Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.9999999982576 (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) chr12:105583877G>AN/A show variant in all transcripts   IGV
HGNC symbol APPL2
Ensembl transcript ID ENST00000539978
Genbank transcript ID N/A
UniProt peptide Q8NEU8
alteration type single base exchange
alteration region CDS
DNA changes c.1169C>T
cDNA.1604C>T
g.46140C>T
AA changes A390V Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 390
frameshift no
known variant Reference ID: rs2272495
databasehomozygous (A/A)heterozygousallele carriers
1000G107724831
ExAC26051940222007
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1860
1.4880.003
(flanking)0.430.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased46143wt: 0.24 / mu: 0.33wt: AGCAACAGCCAGTCT
mu: AGTAACAGCCAGTCT		 CAAC|agcc
Donor increased46133wt: 0.81 / mu: 0.93wt: TTGTTCCCAAAGCAA
mu: TTGTTCCCAAAGTAA		 GTTC|ccaa
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      390MENENDKIVPKATASLPEAEELIA
mutated  not conserved    390MENENDKIVPKVTASLPEAEELI
Ptroglodytes  all identical  ENSPTRG00000005384  433MENENDKIVPKATARLPEAEELI
Mmulatta  all identical  ENSMMUG00000009524  420MENENDKIVPNATASLPEAEELI
Fcatus  all identical  ENSFCAG00000001461  430-ETEDDKIVSQAAVRADDADELI
Mmusculus  all identical  ENSMUSG00000020263  433IEDDN--IVPKATASIPETEELI
Ggallus  not conserved  ENSGALG00000012665  433-PTDNGKTTPSESAGIQDSTQLI
Trubripes  not conserved  ENSTRUG00000016642  432LHTSSG---GSQTGAALEPEDLI
Drerio  all conserved  ENSDARG00000078139  432LPVTSQE-AEKSSVSL-EPEDLI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  not conserved  ENSXETG00000001888  433PQSATSGSATEEPLHECEPEQLI
protein features
start (aa)end (aa)featuredetails 
1428REGIONRequired for RAB5A binding (By similarity).lost
448448CONFLICTT -> A (in Ref. 2).might get lost (downstream of altered splice site)
488637DOMAINPID.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1866 / 1866
position (AA) of stopcodon in wt / mu AA sequence 622 / 622
position of stopcodon in wt / mu cDNA 2301 / 2301
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 436 / 436
chromosome 12
strand -1
last intron/exon boundary 2167
theoretical NMD boundary in CDS 1681
length of CDS 1866
coding sequence (CDS) position 1169
cDNA position
(for ins/del: last normal base / first normal base)		 1604
gDNA position
(for ins/del: last normal base / first normal base)		 46140
chromosomal position
(for ins/del: last normal base / first normal base)		 105583877
original gDNA sequence snippet TGACAAGATTGTTCCCAAAGCAACAGCCAGTCTACCTGAAG
altered gDNA sequence snippet TGACAAGATTGTTCCCAAAGTAACAGCCAGTCTACCTGAAG
original cDNA sequence snippet TGACAAGATTGTTCCCAAAGCAACAGCCAGTCTACCTGAAG
altered cDNA sequence snippet TGACAAGATTGTTCCCAAAGTAACAGCCAGTCTACCTGAAG
wildtype AA sequence MQRVYGAQNE MCLATQQLSK QLLAYEKQNF ALGKGDEEVI STLHYFSKVV DELNLLHTEL
AKQLADTMVL PIIQFREKDL TEVSTLKDLF GLASNEHDLS MAKYSRLPKK KENEKVKTEV
GKEVAAARRK QHLSSLQYYC ALNALQYRKQ MAMMEPMIGF AHGQINFFKK GAEMFSKRMD
SFLSSVADMV QSIQVELEAE AEKMRVSQQE LLSVDESVYT PDSDVAAPQI NRNLIQKAGY
LNLRNKTGLV TTTWERLYFF TQGGNLMCQP RGAVAGGLIQ DLDNCSVMAV DCEDRRYCFQ
ITTPNGKSGI ILQAESRKEN EEWICAINNI SRQIYLTDNP EAVAIKLNQT ALQAVTPITS
FGKKQESSCP SQNLKNSEME NENDKIVPKA TASLPEAEEL IAPGTPIQFD IVLPATEFLD
QNRGSRRTNP FGETEDESFP EAEDSLLQQM FIVRFLGSMA VKTDSTTEVI YEAMRQVLAA
RAIHNIFRMT ESHLMVTSQS LRLIDPQTQV SRANFELTSV TQFAAHQENK RLVGFVIRVP
ESTGEESLST YIFESNSEGE KICYAINLGK EIIEVQKDPE ALAQLMLSIP LTNDGKYVLL
NDQPDDDDGN PNEHRGAESE A*
mutated AA sequence MQRVYGAQNE MCLATQQLSK QLLAYEKQNF ALGKGDEEVI STLHYFSKVV DELNLLHTEL
AKQLADTMVL PIIQFREKDL TEVSTLKDLF GLASNEHDLS MAKYSRLPKK KENEKVKTEV
GKEVAAARRK QHLSSLQYYC ALNALQYRKQ MAMMEPMIGF AHGQINFFKK GAEMFSKRMD
SFLSSVADMV QSIQVELEAE AEKMRVSQQE LLSVDESVYT PDSDVAAPQI NRNLIQKAGY
LNLRNKTGLV TTTWERLYFF TQGGNLMCQP RGAVAGGLIQ DLDNCSVMAV DCEDRRYCFQ
ITTPNGKSGI ILQAESRKEN EEWICAINNI SRQIYLTDNP EAVAIKLNQT ALQAVTPITS
FGKKQESSCP SQNLKNSEME NENDKIVPKV TASLPEAEEL IAPGTPIQFD IVLPATEFLD
QNRGSRRTNP FGETEDESFP EAEDSLLQQM FIVRFLGSMA VKTDSTTEVI YEAMRQVLAA
RAIHNIFRMT ESHLMVTSQS LRLIDPQTQV SRANFELTSV TQFAAHQENK RLVGFVIRVP
ESTGEESLST YIFESNSEGE KICYAINLGK EIIEVQKDPE ALAQLMLSIP LTNDGKYVLL
NDQPDDDDGN PNEHRGAESE A*
speed 1.21 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