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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: ENST00000241125
MT speed 0 s - this script 2.146019 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJA3disease_causing_automatic0.999999954551694simple_aae0N63Ssingle base exchangers121917823show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999954551694 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990685)
  • known disease mutation: rs16978 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:20717240T>CN/A show variant in all transcripts   IGV
HGNC symbol GJA3
Ensembl transcript ID ENST00000241125
Genbank transcript ID NM_021954
UniProt peptide Q9Y6H8
alteration type single base exchange
alteration region CDS
DNA changes c.188A>G
cDNA.365A>G
g.17949A>G
AA changes N63S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 63
frameshift no
known variant Reference ID: rs121917823
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16978 (pathogenic for Zonular pulverulent cataract 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990685)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990685)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990685)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.481
4.9741
(flanking)4.9741
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 205
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      63FTCNTQQPGCENVCYDRAFPISHI
mutated  all conserved    63CESVCYDRAFPISH
Ptroglodytes  all identical  ENSPTRG00000005681  63CENVCYDRAFPISH
Mmulatta  all identical  ENSMMUG00000010524  63CENVCYDRAFPISH
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000048582  63CENVCYDRAFPISH
Ggallus  all identical  ENSGALG00000017137  63CENVCYDKAFPISH
Trubripes  all identical  ENSTRUG00000015739  63CENVCYDEAFPISH
Drerio  all identical  ENSDARG00000021889  63CENVCYDEAFPISH
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000002644  63CENVCYDKAFPISH
protein features
start (aa)end (aa)featuredetails 
4176TOPO_DOMExtracellular (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1308 / 1308
position (AA) of stopcodon in wt / mu AA sequence 436 / 436
position of stopcodon in wt / mu cDNA 1485 / 1485
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 178 / 178
chromosome 13
strand -1
last intron/exon boundary 161
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1308
coding sequence (CDS) position 188
cDNA position
(for ins/del: last normal base / first normal base)		 365
gDNA position
(for ins/del: last normal base / first normal base)		 17949
chromosomal position
(for ins/del: last normal base / first normal base)		 20717240
original gDNA sequence snippet CCAGCAGCCGGGCTGCGAGAACGTCTGCTACGACAGGGCCT
altered gDNA sequence snippet CCAGCAGCCGGGCTGCGAGAGCGTCTGCTACGACAGGGCCT
original cDNA sequence snippet CCAGCAGCCGGGCTGCGAGAACGTCTGCTACGACAGGGCCT
altered cDNA sequence snippet CCAGCAGCCGGGCTGCGAGAGCGTCTGCTACGACAGGGCCT
wildtype AA sequence MGDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEDVWGDEQS DFTCNTQQPG
CENVCYDRAF PISHIRFWAL QIIFVSTPTL IYLGHVLHIV RMEEKKKERE EEEQLKRESP
SPKEPPQDNP SSRDDRGRVR MAGALLRTYV FNIIFKTLFE VGFIAGQYFL YGFELKPLYR
CDRWPCPNTV DCFISRPTEK TIFIIFMLAV ACASLLLNML EIYHLGWKKL KQGVTSRLGP
DASEAPLGTA DPPPLPPSSR PPAVAIGFPP YYAHTAAPLG QARAVGYPGA PPPAADFKLL
ALTEARGKGQ SAKLYNGHHH LLMTEQNWAN QAAERQPPAL KAYPAASTPA APSPVGSSSP
PLAHEAEAGA APLLLDGSGS SLEGSALAGT PEEEEQAVTT AAQMHQPPLP LGDPGRASKA
SRASSGRARP EDLAI*
mutated AA sequence MGDWSFLGRL LENAQEHSTV IGKVWLTVLF IFRILVLGAA AEDVWGDEQS DFTCNTQQPG
CESVCYDRAF PISHIRFWAL QIIFVSTPTL IYLGHVLHIV RMEEKKKERE EEEQLKRESP
SPKEPPQDNP SSRDDRGRVR MAGALLRTYV FNIIFKTLFE VGFIAGQYFL YGFELKPLYR
CDRWPCPNTV DCFISRPTEK TIFIIFMLAV ACASLLLNML EIYHLGWKKL KQGVTSRLGP
DASEAPLGTA DPPPLPPSSR PPAVAIGFPP YYAHTAAPLG QARAVGYPGA PPPAADFKLL
ALTEARGKGQ SAKLYNGHHH LLMTEQNWAN QAAERQPPAL KAYPAASTPA APSPVGSSSP
PLAHEAEAGA APLLLDGSGS SLEGSALAGT PEEEEQAVTT AAQMHQPPLP LGDPGRASKA
SRASSGRARP EDLAI*
speed 0.15 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