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 ENST00000557038
Genbank transcript ID N/A
UniProt peptide O15320
alteration type single base exchange
alteration region CDS
DNA changes c.1972G>A
cDNA.2240G>A
g.83658G>A
AA changes G658R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 658
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      658MFGASRDYFPPGDFPGPPPAPFAM
mutated  not conserved    658MFGASRDYFPPRDF
Ptroglodytes  not conserved  ENSPTRG00000006297  738MFGASRDYFPPRDF
Mmulatta  not conserved  ENSMMUG00000021121  739MFGTSRDYFPPRDFP
Fcatus  no homologue    
Mmusculus  not conserved  ENSMUSG00000021000  740RDYFPPRDFPGPPLPPFP
Ggallus  not conserved  ENSGALG00000010189  1259G-PRECFPVRDL-GLPRPPLP
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000023516  636------DYFPP---RGPHVLPMG
Dmelanogaster  no alignment  FBgn0031842  n/a
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
502804COMPBIASPro-rich.lost
678678MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
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 2175 / 2175
position (AA) of stopcodon in wt / mu AA sequence 725 / 725
position of stopcodon in wt / mu cDNA 2443 / 2443
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 269 / 269
chromosome 14
strand 1
last intron/exon boundary 2277
theoretical NMD boundary in CDS 1958
length of CDS 2175
coding sequence (CDS) position 1972
cDNA position
(for ins/del: last normal base / first normal base)		 2240
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 MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEAT CEKLNRSNSE
LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES KSLKSQVAEA KMTFKIFQMN
EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN KQKVTFEDSK VHAEQVLNDK
ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE NGAYLDNPPK GALKKLIHAA
KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE QASLQSENTH FENENQKLQQ
KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK ISHATEELET YRKRAKDLEE
ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE NAHNRQKLTE TELKFELLEK
DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL LEGPLRLSPL LPGGGGRGSR
GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD QDRRMMFPPP GQSYPDSALP
PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME SSRNDTKDDL GNLNVPDSSL
PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP PPPPGAMFGA SRDYFPPGDF
PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS EFPSGLIPPS NEPATEHPEP
QQET*
mutated AA sequence MLSGLIEEKS KLLEKFSLVQ KEYEGYEVES SLKDASFEKE ATEAQSLEAT CEKLNRSNSE
LEDEILCLEK ELKEEKSKHS EQDELMADIS KRIQSLEDES KSLKSQVAEA KMTFKIFQMN
EERLKIAIKD ALNENSQLQE SQKQLLQEAE VWKEQVSELN KQKVTFEDSK VHAEQVLNDK
ESHIKTLTER LLKMKDWAAM LGEDITDDDN LELEMNSESE NGAYLDNPPK GALKKLIHAA
KLNASLKTLE GERNQIYIQL SEVDKTKEEL TEHIKNLQTE QASLQSENTH FENENQKLQQ
KLKVMTELYQ ENEMKLHRKL TVEENYRLEK EEKLSKVDEK ISHATEELET YRKRAKDLEE
ELERTIHSYQ GQIISHEKKA HDNWLAARNA ERNLNDLRKE NAHNRQKLTE TELKFELLEK
DPYALDVPNT AFGREHSPYG PSPLGWPSSE TRAFLSPPTL LEGPLRLSPL LPGGGGRGSR
GPGNPLDHQI TNERGESSCD RLTDPHRAPS DTGSLSPPWD QDRRMMFPPP GQSYPDSALP
PQRQDRFCSN SGRLSGPAEL RSFNMPSLDK MDGSMPSEME SSRNDTKDDL GNLNVPDSSL
PAENEATGPG FVPPPLAPIR GPLFPVDARG PFLRRGPPFP PPPPGAMFGA SRDYFPPRDF
PGPPPAPFAM RNVYPPRGFP PYLPPRPGFF PPPPHSEGRS EFPSGLIPPS NEPATEHPEP
QQET*
speed 0.76 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