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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000241124
Querying Taster for transcript #2: ENST00000400065
Querying Taster for transcript #3: ENST00000400066
Querying Taster for transcript #4: ENST00000356192
MT speed 0 s - this script 4.188474 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJB6disease_causing_automatic3.74956396284073e-10simple_aae0T5Msingle base exchangers104894414show file
GJB6disease_causing_automatic3.74956396284073e-10simple_aae0T5Msingle base exchangers104894414show file
GJB6disease_causing_automatic3.74956396284073e-10simple_aae0T5Msingle base exchangers104894414show file
GJB6disease_causing_automatic3.74956396284073e-10simple_aae0T5Msingle base exchangers104894414show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 3.74956396284073e-10 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993506)
  • known disease mutation: rs5543 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20797606G>AN/A show variant in all transcripts   IGV
HGNC symbol GJB6
Ensembl transcript ID ENST00000400065
Genbank transcript ID NM_001110221
UniProt peptide O95452
alteration type single base exchange
alteration region CDS
DNA changes c.14C>T
cDNA.309C>T
g.8929C>T
AA changes T5M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 5
frameshift no
known variant Reference ID: rs104894414
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs5543 (pathogenic for Deafness, autosomal dominant 3b) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.3430
0.7450
(flanking)0.2010
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      5 MDWGTLHTFIGGVNKHS
mutated  not conserved    5 MDWGMLHTFIGGVNKHSTSIGK
Ptroglodytes  all identical  ENSPTRG00000005683  5 MDWGTLHTFIGGVNKHSTSIGK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000040055  5 MDWGTLHTVIGGVNKHSTSIGK
Ggallus  not conserved  ENSGALG00000017136  5 MDWGALQTILGGVNKHSTSIGK
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000042707  5 MSWGALYAQLGGVNKHSTSLGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  5 MDWGTLYEVIGGVNRHSTSIGK
protein features
start (aa)end (aa)featuredetails 
122TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 786 / 786
position (AA) of stopcodon in wt / mu AA sequence 262 / 262
position of stopcodon in wt / mu cDNA 1081 / 1081
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 296 / 296
chromosome 13
strand -1
last intron/exon boundary 281
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 786
coding sequence (CDS) position 14
cDNA position
(for ins/del: last normal base / first normal base)		 309
gDNA position
(for ins/del: last normal base / first normal base)		 8929
chromosomal position
(for ins/del: last normal base / first normal base)		 20797606
original gDNA sequence snippet CAGCGCAATGGATTGGGGGACGCTGCACACTTTCATCGGGG
altered gDNA sequence snippet CAGCGCAATGGATTGGGGGATGCTGCACACTTTCATCGGGG
original cDNA sequence snippet CAGCGCAATGGATTGGGGGACGCTGCACACTTTCATCGGGG
altered cDNA sequence snippet CAGCGCAATGGATTGGGGGATGCTGCACACTTTCATCGGGG
wildtype AA sequence MDWGTLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*
mutated AA sequence MDWGMLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*
speed 0.80 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: 3.74956396284073e-10 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993506)
  • known disease mutation: rs5543 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20797606G>AN/A show variant in all transcripts   IGV
HGNC symbol GJB6
Ensembl transcript ID ENST00000241124
Genbank transcript ID NM_006783
UniProt peptide O95452
alteration type single base exchange
alteration region CDS
DNA changes c.14C>T
cDNA.312C>T
g.8929C>T
AA changes T5M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 5
frameshift no
known variant Reference ID: rs104894414
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs5543 (pathogenic for Deafness, autosomal dominant 3b) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.3430
0.7450
(flanking)0.2010
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      5 MDWGTLHTFIGGVNKHS
mutated  not conserved    5 MDWGMLHTFIGGVNKHSTSIGK
Ptroglodytes  all identical  ENSPTRG00000005683  5 MDWGTLHTFIGGVNKHSTSIGK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000040055  5 MDWGTLHTVIGGVNKHSTSIGK
Ggallus  not conserved  ENSGALG00000017136  5 MDWGALQTILGGVNKHSTSIGK
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000042707  5 MSWGALYAQLGGVNKHSTSLGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  5 MDWGTLYEVIGGVNRHSTSIGK
protein features
start (aa)end (aa)featuredetails 
122TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 786 / 786
position (AA) of stopcodon in wt / mu AA sequence 262 / 262
position of stopcodon in wt / mu cDNA 1084 / 1084
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 299 / 299
chromosome 13
strand -1
last intron/exon boundary 284
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 786
coding sequence (CDS) position 14
cDNA position
(for ins/del: last normal base / first normal base)		 312
gDNA position
(for ins/del: last normal base / first normal base)		 8929
chromosomal position
(for ins/del: last normal base / first normal base)		 20797606
original gDNA sequence snippet CAGCGCAATGGATTGGGGGACGCTGCACACTTTCATCGGGG
altered gDNA sequence snippet CAGCGCAATGGATTGGGGGATGCTGCACACTTTCATCGGGG
original cDNA sequence snippet CAGCGCAATGGATTGGGGGACGCTGCACACTTTCATCGGGG
altered cDNA sequence snippet CAGCGCAATGGATTGGGGGATGCTGCACACTTTCATCGGGG
wildtype AA sequence MDWGTLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*
mutated AA sequence MDWGMLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*
speed 0.97 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: 3.74956396284073e-10 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993506)
  • known disease mutation: rs5543 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20797606G>AN/A show variant in all transcripts   IGV
HGNC symbol GJB6
Ensembl transcript ID ENST00000356192
Genbank transcript ID NM_001110219
UniProt peptide O95452
alteration type single base exchange
alteration region CDS
DNA changes c.14C>T
cDNA.635C>T
g.8929C>T
AA changes T5M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 5
frameshift no
known variant Reference ID: rs104894414
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs5543 (pathogenic for Deafness, autosomal dominant 3b) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.3430
0.7450
(flanking)0.2010
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      5 MDWGTLHTFIGGVNKHS
mutated  not conserved    5 MDWGMLHTFIGGVNKHSTSIGK
Ptroglodytes  all identical  ENSPTRG00000005683  5 MDWGTLHTFIGGVNKHSTSIGK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000040055  5 MDWGTLHTVIGGVNKHSTSIGK
Ggallus  not conserved  ENSGALG00000017136  5 MDWGALQTILGGVNKHSTSIGK
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000042707  5 MSWGALYAQLGGVNKHSTSLGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  5 MDWGTLYEVIGGVNRHSTSIGK
protein features
start (aa)end (aa)featuredetails 
122TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 786 / 786
position (AA) of stopcodon in wt / mu AA sequence 262 / 262
position of stopcodon in wt / mu cDNA 1407 / 1407
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 622 / 622
chromosome 13
strand -1
last intron/exon boundary 607
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 786
coding sequence (CDS) position 14
cDNA position
(for ins/del: last normal base / first normal base)		 635
gDNA position
(for ins/del: last normal base / first normal base)		 8929
chromosomal position
(for ins/del: last normal base / first normal base)		 20797606
original gDNA sequence snippet CAGCGCAATGGATTGGGGGACGCTGCACACTTTCATCGGGG
altered gDNA sequence snippet CAGCGCAATGGATTGGGGGATGCTGCACACTTTCATCGGGG
original cDNA sequence snippet CAGCGCAATGGATTGGGGGACGCTGCACACTTTCATCGGGG
altered cDNA sequence snippet CAGCGCAATGGATTGGGGGATGCTGCACACTTTCATCGGGG
wildtype AA sequence MDWGTLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*
mutated AA sequence MDWGMLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*
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: 3.74956396284073e-10 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993506)
  • known disease mutation: rs5543 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20797606G>AN/A show variant in all transcripts   IGV
HGNC symbol GJB6
Ensembl transcript ID ENST00000400066
Genbank transcript ID NM_001110220
UniProt peptide O95452
alteration type single base exchange
alteration region CDS
DNA changes c.14C>T
cDNA.431C>T
g.8929C>T
AA changes T5M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 5
frameshift no
known variant Reference ID: rs104894414
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs5543 (pathogenic for Deafness, autosomal dominant 3b) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993506)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.3430
0.7450
(flanking)0.2010
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      5 MDWGTLHTFIGGVNKHS
mutated  not conserved    5 MDWGMLHTFIGGVNKHSTSIGK
Ptroglodytes  all identical  ENSPTRG00000005683  5 MDWGTLHTFIGGVNKHSTSIGK
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000040055  5 MDWGTLHTVIGGVNKHSTSIGK
Ggallus  not conserved  ENSGALG00000017136  5 MDWGALQTILGGVNKHSTSIGK
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000042707  5 MSWGALYAQLGGVNKHSTSLGK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  5 MDWGTLYEVIGGVNRHSTSIGK
protein features
start (aa)end (aa)featuredetails 
122TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 786 / 786
position (AA) of stopcodon in wt / mu AA sequence 262 / 262
position of stopcodon in wt / mu cDNA 1203 / 1203
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 418 / 418
chromosome 13
strand -1
last intron/exon boundary 403
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 786
coding sequence (CDS) position 14
cDNA position
(for ins/del: last normal base / first normal base)		 431
gDNA position
(for ins/del: last normal base / first normal base)		 8929
chromosomal position
(for ins/del: last normal base / first normal base)		 20797606
original gDNA sequence snippet CAGCGCAATGGATTGGGGGACGCTGCACACTTTCATCGGGG
altered gDNA sequence snippet CAGCGCAATGGATTGGGGGATGCTGCACACTTTCATCGGGG
original cDNA sequence snippet CAGCGCAATGGATTGGGGGACGCTGCACACTTTCATCGGGG
altered cDNA sequence snippet CAGCGCAATGGATTGGGGGATGCTGCACACTTTCATCGGGG
wildtype AA sequence MDWGTLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*
mutated AA sequence MDWGMLHTFI GGVNKHSTSI GKVWITVIFI FRVMILVVAA QEVWGDEQED FVCNTLQPGC
KNVCYDHFFP VSHIRLWALQ LIFVSTPALL VAMHVAYYRH ETTRKFRRGE KRNDFKDIED
IKKQKVRIEG SLWWTYTSSI FFRIIFEAAF MYVFYFLYNG YHLPWVLKCG IDPCPNLVDC
FISRPTEKTV FTIFMISASV ICMLLNVAEL CYLLLKVCFR RSKRAQTQKN HPNHALKESK
QNEMNELISD SGQNAITGFP S*
speed 0.96 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