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MutationTaster - study a chromosomal position

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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: ENST00000366714
MT speed 1.81 s - this script 7.023516 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJC2disease_causing_automatic0.999999930371981simple_aaeaffected0Y272Dsingle base exchangers74315314show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999999930371981 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM041778)
  • known disease mutation: rs2075 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:228346273T>GN/A show variant in all transcripts   IGV
HGNC symbol GJC2
Ensembl transcript ID ENST00000366714
Genbank transcript ID NM_020435
UniProt peptide Q5T442
alteration type single base exchange
alteration region CDS
DNA changes c.814T>G
cDNA.989T>G
g.8721T>G
AA changes Y272D Score: 160 explain score(s)
position(s) of altered AA
if AA alteration in CDS
272
frameshift no
known variant Reference ID: rs74315314
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs2075 (pathogenic for Leukodystrophy, hypomyelinating, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM041778)

known disease mutation at this position, please check HGMD for details (HGMD ID CM041778)
known disease mutation at this position, please check HGMD for details (HGMD ID CM041778)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.6011
4.4331
(flanking)2.9231
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased8715wt: 0.5357 / mu: 0.5617 (marginal change - not scored)wt: AAAAGACGGTCTTCCTGCTGGTTATGTACGTGGTCAGCTGC
mu: AAAAGACGGTCTTCCTGCTGGTTATGGACGTGGTCAGCTGC
 ctgg|TTAT
Acc increased8714wt: 0.44 / mu: 0.58wt: GAAAAGACGGTCTTCCTGCTGGTTATGTACGTGGTCAGCTG
mu: GAAAAGACGGTCTTCCTGCTGGTTATGGACGTGGTCAGCTG
 gctg|GTTA
Donor increased8718wt: 0.80 / mu: 0.93wt: TGGTTATGTACGTGG
mu: TGGTTATGGACGTGG
 GTTA|tgta
distance from splice site 833
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      272PTEKTVFLLVMYVVSCLCLLLNLC
mutated  not conserved    272PTEKTVFLLVMDVVSCLCLLLNL
Ptroglodytes  all identical  ENSPTRG00000002070  272PTEKTVFLLVMYVVSCLCLLLNL
Mmulatta  all identical  ENSMMUG00000023086  272PTEKTVFLLVMYVVSCLCLLLNL
Fcatus  all identical  ENSFCAG00000007130  267PTEKTIFLLVMYVVSCLCLLLNL
Mmusculus  all identical  ENSMUSG00000043448  271PTEKTVFLLVMYVVSCLCLLLNL
Ggallus  all identical  ENSGALG00000005331  237PTEKTIFLLVMYVVSCLCLLLNM
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000073896  236PTEKTIFLLIMYVVSCLCLLLNV
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000006175  236PTEKTVFLLIMYVVSCLCLFLNV
protein features
start (aa)end (aa)featuredetails 
266286TRANSMEMHelical; (Potential).lost
287439TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
371371MOD_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 1320 / 1320
position (AA) of stopcodon in wt / mu AA sequence 440 / 440
position of stopcodon in wt / mu cDNA 1495 / 1495
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 176 / 176
chromosome 1
strand 1
last intron/exon boundary 157
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 1320
coding sequence (CDS) position 814
cDNA position
(for ins/del: last normal base / first normal base)
989
gDNA position
(for ins/del: last normal base / first normal base)
8721
chromosomal position
(for ins/del: last normal base / first normal base)
228346273
original gDNA sequence snippet CGGTCTTCCTGCTGGTTATGTACGTGGTCAGCTGCCTGTGC
altered gDNA sequence snippet CGGTCTTCCTGCTGGTTATGGACGTGGTCAGCTGCCTGTGC
original cDNA sequence snippet CGGTCTTCCTGCTGGTTATGTACGTGGTCAGCTGCCTGTGC
altered cDNA sequence snippet CGGTCTTCCTGCTGGTTATGGACGTGGTCAGCTGCCTGTGC
wildtype AA sequence MTNMSWSFLT RLLEEIHNHS TFVGKVWLTV LVVFRIVLTA VGGEAIYSDE QAKFTCNTRQ
PGCDNVCYDA FAPLSHVRFW VFQIVVISTP SVMYLGYAVH RLARASEQER RRALRRRPGP
RRAPRAHLPP PHAGWPEPAD LGEEEPMLGL GEEEEEEETG AAEGAGEEAE EAGAEEACTK
AVGADGKAAG TPGPTGQHDG RRRIQREGLM RVYVAQLVAR AAFEVAFLVG QYLLYGFEVR
PFFPCSRQPC PHVVDCFVSR PTEKTVFLLV MYVVSCLCLL LNLCEMAHLG LGSAQDAVRG
RRGPPASAPA PAPRPPPCAF PAAAAGLACP PDYSLVVRAA ERARAHDQNL ANLALQALRD
GAAAGDRDRD SSPCVGLPAA SRGPPRAGAP ASRTGSATSA GTVGEQGRPG THERPGAKPR
AGSEKGSASS RDGKTTVWI*
mutated AA sequence MTNMSWSFLT RLLEEIHNHS TFVGKVWLTV LVVFRIVLTA VGGEAIYSDE QAKFTCNTRQ
PGCDNVCYDA FAPLSHVRFW VFQIVVISTP SVMYLGYAVH RLARASEQER RRALRRRPGP
RRAPRAHLPP PHAGWPEPAD LGEEEPMLGL GEEEEEEETG AAEGAGEEAE EAGAEEACTK
AVGADGKAAG TPGPTGQHDG RRRIQREGLM RVYVAQLVAR AAFEVAFLVG QYLLYGFEVR
PFFPCSRQPC PHVVDCFVSR PTEKTVFLLV MDVVSCLCLL LNLCEMAHLG LGSAQDAVRG
RRGPPASAPA PAPRPPPCAF PAAAAGLACP PDYSLVVRAA ERARAHDQNL ANLALQALRD
GAAAGDRDRD SSPCVGLPAA SRGPPRAGAP ASRTGSATSA GTVGEQGRPG THERPGAKPR
AGSEKGSASS RDGKTTVWI*
speed 1.81 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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