Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999945 (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) chr7:157931144C>TN/A show variant in all transcripts   IGV
HGNC symbol PTPRN2
Ensembl transcript ID ENST00000404321
Genbank transcript ID N/A
UniProt peptide Q92932
alteration type single base exchange
alteration region CDS
DNA changes c.1043G>A
cDNA.1043G>A
g.449337G>A
AA changes S348N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 348
frameshift no
known variant Reference ID: rs1130499
databasehomozygous (T/T)heterozygousallele carriers
1000G36911411510
ExAC75371769325230
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.1930
0.4140.007
(flanking)0.4850.015
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased449341wt: 0.28 / mu: 0.58wt: AGTGGCCTGGAGCTG
mu: AATGGCCTGGAGCTG		 TGGC|ctgg
distance from splice site 64
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      348LQRQPAEVRGLSGLELDGMAELMA
mutated  all conserved    348LQRQPAEVRGLNGLELDGMAELM
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  not conserved  ENSFCAG00000007989  282--------------------EAM
Mmusculus  not conserved  ENSMUSG00000056553  318LQ-QNSEVDRLGPLK-EEKADSV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000035970  314LGRQSVNVDTLTPK
Dmelanogaster  no alignment  FBgn0031294  n/a
Celegans  no alignment  B0244.2  n/a
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
22615TOPO_DOMExtracellular (Potential).lost
427428SITECleavage (Potential).might get lost (downstream of altered splice site)
564564CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
616636TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
6371015TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
692692MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
725738HELIXmight get lost (downstream of altered splice site)
742754HELIXmight get lost (downstream of altered splice site)
7451005DOMAINTyrosine-protein phosphatase.might get lost (downstream of altered splice site)
763766TURNmight get lost (downstream of altered splice site)
768770TURNmight get lost (downstream of altered splice site)
771773HELIXmight get lost (downstream of altered splice site)
783785HELIXmight get lost (downstream of altered splice site)
791793TURNmight get lost (downstream of altered splice site)
795797STRANDmight get lost (downstream of altered splice site)
802806STRANDmight get lost (downstream of altered splice site)
811813STRANDmight get lost (downstream of altered splice site)
815819STRANDmight get lost (downstream of altered splice site)
824826HELIXmight get lost (downstream of altered splice site)
827836HELIXmight get lost (downstream of altered splice site)
841844STRANDmight get lost (downstream of altered splice site)
848850STRANDmight get lost (downstream of altered splice site)
862868STRANDmight get lost (downstream of altered splice site)
871882STRANDmight get lost (downstream of altered splice site)
885894STRANDmight get lost (downstream of altered splice site)
895898TURNmight get lost (downstream of altered splice site)
899908STRANDmight get lost (downstream of altered splice site)
913913BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
920934HELIXmight get lost (downstream of altered splice site)
941944STRANDmight get lost (downstream of altered splice site)
945945ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
945945MUTAGENC->S: Loss of activity.might get lost (downstream of altered splice site)
945951REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
946949STRANDmight get lost (downstream of altered splice site)
950966HELIXmight get lost (downstream of altered splice site)
970970MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
974982HELIXmight get lost (downstream of altered splice site)
977977MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
990990BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
9921010HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3117 / 3117
position (AA) of stopcodon in wt / mu AA sequence 1039 / 1039
position of stopcodon in wt / mu cDNA 3117 / 3117
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 1 / 1
chromosome 7
strand -1
last intron/exon boundary 3046
theoretical NMD boundary in CDS 2995
length of CDS 3117
coding sequence (CDS) position 1043
cDNA position
(for ins/del: last normal base / first normal base)		 1043
gDNA position
(for ins/del: last normal base / first normal base)		 449337
chromosomal position
(for ins/del: last normal base / first normal base)		 157931144
original gDNA sequence snippet GGCTGAGGTGAGGGGCCTGAGTGGCCTGGAGCTGGACGGCA
altered gDNA sequence snippet GGCTGAGGTGAGGGGCCTGAATGGCCTGGAGCTGGACGGCA
original cDNA sequence snippet GGCTGAGGTGAGGGGCCTGAGTGGCCTGGAGCTGGACGGCA
altered cDNA sequence snippet GGCTGAGGTGAGGGGCCTGAATGGCCTGGAGCTGGACGGCA
wildtype AA sequence MAVESEYSLL RTEASFPTMK MFCVSHTLPR VEVMFVSGPQ TRERTEPVDP RWQCLVQMWA
GCLLEEGLCG ASEACVNDGV FGRCQKVPAM DFYRYEVSPV ALQRLRVALQ KLSGTGFTWQ
DDYTQYVMDQ ELADLPKTYL RRPEASSPAR PSKHSVGSER RYSREGGAAL ANALRRHLPF
LEALSQAPAS DVLARTHTAQ DRPPAEGDDR FSESILTYVA HTSALTYPPG SRTQLREDLL
PRTLGQLQPD ELSPKVDSGV DRHHLMAALS AYAAQRPPAP PGEGSLEPQY LLRAPSRMPR
PLLAPAAPQK WPSPLGDSED PSSTGDGARI HTLLKDLQRQ PAEVRGLSGL ELDGMAELMA
GLMQGVDHGV ARGSPGRAAL GESGEQADGP KATLRGDSFP DDGVQDDDDR LYQEVHRLSA
TLGGLLQDHG SRLLPGALPF ARPLDMERKK SEHPESSLSS EEETAGVENV KSQTYSKDLL
GQQPHSEPGA AAFGELQNQM PGPSKEEQSL PAGAQEALSD GLQLEVQPSE EEARGYIVTD
RDPLRPEEGR RLVEDVARLL QVPSSAFADV EVLGPAVTFK VSANVQNVTT EDVEKATVDN
KDKLEETSGL KILQTGVGSK SKLKFLPPQA EQEDSTKFIA LTLVSLACIL GVLLASGLIY
CLRHSSQHRL KEKLSGLGGD PGADATAAYQ ELCRQRMATR PPDRPEGPHT SRISSVSSQF
SDGPIPSPSA RSSASSWSEE PVQSNMDIST GHMILSYMED HLKNKNRLEK EWEALCAYQA
EPNSSFVAQR EENVPKNRSL AVLTYDHSRV LLKAENSHSH SDYINASPIM DHDPRNPAYI
ATQGPLPATV ADFWQMVWES GCVVIVMLTP LAENGVRQCY HYWPDEGSNL YHIYEVNLVS
EHIWCEDFLV RSFYLKNLQT NETRTVTQFH FLSWYDRGVP SSSRSLLDFR RKVNKCYRGR
SCPIIVHCSD GAGRSGTYVL IDMVLNKMAK GAKEIDIAAT LEHLRDQRPG MVQTKEQFEF
ALTAVAEEVN AILKALPQ*
mutated AA sequence MAVESEYSLL RTEASFPTMK MFCVSHTLPR VEVMFVSGPQ TRERTEPVDP RWQCLVQMWA
GCLLEEGLCG ASEACVNDGV FGRCQKVPAM DFYRYEVSPV ALQRLRVALQ KLSGTGFTWQ
DDYTQYVMDQ ELADLPKTYL RRPEASSPAR PSKHSVGSER RYSREGGAAL ANALRRHLPF
LEALSQAPAS DVLARTHTAQ DRPPAEGDDR FSESILTYVA HTSALTYPPG SRTQLREDLL
PRTLGQLQPD ELSPKVDSGV DRHHLMAALS AYAAQRPPAP PGEGSLEPQY LLRAPSRMPR
PLLAPAAPQK WPSPLGDSED PSSTGDGARI HTLLKDLQRQ PAEVRGLNGL ELDGMAELMA
GLMQGVDHGV ARGSPGRAAL GESGEQADGP KATLRGDSFP DDGVQDDDDR LYQEVHRLSA
TLGGLLQDHG SRLLPGALPF ARPLDMERKK SEHPESSLSS EEETAGVENV KSQTYSKDLL
GQQPHSEPGA AAFGELQNQM PGPSKEEQSL PAGAQEALSD GLQLEVQPSE EEARGYIVTD
RDPLRPEEGR RLVEDVARLL QVPSSAFADV EVLGPAVTFK VSANVQNVTT EDVEKATVDN
KDKLEETSGL KILQTGVGSK SKLKFLPPQA EQEDSTKFIA LTLVSLACIL GVLLASGLIY
CLRHSSQHRL KEKLSGLGGD PGADATAAYQ ELCRQRMATR PPDRPEGPHT SRISSVSSQF
SDGPIPSPSA RSSASSWSEE PVQSNMDIST GHMILSYMED HLKNKNRLEK EWEALCAYQA
EPNSSFVAQR EENVPKNRSL AVLTYDHSRV LLKAENSHSH SDYINASPIM DHDPRNPAYI
ATQGPLPATV ADFWQMVWES GCVVIVMLTP LAENGVRQCY HYWPDEGSNL YHIYEVNLVS
EHIWCEDFLV RSFYLKNLQT NETRTVTQFH FLSWYDRGVP SSSRSLLDFR RKVNKCYRGR
SCPIIVHCSD GAGRSGTYVL IDMVLNKMAK GAKEIDIAAT LEHLRDQRPG MVQTKEQFEF
ALTAVAEEVN AILKALPQ*
speed 1.43 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