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 ENST00000341749
Genbank transcript ID NM_203354
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.2176G>A
cDNA.2279G>A
g.83658G>A
AA changes G726R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 726
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      726MFGASRDYFPPGDFPGPPPAPFAM
mutated  not conserved    726DYFPPRDFPGPPPAPFA
Ptroglodytes  not conserved  ENSPTRG00000006297  738MFGASRDYFPPRDFP
Mmulatta  not conserved  ENSMMUG00000021121  739MFGTSRDYFPPRDF
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000021000  740RDYFPPRDFPGPPLPPFP
Ggallus  not conserved  ENSGALG00000010189  1259YG-PRECFPVRDL-GLPRPPLP
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000023516  623PP---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 2379 / 2379
position (AA) of stopcodon in wt / mu AA sequence 793 / 793
position of stopcodon in wt / mu cDNA 2482 / 2482
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 104 / 104
chromosome 14
strand 1
last intron/exon boundary 2316
theoretical NMD boundary in CDS 2162
length of CDS 2379
coding sequence (CDS) position 2176
cDNA position
(for ins/del: last normal base / first normal base)		 2279
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 MELKSPEEEV VAALPEGMRP DSNLYGFPWE LVICAAVVGF FAVLFFLWRS FRSVRSRLYV
GREKKLALML SGLIEEKSKL LEKFSLVQKE YEGYEVESSL KDASFEKEAT EAQSLEATCE
KLNRSNSELE DEILCLEKEL KEEKSKHSEQ DELMADISKR IQSLEDESKS LKSQVAEAKM
TFKIFQMNEE RLKIAIKDAL NENSQLQESQ KQLLQEAEVW KEQVSELNKQ KVTFEDSKVH
AEQVLNDKES HIKTLTERLL KMKDWAAMLG EDITDDDNLE LEMNSESENG AYLDNPPKGA
LKKLIHAAKL NASLKTLEGE RNQIYIQLSE VDKTKEELTE HIKNLQTEQA SLQSENTHFE
NENQKLQQKL KVMTELYQEN EMKLHRKLTV EENYRLEKEE KLSKVDEKIS HATEELETYR
KRAKDLEEEL ERTIHSYQGQ IISHEKKAHD NWLAARNAER NLNDLRKENA HNRQKLTETE
LKFELLEKDP YALDVPNTAF GREHSPYGPS PLGWPSSETR AFLSPPTLLE GPLRLSPLLP
GGGGRGSRGP GNPLDHQITN ERGESSCDRL TDPHRAPSDT GSLSPPWDQD RRMMFPPPGQ
SYPDSALPPQ RQDRFCSNSG RLSGPAELRS FNMPSLDKMD GSMPSEMESS RNDTKDDLGN
LNVPDSSLPA ENEATGPGFV PPPLAPIRGP LFPVDARGPF LRRGPPFPPP PPGAMFGASR
DYFPPGDFPG PPPAPFAMRN VYPPRGFPPY LPPRPGFFPP PPHSEGRSEF PSGLIPPSNE
PATEHPEPQQ ET*
mutated AA sequence MELKSPEEEV VAALPEGMRP DSNLYGFPWE LVICAAVVGF FAVLFFLWRS FRSVRSRLYV
GREKKLALML SGLIEEKSKL LEKFSLVQKE YEGYEVESSL KDASFEKEAT EAQSLEATCE
KLNRSNSELE DEILCLEKEL KEEKSKHSEQ DELMADISKR IQSLEDESKS LKSQVAEAKM
TFKIFQMNEE RLKIAIKDAL NENSQLQESQ KQLLQEAEVW KEQVSELNKQ KVTFEDSKVH
AEQVLNDKES HIKTLTERLL KMKDWAAMLG EDITDDDNLE LEMNSESENG AYLDNPPKGA
LKKLIHAAKL NASLKTLEGE RNQIYIQLSE VDKTKEELTE HIKNLQTEQA SLQSENTHFE
NENQKLQQKL KVMTELYQEN EMKLHRKLTV EENYRLEKEE KLSKVDEKIS HATEELETYR
KRAKDLEEEL ERTIHSYQGQ IISHEKKAHD NWLAARNAER NLNDLRKENA HNRQKLTETE
LKFELLEKDP YALDVPNTAF GREHSPYGPS PLGWPSSETR AFLSPPTLLE GPLRLSPLLP
GGGGRGSRGP GNPLDHQITN ERGESSCDRL TDPHRAPSDT GSLSPPWDQD RRMMFPPPGQ
SYPDSALPPQ RQDRFCSNSG RLSGPAELRS FNMPSLDKMD GSMPSEMESS RNDTKDDLGN
LNVPDSSLPA ENEATGPGFV PPPLAPIRGP LFPVDARGPF LRRGPPFPPP PPGAMFGASR
DYFPPRDFPG PPPAPFAMRN VYPPRGFPPY LPPRPGFFPP PPHSEGRSEF PSGLIPPSNE
PATEHPEPQQ ET*
speed 1.55 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