Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999848 (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) chr14:39818028A>GN/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.2110A>G
cDNA.2446A>G
g.83541A>G
AA changes I704V Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 704
frameshift no
known variant Reference ID: rs1140952
databasehomozygous (G/G)heterozygousallele carriers
1000G41910881507
ExAC95161373523251
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.3810
-0.3470
(flanking)0.9680.001
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased83539wt: 0.8806 / mu: 0.9021 (marginal change - not scored)wt: TGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTC
mu: TGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTC		 ctcc|AATC
Acc increased83540wt: 0.68 / mu: 0.87wt: GTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCC
mu: GTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCC		 tcca|ATCA
Acc marginally increased83534wt: 0.9483 / mu: 0.9585 (marginal change - not scored)wt: GGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATT
mu: GGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATT		 tctt|GCTC
Acc marginally increased83535wt: 0.9069 / mu: 0.9174 (marginal change - not scored)wt: GCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTG
mu: GCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTG		 cttg|CTCC
Acc increased83532wt: 0.36 / mu: 0.53wt: CTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCA
mu: CTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCA		 cctc|TTGC
Acc marginally increased83531wt: 0.9921 / mu: 0.9928 (marginal change - not scored)wt: CCTGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCC
mu: CCTGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCC		 acct|CTTG
Acc increased83533wt: 0.70 / mu: 0.86wt: TGGCTTTGTTCCTCCACCTCTTGCTCCAATCAGAGGTCCAT
mu: TGGCTTTGTTCCTCCACCTCTTGCTCCAGTCAGAGGTCCAT		 ctct|TGCT
Donor gained835400.85mu: GCTCCAGTCAGAGGT TCCA|gtca
distance from splice site 82
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      704GPGFVPPPLAPIRGPLFPVDARGP
mutated  all conserved    704GPGFVPPPLAPVRGPLFPVDARG
Ptroglodytes  all identical  ENSPTRG00000006297  699GPGFVPPPLAPIRGPLFPVDTRG
Mmulatta  all identical  ENSMMUG00000021121  700GPGFVPPPLAPIRGPLFPVDTRG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000021000  701GRGFFPPPFPPVRDPLFPVDPRS
Ggallus  all conserved  ENSGALG00000010189  1220SSGFGPPPFPPVRPPTMPMDPRG
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000023516  600GP--LPPPGPPLMSMPPPMDPRD
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 2110
cDNA position
(for ins/del: last normal base / first normal base)		 2446
gDNA position
(for ins/del: last normal base / first normal base)		 83541
chromosomal position
(for ins/del: last normal base / first normal base)		 39818028
original gDNA sequence snippet TTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCA
altered gDNA sequence snippet TTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCCA
original cDNA sequence snippet TTCCTCCACCTCTTGCTCCAATCAGAGGTCCATTGTTTCCA
altered cDNA sequence snippet TTCCTCCACCTCTTGCTCCAGTCAGAGGTCCATTGTTTCCA
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 LAPVRGPLFP VDARGPFLRR
GPPFPPPPPG AMFGASRDYF PPGDFPGPPP APFAMRNVYP PRGFPPYLPP RPGFFPPPPH
SEGRSEFPSG LIPPSNEPAT EHPEPQQET*
speed 1.08 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