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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: ENST00000382114
MT speed 1.44 s - this script 5.216307 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
LGI2polymorphism_automatic0.973561168075257simple_aaeaffectedG61Ssingle base exchangers74901868show file

Taster files

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documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0264388319247426 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr4:25032135C>TN/A show variant in all transcripts   IGV
HGNC symbol LGI2
Ensembl transcript ID ENST00000382114
Genbank transcript ID NM_018176
UniProt peptide Q8N0V4
alteration type single base exchange
alteration region CDS
DNA changes c.181G>A
cDNA.367G>A
g.367G>A
AA changes G61S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS
61
frameshift no
known variant Reference ID: rs74901868
databasehomozygous (T/T)heterozygousallele carriers
1000G82737819
ExAC10061089911905
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7971
1.251
(flanking)0.1070.999
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased367wt: 0.83 / mu: 0.99wt: TGCCGGGCGACATCA
mu: TGCCGAGCGACATCA
 CCGG|gcga
Donor gained3620.98mu: GATCGTGCCGAGCGA TCGT|gccg
distance from splice site 17
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      61VGSSWVPRIVPGDISSLSLVNGTF
mutated  not conserved    61SDISSLSLVNGT
Ptroglodytes  all identical  ENSPTRG00000015958  61GDISSLSLVNGT
Mmulatta  all identical  ENSMMUG00000009154  61GDISSLSLVNGT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000039252  58GDISSLSLVNGT
Ggallus  not conserved  ENSGALG00000014389  42MGAAGAPRSLPAGFGSLSLVNGT
Trubripes  all identical  ENSTRUG00000006766  80VGISSVPRSPPGDIGSLSIVNGT
Drerio  not conserved  ENSDARG00000089957  52VGSSYVPRYIPNDVSSLSIVNGT
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000002120  95GDISSLSLVNGT
protein features
start (aa)end (aa)featuredetails 
2965DOMAINLRRNT.lost
7070CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
86107REPEATLRR 1.might get lost (downstream of altered splice site)
110131REPEATLRR 2.might get lost (downstream of altered splice site)
134155REPEATLRR 3.might get lost (downstream of altered splice site)
167217DOMAINLRRCT.might get lost (downstream of altered splice site)
186186CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
218261REPEATEAR 1.might get lost (downstream of altered splice site)
264307REPEATEAR 2.might get lost (downstream of altered splice site)
271271CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
310358REPEATEAR 3.might get lost (downstream of altered splice site)
359403REPEATEAR 4.might get lost (downstream of altered splice site)
402402CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
406450REPEATEAR 5.might get lost (downstream of altered splice site)
451494REPEATEAR 6.might get lost (downstream of altered splice site)
497540REPEATEAR 7.might get lost (downstream of altered splice site)
524524CONFLICTF -> L (in Ref. 2; CAD32305 and 5; BAB67809).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1638 / 1638
position (AA) of stopcodon in wt / mu AA sequence 546 / 546
position of stopcodon in wt / mu cDNA 1824 / 1824
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 187 / 187
chromosome 4
strand -1
last intron/exon boundary 1007
theoretical NMD boundary in CDS 770
length of CDS 1638
coding sequence (CDS) position 181
cDNA position
(for ins/del: last normal base / first normal base)
367
gDNA position
(for ins/del: last normal base / first normal base)
367
chromosomal position
(for ins/del: last normal base / first normal base)
25032135
original gDNA sequence snippet GGGTGCCCAGGATCGTGCCGGGCGACATCAGCTCCCTGTGA
altered gDNA sequence snippet GGGTGCCCAGGATCGTGCCGAGCGACATCAGCTCCCTGTGA
original cDNA sequence snippet GGGTGCCCAGGATCGTGCCGGGCGACATCAGCTCCCTGAGC
altered cDNA sequence snippet GGGTGCCCAGGATCGTGCCGAGCGACATCAGCTCCCTGAGC
wildtype AA sequence MALRRGGCGA LGLLLLLLGA ACLIPRSAQV RRLARCPATC SCTKESIICV GSSWVPRIVP
GDISSLSLVN GTFSEIKDRM FSHLPSLQLL LLNSNSFTII RDDAFAGLFH LEYLFIEGNK
IETISRNAFR GLRDLTHLSL ANNHIKALPR DVFSDLDSLI ELDLRGNKFE CDCKAKWLYL
WLKMTNSTVS DVLCIGPPEY QEKKLNDVTS FDYECTTTDF VVHQTLPYQS VSVDTFNSKN
DVYVAIAQPS MENCMVLEWD HIEMNFRSYD NITGQSIVGC KAILIDDQVF VVVAQLFGGS
HIYKYDESWT KFVKFQDIEV SRISKPNDIE LFQIDDETFF VIADSSKAGL STVYKWNSKG
FYSYQSLHEW FRDTDAEFVD IDGKSHLILS SRSQVPIILQ WNKSSKKFVP HGDIPNMEDV
LAVKSFRMQN TLYLSLTRFI GDSRVMRWNS KQFVEIQALP SRGAMTLQPF SFKDNHYLAL
GSDYTFSQIY QWDKEKQLFK KFKEIYVQAP RSFTAVSTDR RDFFFASSFK GKTKIFEHII
VDLSL*
mutated AA sequence MALRRGGCGA LGLLLLLLGA ACLIPRSAQV RRLARCPATC SCTKESIICV GSSWVPRIVP
SDISSLSLVN GTFSEIKDRM FSHLPSLQLL LLNSNSFTII RDDAFAGLFH LEYLFIEGNK
IETISRNAFR GLRDLTHLSL ANNHIKALPR DVFSDLDSLI ELDLRGNKFE CDCKAKWLYL
WLKMTNSTVS DVLCIGPPEY QEKKLNDVTS FDYECTTTDF VVHQTLPYQS VSVDTFNSKN
DVYVAIAQPS MENCMVLEWD HIEMNFRSYD NITGQSIVGC KAILIDDQVF VVVAQLFGGS
HIYKYDESWT KFVKFQDIEV SRISKPNDIE LFQIDDETFF VIADSSKAGL STVYKWNSKG
FYSYQSLHEW FRDTDAEFVD IDGKSHLILS SRSQVPIILQ WNKSSKKFVP HGDIPNMEDV
LAVKSFRMQN TLYLSLTRFI GDSRVMRWNS KQFVEIQALP SRGAMTLQPF SFKDNHYLAL
GSDYTFSQIY QWDKEKQLFK KFKEIYVQAP RSFTAVSTDR RDFFFASSFK GKTKIFEHII
VDLSL*
speed 1.44 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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