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 ENST00000454776
Genbank transcript ID N/A
UniProt peptide Q5I0G3
alteration type single base exchange
alteration region CDS
DNA changes c.1527A>C
cDNA.1542A>C
g.27038A>C
AA changes E509D Score: 45 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 509
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      509FEKPQSLEFLNEFEGKTVES*
mutated  all conserved    509FEKPQSLEFLNDFEGKTVES
Ptroglodytes  all conserved  ENSPTRG00000012847  509FEKPQSLEFLNDFEGKTVES
Mmulatta  not conserved  ENSMMUG00000017734  509FEKPQSLEFLNGFEGKTVES
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 1554 / 1554
position (AA) of stopcodon in wt / mu AA sequence 518 / 518
position of stopcodon in wt / mu cDNA 1569 / 1569
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 16 / 16
chromosome 2
strand -1
last intron/exon boundary 1541
theoretical NMD boundary in CDS 1475
length of CDS 1554
coding sequence (CDS) position 1527
cDNA position
(for ins/del: last normal base / first normal base)		 1542
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 MAKFVIAGRA DCPYYAKTEL VADYLQKNLP DFRIHKITQR PEVWEDWLKD VCEKNKWSHK
NSPIIWRELL DRGGKGLLLG GYNEFLEHAQ LYYDVTSSMT TELMMVIAQE NLGAHIEKEQ
EEEALKTCIN PLQVWITSAS APACYNLIPI LTSGEVFGMH TEISITLFDN KQAEEHLKSL
VVETQDLASP VLRSVSICTK VEEAFRQAHV IVVLDDSTNK EVFTLEDCLR SRVPLCRLYG
YLIEKNAHES VRVIVGGRTF VNLKTVLLMR YAPRIAHNII AVALGVEGEA KAILARKLKT
APSYIKDVII WGNISGNNYV DLRKTRVYRY ESAIWGPLHY SRPVLNLIFD SEWVKREFVA
ILKNLTTTGR QFGGILAAHS IATTLKYWYH GSPPGEIVSL GILSEGQFGI PKGIVFSMPV
KFENGTWVVL TDLKDVEISE QIMTRMTSDL IQEKLVALGD KIHFQPYQSG HKDLVPDEEK
NLAMSDAEFP NQIPQTTFEK PQSLEFLNEF EGKTVES*
mutated AA sequence MAKFVIAGRA DCPYYAKTEL VADYLQKNLP DFRIHKITQR PEVWEDWLKD VCEKNKWSHK
NSPIIWRELL DRGGKGLLLG GYNEFLEHAQ LYYDVTSSMT TELMMVIAQE NLGAHIEKEQ
EEEALKTCIN PLQVWITSAS APACYNLIPI LTSGEVFGMH TEISITLFDN KQAEEHLKSL
VVETQDLASP VLRSVSICTK VEEAFRQAHV IVVLDDSTNK EVFTLEDCLR SRVPLCRLYG
YLIEKNAHES VRVIVGGRTF VNLKTVLLMR YAPRIAHNII AVALGVEGEA KAILARKLKT
APSYIKDVII WGNISGNNYV DLRKTRVYRY ESAIWGPLHY SRPVLNLIFD SEWVKREFVA
ILKNLTTTGR QFGGILAAHS IATTLKYWYH GSPPGEIVSL GILSEGQFGI PKGIVFSMPV
KFENGTWVVL TDLKDVEISE QIMTRMTSDL IQEKLVALGD KIHFQPYQSG HKDLVPDEEK
NLAMSDAEFP NQIPQTTFEK PQSLEFLNDF EGKTVES*
speed 1.11 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