLYDNA
GKKHGGLWWT YLFSLIFKLI IEFLFLYLLH TLWHGFNMPR LVQCANVAPC PNIVDCYIAR
PTEKKIFTYF MVGASAVCIV LTICELCYLI CHRVLRGLHK DKPRGGCSPS SSASRASTCR
CHHKLVEAGE VDPDPGNNKL QASAPNLTPI *
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
back to results table

Problems