Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999998205 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr10:85981801T>GN/A show variant in all transcripts   IGV
HGNC symbol LRIT2
Ensembl transcript ID ENST00000538192
Genbank transcript ID N/A
UniProt peptide A6NDA9
alteration type single base exchange
alteration region CDS
DNA changes c.1558A>C
cDNA.1627A>C
g.3545A>C
AA changes T520P Score: 38 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 520
frameshift no
known variant Reference ID: rs6585847
databasehomozygous (G/G)heterozygousallele carriers
1000G83511101945
ExAC15107255317660
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4890.059
1.7470.059
(flanking)-0.340.009
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased3552wt: 0.20 / mu: 0.70wt: AGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCCAAGGATG
mu: AGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGATG		 ctgc|AGCC
Acc increased3554wt: 0.27 / mu: 0.64wt: CCCCCAGCTGCACCCCTGCAGCCCCGCAGTCCAAGGATGGC
mu: CCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGATGGC		 gcag|CCCC
Acc gained35500.56mu: AAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCCAAGGA ccct|GCAG
distance from splice site 636
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      520GCLHRRKAPSCTPAAPQSKDGSFR
mutated  not conserved    520GCLHRRKAPSCPPAAPQSKDGSF
Ptroglodytes  not conserved  ENSPTRG00000029854  520CCLHRRKAPSCPPAAPQSKDGSF
Mmulatta  not conserved  ENSMMUG00000000659  510YCLHCRKAPSCPPAAPQCRDGSF
Fcatus  not conserved  ENSFCAG00000001653  510CCPHRRKAPRCPRAVPQHRDCSY
Mmusculus  not conserved  ENSMUSG00000043418  510RCPLHRKTLRCPQAVPQCKDNSF
Ggallus  not conserved  ENSGALG00000002307  460CPAAWPRRRRG--
Trubripes  not conserved  ENSTRUG00000011830  471GCL-ERCVDLCKKHGTQGHNLRG
Drerio  not conserved  ENSDARG00000030626  509LWRNRRHAELSNPTG--DRQGTF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000005631  516LCRRKHKAQK-TLKKDNTKESTF
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1683 / 1683
position (AA) of stopcodon in wt / mu AA sequence 561 / 561
position of stopcodon in wt / mu cDNA 1752 / 1752
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 70 / 70
chromosome 10
strand -1
last intron/exon boundary 992
theoretical NMD boundary in CDS 872
length of CDS 1683
coding sequence (CDS) position 1558
cDNA position
(for ins/del: last normal base / first normal base)		 1627
gDNA position
(for ins/del: last normal base / first normal base)		 3545
chromosomal position
(for ins/del: last normal base / first normal base)		 85981801
original gDNA sequence snippet GCAGGAAAGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCC
altered gDNA sequence snippet GCAGGAAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCC
original cDNA sequence snippet GCAGGAAAGCCCCCAGCTGCACCCCTGCAGCCCCGCAGTCC
altered cDNA sequence snippet GCAGGAAAGCCCCCAGCTGCCCCCCTGCAGCCCCGCAGTCC
wildtype AA sequence MASVFHYFLL VLVFLDTHAA QPFCLPGCTC SEESFGRTLQ CTSVSLGKIP GNLSEEFKQV
RIENSPLFEM PQGSFINMST LEYLWLNFNN ISVIHLGALE HLPELRELRL EGNKLCSVPW
TAFRATPLLR VLDLKRNKID ALPELALQFL VSLTYLDLSS NRLTVVSKSV FLNWPAYQKC
RQPDCGAEIL SSLVVALHDN PWVCDCRLRG LVQFVKSITL PVILVNSYLI CQGPLSKAGQ
LFHETELSAC MKPQISTPSA NITIRAGQNV TLRCLAQASP SPSIAWTYPL SMWREFDGLL
GGKHLTPVLT SSTGEDTALS ELAIPAAHLV DSGNYTCMAS NSIGKSNLVI SLHVQPAQAL
HAPDSLSIPS EGNAYIDLRV VKQTVHGILL EWLAVADTSK EEWFTLYIAS DEAFRKEVVH
IGPGINTYAV DDLLPGTKYE ACLSLEGQPP HQGQCVAFVT GRDAGGLEAR EHLLHVTVVL
CVVLLAVPVG AYAWAAQGPC SCSKWVLRGC LHRRKAPSCT PAAPQSKDGS FREHPAVCDD
GEGHIDTEGD KEKGGTEDNS *
mutated AA sequence MASVFHYFLL VLVFLDTHAA QPFCLPGCTC SEESFGRTLQ CTSVSLGKIP GNLSEEFKQV
RIENSPLFEM PQGSFINMST LEYLWLNFNN ISVIHLGALE HLPELRELRL EGNKLCSVPW
TAFRATPLLR VLDLKRNKID ALPELALQFL VSLTYLDLSS NRLTVVSKSV FLNWPAYQKC
RQPDCGAEIL SSLVVALHDN PWVCDCRLRG LVQFVKSITL PVILVNSYLI CQGPLSKAGQ
LFHETELSAC MKPQISTPSA NITIRAGQNV TLRCLAQASP SPSIAWTYPL SMWREFDGLL
GGKHLTPVLT SSTGEDTALS ELAIPAAHLV DSGNYTCMAS NSIGKSNLVI SLHVQPAQAL
HAPDSLSIPS EGNAYIDLRV VKQTVHGILL EWLAVADTSK EEWFTLYIAS DEAFRKEVVH
IGPGINTYAV DDLLPGTKYE ACLSLEGQPP HQGQCVAFVT GRDAGGLEAR EHLLHVTVVL
CVVLLAVPVG AYAWAAQGPC SCSKWVLRGC LHRRKAPSCP PAAPQSKDGS FREHPAVCDD
GEGHIDTEGD KEKGGTEDNS *
speed 1.25 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