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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: ENST00000366714
MT speed 0 s - this script 2.483054 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
GJC2disease_causing_automatic0.999988914478572simple_aaeaffected0P90Ssingle base exchangers74315312show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999988914478572 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM041776)
  • known disease mutation: rs2072 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:228345727C>TN/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.268C>T
cDNA.443C>T
g.8175C>T
AA changes P90S Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 90
frameshift no
known variant Reference ID: rs74315312
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs2072 (pathogenic for Leukodystrophy, hypomyelinating, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM041776)

known disease mutation at this position, please check HGMD for details (HGMD ID CM041776)
known disease mutation at this position, please check HGMD for details (HGMD ID CM041776)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.040.986
2.7520.997
(flanking)2.9030.99
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8185wt: 0.43 / mu: 0.72wt: CATCTCCACGCCCTCGGTCATGTACCTGGGCTACGCCGTGC
mu: CATCTCCACGTCCTCGGTCATGTACCTGGGCTACGCCGTGC		 tcat|GTAC
Acc increased8180wt: 0.68 / mu: 0.76wt: GTGGTCATCTCCACGCCCTCGGTCATGTACCTGGGCTACGC
mu: GTGGTCATCTCCACGTCCTCGGTCATGTACCTGGGCTACGC		 ctcg|GTCA
Acc marginally increased8181wt: 0.2381 / mu: 0.2412 (marginal change - not scored)wt: TGGTCATCTCCACGCCCTCGGTCATGTACCTGGGCTACGCC
mu: TGGTCATCTCCACGTCCTCGGTCATGTACCTGGGCTACGCC		 tcgg|TCAT
Acc marginally increased8173wt: 0.8764 / mu: 0.9340 (marginal change - not scored)wt: CCAGATTGTGGTCATCTCCACGCCCTCGGTCATGTACCTGG
mu: CCAGATTGTGGTCATCTCCACGTCCTCGGTCATGTACCTGG		 ccac|GCCC
Acc marginally increased8184wt: 0.2844 / mu: 0.3291 (marginal change - not scored)wt: TCATCTCCACGCCCTCGGTCATGTACCTGGGCTACGCCGTG
mu: TCATCTCCACGTCCTCGGTCATGTACCTGGGCTACGCCGTG		 gtca|TGTA
Donor marginally increased8180wt: 0.9913 / mu: 0.9918 (marginal change - not scored)wt: CCCTCGGTCATGTAC
mu: TCCTCGGTCATGTAC		 CTCG|gtca
Donor gained81680.84mu: GTCATCTCCACGTCC CATC|tcca
distance from splice site 287
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      90FWVFQIVVISTPSVMYLGYAVHRL
mutated  not conserved    90FWVFQIVVISTSSVMYLGYAVHR
Ptroglodytes  all identical  ENSPTRG00000002070  90FWVFQIVVISTPSVMYLGYAVHR
Mmulatta  all identical  ENSMMUG00000023086  90FWVFQIVVISTPSVMYLGYAVHR
Fcatus  all identical  ENSFCAG00000007130  90FWVFQIVVISTPSVMYLGYAVHR
Mmusculus  all identical  ENSMUSG00000043448  90FWVFQIVVISTPSVMYLGYAVHR
Ggallus  all identical  ENSGALG00000005331  87FWVFQIIMISTPSVMYLGYAIHR
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000073896  87FWVFQIIMISTPSVMYLGYAIHK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000006175  90FWVFQIIMISAPSVMYLGYAIHR
protein features
start (aa)end (aa)featuredetails 
7999TRANSMEMHelical; (Potential).lost
100216TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
143176COMPBIASGlu-rich.might get lost (downstream of altered splice site)
217237TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
238265TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
252252CONFLICTH -> Q (in Ref. 1; AAB94511).might get lost (downstream of altered splice site)
266286TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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 268
cDNA position
(for ins/del: last normal base / first normal base)		 443
gDNA position
(for ins/del: last normal base / first normal base)		 8175
chromosomal position
(for ins/del: last normal base / first normal base)		 228345727
original gDNA sequence snippet AGATTGTGGTCATCTCCACGCCCTCGGTCATGTACCTGGGC
altered gDNA sequence snippet AGATTGTGGTCATCTCCACGTCCTCGGTCATGTACCTGGGC
original cDNA sequence snippet AGATTGTGGTCATCTCCACGCCCTCGGTCATGTACCTGGGC
altered cDNA sequence snippet AGATTGTGGTCATCTCCACGTCCTCGGTCATGTACCTGGGC
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 VFQIVVISTS 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*
speed 0.41 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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