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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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000282561
MT speed 0 s - this script 5.110569 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJA1disease_causing_automatic0.999999992028688simple_aaeaffected0Y17Ssingle base exchangers104893961show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999992028688 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030451)
  • known disease mutation: rs16982 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:121768043A>CN/A show variant in all transcripts   IGV
HGNC symbol GJA1
Ensembl transcript ID ENST00000282561
Genbank transcript ID NM_000165
UniProt peptide P17302
alteration type single base exchange
alteration region CDS
DNA changes c.50A>C
cDNA.207A>C
g.11206A>C
AA changes Y17S Score: 144 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 17
frameshift no
known variant Reference ID: rs104893961
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16982 (pathogenic for Oculodentodigital dysplasia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030451)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030451)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030451)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2421
5.3021
(flanking)0.511
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased11217wt: 0.34 / mu: 0.70wt: TTCAAGCCTACTCAACTGCTGGAGGGAAGGTGTGGCTGTCA
mu: TTCAAGCCTCCTCAACTGCTGGAGGGAAGGTGTGGCTGTCA		 gctg|GAGG
Acc gained112130.47mu: AAGGTTCAAGCCTCCTCAACTGCTGGAGGGAAGGTGTGGCT aact|GCTG
distance from splice site 66
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      17ALGKLLDKVQAYSTAGGKVWLSVL
mutated  not conserved    17ALGKLLDKVQASSTAGGKVWLSV
Ptroglodytes  all identical  ENSPTRG00000018560  17ALGKLLDKVQAYSTAGGKVWLSV
Mmulatta  all identical  ENSMMUG00000005225  17ALGKLLDKVQAYSTAGGKVWLSV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000050953  17ALGKLLDKVQAYSTAGGKVWLSV
Ggallus  all identical  ENSGALG00000014873  17ALGKLLDKVQAYSTAGGKVWLSV
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000041799  17ALGRLLDKVQAYSTAGGKVWLSV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000025411  17ALGRLLDKVQAYSTAGGKVWLSV
protein features
start (aa)end (aa)featuredetails 
1436TRANSMEMHelical; (Potential).lost
3776TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
5454DISULFIDmight get lost (downstream of altered splice site)
7799TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
100154TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
155177TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
178208TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
187187DISULFIDmight get lost (downstream of altered splice site)
192192DISULFIDmight get lost (downstream of altered splice site)
198198DISULFIDmight get lost (downstream of altered splice site)
209231TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
232382TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
240242HELIXmight get lost (downstream of altered splice site)
246253HELIXmight get lost (downstream of altered splice site)
247247MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
255257HELIXmight get lost (downstream of altered splice site)
262262MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
306306MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
313313MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
314314MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
325325MOD_RESPhosphoserine; by CK1.might get lost (downstream of altered splice site)
326326MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
328328MOD_RESPhosphoserine; by CK1.might get lost (downstream of altered splice site)
330330MOD_RESPhosphoserine; by CK1.might get lost (downstream of altered splice site)
365365MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
368368MOD_RESPhosphoserine; by PKC/PRKCG (By similarity).might get lost (downstream of altered splice site)
369369MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
373373MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1149 / 1149
position (AA) of stopcodon in wt / mu AA sequence 383 / 383
position of stopcodon in wt / mu cDNA 1306 / 1306
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 158 / 158
chromosome 6
strand 1
last intron/exon boundary 142
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1149
coding sequence (CDS) position 50
cDNA position
(for ins/del: last normal base / first normal base)		 207
gDNA position
(for ins/del: last normal base / first normal base)		 11206
chromosomal position
(for ins/del: last normal base / first normal base)		 121768043
original gDNA sequence snippet CCTTGACAAGGTTCAAGCCTACTCAACTGCTGGAGGGAAGG
altered gDNA sequence snippet CCTTGACAAGGTTCAAGCCTCCTCAACTGCTGGAGGGAAGG
original cDNA sequence snippet CCTTGACAAGGTTCAAGCCTACTCAACTGCTGGAGGGAAGG
altered cDNA sequence snippet CCTTGACAAGGTTCAAGCCTCCTCAACTGCTGGAGGGAAGG
wildtype AA sequence MGDWSALGKL LDKVQAYSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG
CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG
VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL LIQWYIYGFS
LSAVYTCKRD PCPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELFY VFFKGVKDRV
KGKSDPYHAT SGALSPAKDC GSQKYAYFNG CSSPTAPLSP MSPPGYKLVT GDRNNSSCRN
YNKQASEQNW ANYSAEQNRM GQAGSTISNS HAQPFDFPDD NQNSKKLAAG HELQPLAIVD
QRPSSRASSR ASSRPRPDDL EI*
mutated AA sequence MGDWSALGKL LDKVQASSTA GGKVWLSVLF IFRILLLGTA VESAWGDEQS AFRCNTQQPG
CENVCYDKSF PISHVRFWVL QIIFVSVPTL LYLAHVFYVM RKEEKLNKKE EELKVAQTDG
VNVDMHLKQI EIKKFKYGIE EHGKVKMRGG LLRTYIISIL FKSIFEVAFL LIQWYIYGFS
LSAVYTCKRD PCPHQVDCFL SRPTEKTIFI IFMLVVSLVS LALNIIELFY VFFKGVKDRV
KGKSDPYHAT SGALSPAKDC GSQKYAYFNG CSSPTAPLSP MSPPGYKLVT GDRNNSSCRN
YNKQASEQNW ANYSAEQNRM GQAGSTISNS HAQPFDFPDD NQNSKKLAAG HELQPLAIVD
QRPSSRASSR ASSRPRPDDL EI*
speed 1.35 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
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Problems