Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
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 0 s - this script 3.130724 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJB2disease_causing_automatic0.999999998232433simple_aaeaffected0H73Rsingle base exchangers121912968show file
GJB2disease_causing_automatic0.999999998232433simple_aaeaffected0H73Rsingle base exchangers121912968show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999998232433 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM081298)
  • known disease mutation: rs17037 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20763503T>CN/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.218A>G
cDNA.356A>G
g.3535A>G
AA changes H73R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 73
frameshift no
known variant Reference ID: rs121912968
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17037 (pathogenic for Palmoplantar keratoderma-deafness syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM081298)

known disease mutation at this position, please check HGMD for details (HGMD ID CM081298)
known disease mutation at this position, please check HGMD for details (HGMD ID CM081298)
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)6.0851
5.0251
(flanking)6.0851
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased3529wt: 0.46 / mu: 0.55wt: CTACGATCACTACTTCCCCATCTCCCACATCCGGCTATGGG
mu: CTACGATCACTACTTCCCCATCTCCCGCATCCGGCTATGGG		 ccat|CTCC
Acc increased3527wt: 0.41 / mu: 0.66wt: TGCTACGATCACTACTTCCCCATCTCCCACATCCGGCTATG
mu: TGCTACGATCACTACTTCCCCATCTCCCGCATCCGGCTATG		 cccc|ATCT
Acc marginally increased3531wt: 0.9550 / mu: 0.9788 (marginal change - not scored)wt: ACGATCACTACTTCCCCATCTCCCACATCCGGCTATGGGCC
mu: ACGATCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCC		 atct|CCCA
Acc increased3532wt: 0.33 / mu: 0.37wt: CGATCACTACTTCCCCATCTCCCACATCCGGCTATGGGCCC
mu: CGATCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCC		 tctc|CCAC
Acc marginally increased3536wt: 0.9719 / mu: 0.9751 (marginal change - not scored)wt: CACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCA
mu: CACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCCTGCA		 ccac|ATCC
Acc marginally increased3534wt: 0.9628 / mu: 0.9820 (marginal change - not scored)wt: ATCACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTG
mu: ATCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCCTG		 tccc|ACAT
distance from splice site 240
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      73NVCYDHYFPISHIRLWALQLIFVS
mutated  not conserved    73NVCYDHYFPISRIRLWALQLIFV
Ptroglodytes  all identical  ENSPTRG00000031248  73NVCYDHYFPISHIRLWALQLIFV
Mmulatta  all identical  ENSMMUG00000010522  73NVCYDHYFPISHIRLWALQLIFV
Fcatus  all identical  ENSFCAG00000006961  73NVCYDHYFPISHIRLWALQLIFV
Mmusculus  all identical  ENSMUSG00000046352  73NVCYDHHFPISHIRLWALQLIMV
Ggallus  all identical  ENSGALG00000017136  73NVCYDHFFPISHIRLWALQLIFV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042707  73NVCYDHFFPVSHIRFWCLQLIFV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  73NVCYDHHFPVSHIRLWCLQLIFV
protein features
start (aa)end (aa)featuredetails 
4175TOPO_DOMExtracellular (Potential).lost
7383HELIXlost
7698TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
85105HELIXmight get lost (downstream of altered splice site)
8686CONFLICTT -> S (in Ref. 1; AAD21314).might get lost (downstream of altered splice site)
99131TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
106108TURNmight get lost (downstream of altered splice site)
112112CONFLICTK -> N (in Ref. 4; AAY25170).might get lost (downstream of altered splice site)
126130TURNmight get lost (downstream of altered splice site)
131156HELIXmight get lost (downstream of altered splice site)
132154TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
155192TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
157159TURNmight get lost (downstream of altered splice site)
160162STRANDmight get lost (downstream of altered splice site)
165169STRANDmight get lost (downstream of altered splice site)
169169DISULFIDmight get lost (downstream of altered splice site)
174174DISULFIDmight get lost (downstream of altered splice site)
174181STRANDmight get lost (downstream of altered splice site)
180180DISULFIDmight get lost (downstream of altered splice site)
185215HELIXmight get lost (downstream of altered splice site)
193215TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
216226TOPO_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 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 218
cDNA position
(for ins/del: last normal base / first normal base)		 356
gDNA position
(for ins/del: last normal base / first normal base)		 3535
chromosomal position
(for ins/del: last normal base / first normal base)		 20763503
original gDNA sequence snippet TCACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGC
altered gDNA sequence snippet TCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCCTGC
original cDNA sequence snippet TCACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGC
altered cDNA sequence snippet TCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCCTGC
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 ISRIRLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*
speed 0.74 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: 0.999999998232433 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM081298)
  • known disease mutation: rs17037 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20763503T>CN/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.218A>G
cDNA.417A>G
g.3535A>G
AA changes H73R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 73
frameshift no
known variant Reference ID: rs121912968
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17037 (pathogenic for Palmoplantar keratoderma-deafness syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM081298)

known disease mutation at this position, please check HGMD for details (HGMD ID CM081298)
known disease mutation at this position, please check HGMD for details (HGMD ID CM081298)
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)6.0851
5.0251
(flanking)6.0851
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased3529wt: 0.46 / mu: 0.55wt: CTACGATCACTACTTCCCCATCTCCCACATCCGGCTATGGG
mu: CTACGATCACTACTTCCCCATCTCCCGCATCCGGCTATGGG		 ccat|CTCC
Acc increased3527wt: 0.41 / mu: 0.66wt: TGCTACGATCACTACTTCCCCATCTCCCACATCCGGCTATG
mu: TGCTACGATCACTACTTCCCCATCTCCCGCATCCGGCTATG		 cccc|ATCT
Acc marginally increased3531wt: 0.9550 / mu: 0.9788 (marginal change - not scored)wt: ACGATCACTACTTCCCCATCTCCCACATCCGGCTATGGGCC
mu: ACGATCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCC		 atct|CCCA
Acc increased3532wt: 0.33 / mu: 0.37wt: CGATCACTACTTCCCCATCTCCCACATCCGGCTATGGGCCC
mu: CGATCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCC		 tctc|CCAC
Acc marginally increased3536wt: 0.9719 / mu: 0.9751 (marginal change - not scored)wt: CACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGCA
mu: CACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCCTGCA		 ccac|ATCC
Acc marginally increased3534wt: 0.9628 / mu: 0.9820 (marginal change - not scored)wt: ATCACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTG
mu: ATCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCCTG		 tccc|ACAT
distance from splice site 417
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      73NVCYDHYFPISHIRLWALQLIFVS
mutated  not conserved    73NVCYDHYFPISRIRLWALQLIFV
Ptroglodytes  all identical  ENSPTRG00000031248  73NVCYDHYFPISHIRLWALQLIFV
Mmulatta  all identical  ENSMMUG00000010522  73NVCYDHYFPISHIRLWALQLIFV
Fcatus  all identical  ENSFCAG00000006961  73NVCYDHYFPISHIRLWALQLIFV
Mmusculus  all identical  ENSMUSG00000046352  73NVCYDHHFPISHIRLWALQLIMV
Ggallus  all identical  ENSGALG00000017136  73NVCYDHFFPISHIRLWALQLIFV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042707  73NVCYDHFFPVSHIRFWCLQLIFV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  73NVCYDHHFPVSHIRLWCLQLIFV
protein features
start (aa)end (aa)featuredetails 
4175TOPO_DOMExtracellular (Potential).lost
7383HELIXlost
7698TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
85105HELIXmight get lost (downstream of altered splice site)
8686CONFLICTT -> S (in Ref. 1; AAD21314).might get lost (downstream of altered splice site)
99131TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
106108TURNmight get lost (downstream of altered splice site)
112112CONFLICTK -> N (in Ref. 4; AAY25170).might get lost (downstream of altered splice site)
126130TURNmight get lost (downstream of altered splice site)
131156HELIXmight get lost (downstream of altered splice site)
132154TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
155192TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
157159TURNmight get lost (downstream of altered splice site)
160162STRANDmight get lost (downstream of altered splice site)
165169STRANDmight get lost (downstream of altered splice site)
169169DISULFIDmight get lost (downstream of altered splice site)
174174DISULFIDmight get lost (downstream of altered splice site)
174181STRANDmight get lost (downstream of altered splice site)
180180DISULFIDmight get lost (downstream of altered splice site)
185215HELIXmight get lost (downstream of altered splice site)
193215TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
216226TOPO_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 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 218
cDNA position
(for ins/del: last normal base / first normal base)		 417
gDNA position
(for ins/del: last normal base / first normal base)		 3535
chromosomal position
(for ins/del: last normal base / first normal base)		 20763503
original gDNA sequence snippet TCACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGC
altered gDNA sequence snippet TCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCCTGC
original cDNA sequence snippet TCACTACTTCCCCATCTCCCACATCCGGCTATGGGCCCTGC
altered cDNA sequence snippet TCACTACTTCCCCATCTCCCGCATCCGGCTATGGGCCCTGC
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 ISRIRLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG ICILLNVTEL CYLLIRYCSG KSKKPV*
speed 0.40 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

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