Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999728047416 (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) chr14:39818145G>AN/A show variant in all transcripts   IGV
HGNC symbol MIA2
Ensembl transcript ID ENST00000396158
Genbank transcript ID NM_001247989
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.2227G>A
cDNA.2563G>A
g.83658G>A
AA changes G743R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 743
frameshift no
known variant Reference ID: rs1060878
databasehomozygous (A/A)heterozygousallele carriers
1000G25910381297
ExAC77341729925033
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3620.999
0.3260.999
(flanking)3.541
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased83655wt: 0.24 / mu: 0.37wt: CTTCTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCA
mu: CTTCTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCA		 ccac|CAGG
Acc marginally increased83658wt: 0.6961 / mu: 0.7634 (marginal change - not scored)wt: CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA
mu: CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA		 ccag|GGGA
Donor increased83658wt: 0.65 / mu: 0.95wt: CACCAGGGGATTTCC
mu: CACCAAGGGATTTCC		 CCAG|ggga
Donor increased83654wt: 0.22 / mu: 0.85wt: TTTCCACCAGGGGAT
mu: TTTCCACCAAGGGAT		 TCCA|ccag
Acc gained836600.60mu: CGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCACC aagg|GATT
Donor gained836530.94mu: TTTTCCACCAAGGGA TTCC|acca
distance from splice site 37
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      743MFGASRDYFPPGDFPGPPPAPFAM
mutated  not conserved    743MFGASRDYFPPRDFPGPPPAPFA
Ptroglodytes  not conserved  ENSPTRG00000006297  738MFGASRDYFPPRDFPGPPPAPFA
Mmulatta  not conserved  ENSMMUG00000021121  739MFGTSRDYFPPRDFPGPPHAPFA
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000021000  740IYAAPRDYFPPRDFPGPPLPPFP
Ggallus  not conserved  ENSGALG00000010189  1259IYG-PRECFPVRDL-GLPRPPLP
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000023516  625--DYFPP---RGPHVLPMG
Dmelanogaster  no alignment  FBgn0031842  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
502804COMPBIASPro-rich.lost
776776CONFLICTS -> F (in Ref. 2; AAN77610).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2430 / 2430
position (AA) of stopcodon in wt / mu AA sequence 810 / 810
position of stopcodon in wt / mu cDNA 2766 / 2766
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 337 / 337
chromosome 14
strand 1
last intron/exon boundary 2600
theoretical NMD boundary in CDS 2213
length of CDS 2430
coding sequence (CDS) position 2227
cDNA position
(for ins/del: last normal base / first normal base)		 2563
gDNA position
(for ins/del: last normal base / first normal base)		 83658
chromosomal position
(for ins/del: last normal base / first normal base)		 39818145
original gDNA sequence snippet CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA
altered gDNA sequence snippet CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA
original cDNA sequence snippet CTCGAGATTATTTTCCACCAGGGGATTTCCCAGGTCCACCA
altered cDNA sequence snippet CTCGAGATTATTTTCCACCAAGGGATTTCCCAGGTCCACCA
wildtype AA sequence MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEVE NQMATCEKLN RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS
LEDESKSLKS QVAEAKMTFK IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ
VSELNKQKVT FEDSKVHAEQ VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM
NSESENGAYL DNPPKGALKK LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK
NLQTEQASLQ SENTHFENEN QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS
KVDEKISHAT EELETYRKRA KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN
DLRKENAHNR QKLTETELKF ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL
SPPTLLEGPL RLSPLLPGGG GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL
SPPWDQDRRM MFPPPGQSYP DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM
PSEMESSRND TKDDLGNLNV PDSSLPAENE ATGPGFVPPP LAPIRGPLFP VDARGPFLRR
GPPFPPPPPG AMFGASRDYF PPGDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH
SEGRSEFPSG LIPPSNEPAT EHPEPQQET*
mutated AA sequence MEEPGVTPQP YLGLLLEELR RVVAALPEGM RPDSNLYGFP WELVICAAVV GFFAVLFFLW
RSFRSVRSRL YVGREKKLAL MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE
ATEAQSLEVE NQMATCEKLN RSNSELEDEI LCLEKELKEE KSKHSEQDEL MADISKRIQS
LEDESKSLKS QVAEAKMTFK IFQMNEERLK IAIKDALNEN SQLQESQKQL LQEAEVWKEQ
VSELNKQKVT FEDSKVHAEQ VLNDKESHIK TLTERLLKMK DWAAMLGEDI TDDDNLELEM
NSESENGAYL DNPPKGALKK LIHAAKLNAS LKTLEGERNQ IYIQLSEVDK TKEELTEHIK
NLQTEQASLQ SENTHFENEN QKLQQKLKVM TELYQENEMK LHRKLTVEEN YRLEKEEKLS
KVDEKISHAT EELETYRKRA KDLEEELERT IHSYQGQIIS HEKKAHDNWL AARNAERNLN
DLRKENAHNR QKLTETELKF ELLEKDPYAL DVPNTAFGRE HSPYGPSPLG WPSSETRAFL
SPPTLLEGPL RLSPLLPGGG GRGSRGPGNP LDHQITNERG ESSCDRLTDP HRAPSDTGSL
SPPWDQDRRM MFPPPGQSYP DSALPPQRQD RFCSNSGRLS GPAELRSFNM PSLDKMDGSM
PSEMESSRND TKDDLGNLNV PDSSLPAENE ATGPGFVPPP LAPIRGPLFP VDARGPFLRR
GPPFPPPPPG AMFGASRDYF PPRDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH
SEGRSEFPSG LIPPSNEPAT EHPEPQQET*
speed 0.99 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