Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999672758 (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) chr19:55143157G>AN/A show variant in all transcripts   IGV
HGNC symbol LILRB1
Ensembl transcript ID ENST00000427581
Genbank transcript ID N/A
UniProt peptide Q8NHL6
alteration type single base exchange
alteration region CDS
DNA changes c.385G>A
cDNA.718G>A
g.57812G>A
AA changes A129T Score: 58 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 129
frameshift no
known variant Reference ID: rs12460501
databasehomozygous (A/A)heterozygousallele carriers
1000G191689880
ExAC29091697819887
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.480.011
-0.0420.034
(flanking)1.4870.103
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 increased57803wt: 0.7336 / mu: 0.8042 (marginal change - not scored)wt: TCCCCATCCCATCCATCACCTGGGAACATGCAGGGCGGTAT
mu: TCCCCATCCCATCCATCACCTGGGAACATACAGGGCGGTAT		 acct|GGGA
Donor increased57804wt: 0.73 / mu: 0.93wt: CACCTGGGAACATGC
mu: CACCTGGGAACATAC		 CCTG|ggaa
Donor marginally increased57814wt: 0.7674 / mu: 0.7820 (marginal change - not scored)wt: CATGCAGGGCGGTAT
mu: CATACAGGGCGGTAT		 TGCA|gggc
Donor increased57803wt: 0.42 / mu: 0.55wt: TCACCTGGGAACATG
mu: TCACCTGGGAACATA		 ACCT|ggga
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      129QFPIPSITWEHAGRYRCYYGSDTA
mutated  not conserved    129IPSITWEHTGRYRCYYGSDT
Ptroglodytes  all identical  ENSPTRG00000011467  93QFPIPPITWEDAGRYRCYYGSHT
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
24461TOPO_DOMExtracellular (Potential).lost
116221DOMAINIg-like C2-type 2.lost
126131STRANDlost
133136STRANDmight get lost (downstream of altered splice site)
141146STRANDmight get lost (downstream of altered splice site)
145145DISULFIDmight get lost (downstream of altered splice site)
152159STRANDmight get lost (downstream of altered splice site)
157157DISULFIDmight get lost (downstream of altered splice site)
167167DISULFIDmight get lost (downstream of altered splice site)
167169STRANDmight get lost (downstream of altered splice site)
172174HELIXmight get lost (downstream of altered splice site)
179184STRANDmight get lost (downstream of altered splice site)
193200STRANDmight get lost (downstream of altered splice site)
197197DISULFIDmight get lost (downstream of altered splice site)
204208STRANDmight get lost (downstream of altered splice site)
215220STRANDmight get lost (downstream of altered splice site)
222312DOMAINIg-like C2-type 3.might get lost (downstream of altered splice site)
246246DISULFIDPotential.might get lost (downstream of altered splice site)
281281CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
297297DISULFIDPotential.might get lost (downstream of altered splice site)
302302CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
313409DOMAINIg-like C2-type 4.might get lost (downstream of altered splice site)
341341CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
346346DISULFIDPotential.might get lost (downstream of altered splice site)
397397DISULFIDPotential.might get lost (downstream of altered splice site)
462482TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
483650TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
531536MOTIFITIM motif 1.might get lost (downstream of altered splice site)
533533MUTAGENY->F: Impairs receptor phosphorylation and abolishes inhibition of serotonin release. No effect on PTPN6 binding; when associated with F-562.might get lost (downstream of altered splice site)
533533MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
557557CONFLICTP -> L (in Ref. 4; AAL36989).might get lost (downstream of altered splice site)
560565MOTIFITIM motif 2.might get lost (downstream of altered splice site)
562562MUTAGENY->F: No effect on PTPN6 binding; when associated with F-533.might get lost (downstream of altered splice site)
612617MOTIFITIM motif 3.might get lost (downstream of altered splice site)
614614MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
614614MUTAGENY->F: No effect on PTPN6 binding. Abolishes PTPN6 binding; when associated with F-644.might get lost (downstream of altered splice site)
642647MOTIFITIM motif 4.might get lost (downstream of altered splice site)
644644MOD_RESPhosphotyrosine.might get lost (downstream of altered splice site)
644644MUTAGENY->F: Reduces PTPN6 binding. Abolishes PTPN6 binding; when associated with F- 614.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2106 / 2106
position (AA) of stopcodon in wt / mu AA sequence 702 / 702
position of stopcodon in wt / mu cDNA 2439 / 2439
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 334 / 334
chromosome 19
strand 1
last intron/exon boundary 2293
theoretical NMD boundary in CDS 1909
length of CDS 2106
coding sequence (CDS) position 385
cDNA position
(for ins/del: last normal base / first normal base)		 718
gDNA position
(for ins/del: last normal base / first normal base)		 57812
chromosomal position
(for ins/del: last normal base / first normal base)		 55143157
original gDNA sequence snippet CATCCATCACCTGGGAACATGCAGGGCGGTATCGCTGTTAC
altered gDNA sequence snippet CATCCATCACCTGGGAACATACAGGGCGGTATCGCTGTTAC
original cDNA sequence snippet CATCCATCACCTGGGAACATGCAGGGCGGTATCGCTGTTAC
altered cDNA sequence snippet CATCCATCACCTGGGAACATACAGGGCGGTATCGCTGTTAC
wildtype AA sequence MRRRTQPPIG HTLCVSLSCQ HRGLIHPQSR AVGGDAMTPI LTVLICLGLS LGPRTHVQAG
HLPKPTLWAE PGSVITQGSP VTLRCQGGQE TQEYRLYREK KTALWITRIP QELVKKGQFP
IPSITWEHAG RYRCYYGSDT AGRSESSDPL ELVVTGAYIK PTLSAQPSPV VNSGGNVILQ
CDSQVAFDGF SLCKEGEDEH PQCLNSQPHA RGSSRAIFSV GPVSPSRRWW YRCYAYDSNS
PYEWSLPSDL LELLVLGVSK KPSLSVQPGP IVAPEETLTL QCGSDAGYNR FVLYKDGERD
FLQLAGAQPQ AGLSQANFTL GPVSRSYGGQ YRCYGAHNLS SEWSAPSDPL DILIAGQFYD
RVSLSVQPGP TVASGENVTL LCQSQGWMQT FLLTKEGAAD DPWRLRSTYQ SQKYQAEFPM
GPVTSAHAGT YRCYGSQSSK PYLLTHPSDP LELVVSGPSG GPSSPTTGPT STSAGPEDQP
LTPTGSDPQS APGLGSGAGT RAAGLGRHLG VVIGILVAVI LLLLLLLLLF LILRHRRQGK
HWTSTQRKAD FQHPAGAVGP EPTDRGLQWR SSPAADAQEE NLYAAVKHTQ PEDGVEMDTR
QSPHDEDPQA VTYAEVKHSR PRREMASPPS PLSGEFLDTK DRQAEEDRQM DTEAAASEAP
QDVTYAQLHS LTLRREATEP PPSQEGPSPA VPSIYATLAI H*
mutated AA sequence MRRRTQPPIG HTLCVSLSCQ HRGLIHPQSR AVGGDAMTPI LTVLICLGLS LGPRTHVQAG
HLPKPTLWAE PGSVITQGSP VTLRCQGGQE TQEYRLYREK KTALWITRIP QELVKKGQFP
IPSITWEHTG RYRCYYGSDT AGRSESSDPL ELVVTGAYIK PTLSAQPSPV VNSGGNVILQ
CDSQVAFDGF SLCKEGEDEH PQCLNSQPHA RGSSRAIFSV GPVSPSRRWW YRCYAYDSNS
PYEWSLPSDL LELLVLGVSK KPSLSVQPGP IVAPEETLTL QCGSDAGYNR FVLYKDGERD
FLQLAGAQPQ AGLSQANFTL GPVSRSYGGQ YRCYGAHNLS SEWSAPSDPL DILIAGQFYD
RVSLSVQPGP TVASGENVTL LCQSQGWMQT FLLTKEGAAD DPWRLRSTYQ SQKYQAEFPM
GPVTSAHAGT YRCYGSQSSK PYLLTHPSDP LELVVSGPSG GPSSPTTGPT STSAGPEDQP
LTPTGSDPQS APGLGSGAGT RAAGLGRHLG VVIGILVAVI LLLLLLLLLF LILRHRRQGK
HWTSTQRKAD FQHPAGAVGP EPTDRGLQWR SSPAADAQEE NLYAAVKHTQ PEDGVEMDTR
QSPHDEDPQA VTYAEVKHSR PRREMASPPS PLSGEFLDTK DRQAEEDRQM DTEAAASEAP
QDVTYAQLHS LTLRREATEP PPSQEGPSPA VPSIYATLAI H*
speed 1.17 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