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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 2.14 s - this script 6.309115 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJB2disease_causing_automatic0.99999999999291simple_aaeaffected0C202Fsingle base exchangers104894406show file
GJB2disease_causing_automatic0.99999999999291simple_aaeaffected0C202Fsingle base exchangers104894406show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.99999999999291 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM001172)
  • known disease mutation: rs17018 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20763116C>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.605G>T
cDNA.743G>T
g.3922G>T
AA changes C202F Score: 205 explain score(s)
position(s) of altered AA
if AA alteration in CDS
202
frameshift no
known variant Reference ID: rs104894406
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17018 (pathogenic for Deafness, autosomal dominant 3a) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001172)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001172)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001172)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4271
6.2481
(flanking)5.1591
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased3932wt: 0.36 / mu: 0.60wt: TCTGGAATTTGCATCCTGCTGAATGTCACTGAATTGTGTTA
mu: TCTGGAATTTTCATCCTGCTGAATGTCACTGAATTGTGTTA
 gctg|AATG
Acc increased3933wt: 0.22 / mu: 0.65wt: CTGGAATTTGCATCCTGCTGAATGTCACTGAATTGTGTTAT
mu: CTGGAATTTTCATCCTGCTGAATGTCACTGAATTGTGTTAT
 ctga|ATGT
Acc gained39280.51mu: AGTGTCTGGAATTTTCATCCTGCTGAATGTCACTGAATTGT tcct|GCTG
Acc gained39300.35mu: TGTCTGGAATTTTCATCCTGCTGAATGTCACTGAATTGTGT ctgc|TGAA
distance from splice site 627
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      202FTVFMIAVSGICILLNVTELCYLL
mutated  not conserved    202FTVFMIAVSGIFILLNVTELCYL
Ptroglodytes  all identical  ENSPTRG00000031248  202FTVFMIAVSGICILLNVTELCYL
Mmulatta  all identical  ENSMMUG00000010522  202FTVFMIAVSGICILLNVTELCYL
Fcatus  all identical  ENSFCAG00000006961  202FTVFMIAVSGICILLNVTELCYL
Mmusculus  all identical  ENSMUSG00000046352  202FTVFMISVSGICILLNITELCYL
Ggallus  all identical  ENSGALG00000017136  202FTIFMIAVSSICILLNVAELCYL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042707  204FTIFMVGSSAICIVLNVAELAYL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  201FTIFMIIVSGICMVLNVMELCYL
protein features
start (aa)end (aa)featuredetails 
185215HELIXlost
193215TRANSMEMHelical; (Potential).lost
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 605
cDNA position
(for ins/del: last normal base / first normal base)
743
gDNA position
(for ins/del: last normal base / first normal base)
3922
chromosomal position
(for ins/del: last normal base / first normal base)
20763116
original gDNA sequence snippet GATTGCAGTGTCTGGAATTTGCATCCTGCTGAATGTCACTG
altered gDNA sequence snippet GATTGCAGTGTCTGGAATTTTCATCCTGCTGAATGTCACTG
original cDNA sequence snippet GATTGCAGTGTCTGGAATTTGCATCCTGCTGAATGTCACTG
altered cDNA sequence snippet GATTGCAGTGTCTGGAATTTTCATCCTGCTGAATGTCACTG
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 ISHIRLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG IFILLNVTEL CYLLIRYCSG KSKKPV*
speed 0.72 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: 0.99999999999291 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM001172)
  • known disease mutation: rs17018 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20763116C>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.605G>T
cDNA.804G>T
g.3922G>T
AA changes C202F Score: 205 explain score(s)
position(s) of altered AA
if AA alteration in CDS
202
frameshift no
known variant Reference ID: rs104894406
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs17018 (pathogenic for Deafness, autosomal dominant 3a) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001172)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001172)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001172)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4271
6.2481
(flanking)5.1591
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased3932wt: 0.36 / mu: 0.60wt: TCTGGAATTTGCATCCTGCTGAATGTCACTGAATTGTGTTA
mu: TCTGGAATTTTCATCCTGCTGAATGTCACTGAATTGTGTTA
 gctg|AATG
Acc increased3933wt: 0.22 / mu: 0.65wt: CTGGAATTTGCATCCTGCTGAATGTCACTGAATTGTGTTAT
mu: CTGGAATTTTCATCCTGCTGAATGTCACTGAATTGTGTTAT
 ctga|ATGT
Acc gained39280.51mu: AGTGTCTGGAATTTTCATCCTGCTGAATGTCACTGAATTGT tcct|GCTG
Acc gained39300.35mu: TGTCTGGAATTTTCATCCTGCTGAATGTCACTGAATTGTGT ctgc|TGAA
distance from splice site 804
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      202FTVFMIAVSGICILLNVTELCYLL
mutated  not conserved    202FTVFMIAVSGIFILLNVTELCYL
Ptroglodytes  all identical  ENSPTRG00000031248  202FTVFMIAVSGICILLNVTELCYL
Mmulatta  all identical  ENSMMUG00000010522  202FTVFMIAVSGICILLNVTELCYL
Fcatus  all identical  ENSFCAG00000006961  202FTVFMIAVSGICILLNVTELCYL
Mmusculus  all identical  ENSMUSG00000046352  202FTVFMISVSGICILLNITELCYL
Ggallus  all identical  ENSGALG00000017136  202FTIFMIAVSSICILLNVAELCYL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000042707  204FTIFMVGSSAICIVLNVAELAYL
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000026112  201FTIFMIIVSGICMVLNVMELCYL
protein features
start (aa)end (aa)featuredetails 
185215HELIXlost
193215TRANSMEMHelical; (Potential).lost
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 605
cDNA position
(for ins/del: last normal base / first normal base)
804
gDNA position
(for ins/del: last normal base / first normal base)
3922
chromosomal position
(for ins/del: last normal base / first normal base)
20763116
original gDNA sequence snippet GATTGCAGTGTCTGGAATTTGCATCCTGCTGAATGTCACTG
altered gDNA sequence snippet GATTGCAGTGTCTGGAATTTTCATCCTGCTGAATGTCACTG
original cDNA sequence snippet GATTGCAGTGTCTGGAATTTGCATCCTGCTGAATGTCACTG
altered cDNA sequence snippet GATTGCAGTGTCTGGAATTTTCATCCTGCTGAATGTCACTG
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 ISHIRLWALQ LIFVSTPALL VAMHVAYRRH EKKRKFIKGE IKSEFKDIEE
IKTQKVRIEG SLWWTYTSSI FFRVIFEAAF MYVFYVMYDG FSMQRLVKCN AWPCPNTVDC
FVSRPTEKTV FTVFMIAVSG IFILLNVTEL CYLLIRYCSG KSKKPV*
speed 1.42 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