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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: ENST00000382848
Querying Taster for transcript #2: ENST00000382844
MT speed 2.73 s - this script 7.542237 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJB2disease_causing_automatic0.999999980252715simple_aae0R75Wsingle base exchangers104894402show file
GJB2disease_causing_automatic0.999999980252715simple_aae0R75Wsingle base exchangers104894402show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999980252715 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980925)
  • known disease mutation: rs17011 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20763498G>AN/A show variant in all transcripts   IGV
HGNC symbol GJB2
Ensembl transcript ID ENST00000382848
Genbank transcript ID NM_004004
UniProt peptide P29033
alteration type single base exchange
alteration region CDS
DNA changes c.223C>T
cDNA.361C>T
g.3540C>T
AA changes R75W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
75
frameshift no
known variant Reference ID: rs104894402
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17011 (pathogenic for Hereditary palmoplantar keratoderma|Deafness, autosomal dominant 3a|Nonsyndromic hearing loss and deafness|Autosomal recessive non-syndromic sensorineural deafness type DFNB|none provided|Rare genetic deafness) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980925)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Max, Transcription Factor, Max TF binding
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor
Gabp, Transcription Factor, Gabp TF binding (1)
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)6.0141
3.0711
(flanking)2.3921
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 increased3536wt: 0.9719 / mu: 0.9771 (marginal change - not scored)wt: CACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCA
mu: CACTACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCA
 ccac|ATCC
Acc marginally increased3540wt: 0.9595 / mu: 0.9596 (marginal change - not scored)wt: ACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCAGCTG
mu: ACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCAGCTG
 atcc|GGCT
Acc marginally increased3538wt: 0.8764 / mu: 0.9564 (marginal change - not scored)wt: CTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCAGC
mu: CTACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCAGC
 acat|CCGG
Acc marginally increased3531wt: 0.9550 / mu: 0.9608 (marginal change - not scored)wt: ACGATCACTACTTCCCCATCTCCCACATCCGGCTATGGGCC
mu: ACGATCACTACTTCCCCATCTCCCACATCTGGCTATGGGCC
 atct|CCCA
distance from splice site 245
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      75CYDHYFPISHIRLWALQLIFVSTP
mutated  not conserved    75CYDHYFPISHIWLWALQLIFVST
Ptroglodytes  all identical  ENSPTRG00000031248  75CYDHYFPISHIRLWALQLIFVST
Mmulatta  all identical  ENSMMUG00000010522  75CYDHYFPISHIRLWALQLIFVST
Fcatus  all identical  ENSFCAG00000006961  75CYDHYFPISHIRLWALQLIFVST
Mmusculus  all identical  ENSMUSG00000046352  75CYDHHFPISHIRLWALQLIMVST
Ggallus  all identical  ENSGALG00000017136  75CYDHFFPISHIRLWALQLIFVST
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042707  75CYDHFFPVSHIRFWCLQLIFVST
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  75CYDHHFPVSHIRLWCLQLIFVAT
protein features
start (aa)end (aa)featuredetails 
4175TOPO_DOMExtracellular (Potential).lost
7383HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 681 / 681
position (AA) of stopcodon in wt / mu AA sequence 227 / 227
position of stopcodon in wt / mu cDNA 819 / 819
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 139 / 139
chromosome 13
strand -1
last intron/exon boundary 117
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 681
coding sequence (CDS) position 223
cDNA position
(for ins/del: last normal base / first normal base)
361
gDNA position
(for ins/del: last normal base / first normal base)
3540
chromosomal position
(for ins/del: last normal base / first normal base)
20763498
original gDNA sequence snippet ACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCAGCTG
altered gDNA sequence snippet ACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCAGCTG
original cDNA sequence snippet ACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCAGCTG
altered cDNA sequence snippet ACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCAGCTG
wildtype AA sequence MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC
KNVCYDHYFP ISHIRLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*
mutated AA sequence MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC
KNVCYDHYFP ISHIWLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*
speed 1.39 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: 0.999999980252715 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980925)
  • known disease mutation: rs17011 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20763498G>AN/A show variant in all transcripts   IGV
HGNC symbol GJB2
Ensembl transcript ID ENST00000382844
Genbank transcript ID N/A
UniProt peptide P29033
alteration type single base exchange
alteration region CDS
DNA changes c.223C>T
cDNA.422C>T
g.3540C>T
AA changes R75W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
75
frameshift no
known variant Reference ID: rs104894402
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17011 (pathogenic for Hereditary palmoplantar keratoderma|Deafness, autosomal dominant 3a|Nonsyndromic hearing loss and deafness|Autosomal recessive non-syndromic sensorineural deafness type DFNB|none provided|Rare genetic deafness) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980925)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Max, Transcription Factor, Max TF binding
Gabp, Transcription Factor, Gabp TF binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
CTCF, Transcription Factor, CCCTC-binding factor
Gabp, Transcription Factor, Gabp TF binding (1)
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)6.0141
3.0711
(flanking)2.3921
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 increased3536wt: 0.9719 / mu: 0.9771 (marginal change - not scored)wt: CACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCA
mu: CACTACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCA
 ccac|ATCC
Acc marginally increased3540wt: 0.9595 / mu: 0.9596 (marginal change - not scored)wt: ACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCAGCTG
mu: ACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCAGCTG
 atcc|GGCT
Acc marginally increased3538wt: 0.8764 / mu: 0.9564 (marginal change - not scored)wt: CTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCAGC
mu: CTACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCAGC
 acat|CCGG
Acc marginally increased3531wt: 0.9550 / mu: 0.9608 (marginal change - not scored)wt: ACGATCACTACTTCCCCATCTCCCACATCCGGCTATGGGCC
mu: ACGATCACTACTTCCCCATCTCCCACATCTGGCTATGGGCC
 atct|CCCA
distance from splice site 422
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      75CYDHYFPISHIRLWALQLIFVSTP
mutated  not conserved    75CYDHYFPISHIWLWALQLIFVST
Ptroglodytes  all identical  ENSPTRG00000031248  75CYDHYFPISHIRLWALQLIFVST
Mmulatta  all identical  ENSMMUG00000010522  75CYDHYFPISHIRLWALQLIFVST
Fcatus  all identical  ENSFCAG00000006961  75CYDHYFPISHIRLWALQLIFVST
Mmusculus  all identical  ENSMUSG00000046352  75CYDHHFPISHIRLWALQLIMVST
Ggallus  all identical  ENSGALG00000017136  75CYDHFFPISHIRLWALQLIFVST
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042707  75CYDHFFPVSHIRFWCLQLIFVST
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  75CYDHHFPVSHIRLWCLQLIFVAT
protein features
start (aa)end (aa)featuredetails 
4175TOPO_DOMExtracellular (Potential).lost
7383HELIXlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 681 / 681
position (AA) of stopcodon in wt / mu AA sequence 227 / 227
position of stopcodon in wt / mu cDNA 880 / 880
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 200 / 200
chromosome 13
strand -1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 681
coding sequence (CDS) position 223
cDNA position
(for ins/del: last normal base / first normal base)
422
gDNA position
(for ins/del: last normal base / first normal base)
3540
chromosomal position
(for ins/del: last normal base / first normal base)
20763498
original gDNA sequence snippet ACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCAGCTG
altered gDNA sequence snippet ACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCAGCTG
original cDNA sequence snippet ACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCAGCTG
altered cDNA sequence snippet ACTTCCCCATCTCCCACATCTGGCTATGGGCCCTGCAGCTG
wildtype AA sequence MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC
KNVCYDHYFP ISHIRLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*
mutated AA sequence MDWGTLQTIL GGVNKHSTSI GKIWLTVLFI FRIMILVVAA KEVWGDEQAD FVCNTLQPGC
KNVCYDHYFP ISHIWLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*
speed 1.34 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