Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.99999999999999 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:207603234T>GN/A show variant in all transcripts   IGV
HGNC symbol MDH1B
Ensembl transcript ID ENST00000449792
Genbank transcript ID N/A
UniProt peptide Q5I0G3
alteration type single base exchange
alteration region CDS
DNA changes c.1236A>C
cDNA.1472A>C
g.27038A>C
AA changes E412D Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 412
frameshift no
known variant Reference ID: rs2287631
databasehomozygous (G/G)heterozygousallele carriers
1000G50710781585
ExAC60101991425924
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.1150.054
-0.880.029
(flanking)-0.0490.099
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost27036.5sequence motif lost- wt: taca|GAAT
 mu: taca.GACT
Acc marginally increased27035wt: 0.9900 / mu: 0.9908 (marginal change - not scored)wt: TTTCATTCTTTTCCTTTTACAGAATTTGAAGGCAAAACCGT
mu: TTTCATTCTTTTCCTTTTACAGACTTTGAAGGCAAAACCGT		 taca|GAAT
Acc marginally increased27030wt: 0.9799 / mu: 0.9810 (marginal change - not scored)wt: TGTCTTTTCATTCTTTTCCTTTTACAGAATTTGAAGGCAAA
mu: TGTCTTTTCATTCTTTTCCTTTTACAGACTTTGAAGGCAAA		 cctt|TTAC
Acc marginally increased27034wt: 0.9912 / mu: 0.9919 (marginal change - not scored)wt: TTTTCATTCTTTTCCTTTTACAGAATTTGAAGGCAAAACCG
mu: TTTTCATTCTTTTCCTTTTACAGACTTTGAAGGCAAAACCG		 ttac|AGAA
Acc marginally increased27033wt: 0.9934 / mu: 0.9940 (marginal change - not scored)wt: CTTTTCATTCTTTTCCTTTTACAGAATTTGAAGGCAAAACC
mu: CTTTTCATTCTTTTCCTTTTACAGACTTTGAAGGCAAAACC		 ttta|CAGA
Donor marginally increased27039wt: 0.9040 / mu: 0.9303 (marginal change - not scored)wt: CAGAATTTGAAGGCA
mu: CAGACTTTGAAGGCA		 GAAT|ttga
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      412FEKPQSLEFLNEFEGKTVES*
mutated  all conserved    412FEKPQSLEFLNDFEGKTVES
Ptroglodytes  all conserved  ENSPTRG00000012847  510FEKPQSLEFLNDFEGKTVES
Mmulatta  not conserved  ENSMMUG00000017734  510FEKPQSLEFLNGFEGKTVES
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000025963  n/a
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no alignment  ENSDARG00000018008  n/a
Dmelanogaster  no alignment  FBgn0262782  n/a
Celegans  no alignment  F46E10.10  n/a
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1263 / 1263
position (AA) of stopcodon in wt / mu AA sequence 421 / 421
position of stopcodon in wt / mu cDNA 1499 / 1499
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 237 / 237
chromosome 2
strand -1
last intron/exon boundary 1471
theoretical NMD boundary in CDS 1184
length of CDS 1263
coding sequence (CDS) position 1236
cDNA position
(for ins/del: last normal base / first normal base)		 1472
gDNA position
(for ins/del: last normal base / first normal base)		 27038
chromosomal position
(for ins/del: last normal base / first normal base)		 207603234
original gDNA sequence snippet CATTCTTTTCCTTTTACAGAATTTGAAGGCAAAACCGTGGA
altered gDNA sequence snippet CATTCTTTTCCTTTTACAGACTTTGAAGGCAAAACCGTGGA
original cDNA sequence snippet AGTCTTGAGTTCCTAAATGAATTTGAAGGCAAAACCGTGGA
altered cDNA sequence snippet AGTCTTGAGTTCCTAAATGACTTTGAAGGCAAAACCGTGGA
wildtype AA sequence MTTELMMVIA QENLGAHIEK EQEEEALKTC INPLQVWITS ASAPACYNLI PILTSGEVFG
MHTEISITLF DNKQAEEHLK SLVVETQDLA SPVLRSVSIC TKVEEAFRQA HVIVVLDDST
NKEVFTLEDC LRSRVPLCRL YGYLIEKNAH ESVRVIVGGR TFVNLKTVLL MRYAPRIAHN
IIAVALGVEG EAKAILARKL KTAPSYIKDV IIWGNISGNN YVDLRKTRVY RYESAIWGPL
HYSRPVLNLI FDSEWVKREF VAILKNLTTT GRQFGGILAA HSIATTLKYW YHGSPPGEIV
SLGILSEGQF GIPKGIVFSM PVKFENGTWV VLTDLKDVEI SEQIMTRMTS DLIQEKLVAL
GDKIHFQPYQ SGHKDLVPDE EKNLAMSDAA EFPNQIPQTT FEKPQSLEFL NEFEGKTVES
*
mutated AA sequence MTTELMMVIA QENLGAHIEK EQEEEALKTC INPLQVWITS ASAPACYNLI PILTSGEVFG
MHTEISITLF DNKQAEEHLK SLVVETQDLA SPVLRSVSIC TKVEEAFRQA HVIVVLDDST
NKEVFTLEDC LRSRVPLCRL YGYLIEKNAH ESVRVIVGGR TFVNLKTVLL MRYAPRIAHN
IIAVALGVEG EAKAILARKL KTAPSYIKDV IIWGNISGNN YVDLRKTRVY RYESAIWGPL
HYSRPVLNLI FDSEWVKREF VAILKNLTTT GRQFGGILAA HSIATTLKYW YHGSPPGEIV
SLGILSEGQF GIPKGIVFSM PVKFENGTWV VLTDLKDVEI SEQIMTRMTS DLIQEKLVAL
GDKIHFQPYQ SGHKDLVPDE EKNLAMSDAA EFPNQIPQTT FEKPQSLEFL NDFEGKTVES
*
speed 0.86 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