Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999997232 (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) chr19:868115C>TN/A show variant in all transcripts   IGV
HGNC symbol MED16
Ensembl transcript ID ENST00000589119
Genbank transcript ID N/A
UniProt peptide Q9Y2X0
alteration type single base exchange
alteration region CDS
DNA changes c.2620G>A
cDNA.2620G>A
g.25104G>A
AA changes E874K Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 874
frameshift no
known variant Reference ID: rs13090
databasehomozygous (T/T)heterozygousallele carriers
1000G213775988
ExAC40722065724729
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.6530.015
-0.1790.008
(flanking)-0.2430.005
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased25100wt: 0.81 / mu: 0.94wt: CTGCATCCAGAGGAC
mu: CTGCATCCAAAGGAC		 GCAT|ccag
Donor marginally increased25105wt: 0.9235 / mu: 0.9555 (marginal change - not scored)wt: TCCAGAGGACCGTCC
mu: TCCAAAGGACCGTCC		 CAGA|ggac
distance from splice site 137
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      874RTPRSLDHLHPEDRP*
mutated  all conserved    874RTPRSLDHLHPKDRP
Ptroglodytes  no alignment  ENSPTRG00000010168  n/a
Mmulatta  all identical  ENSMMUG00000009677  872GTPRSLDHPHPEDR
Fcatus  no homologue    
Mmusculus  no alignment  ENSMUSG00000013833  n/a
Ggallus  no alignment  ENSGALG00000001978  n/a
Trubripes  no alignment  ENSTRUG00000007850  n/a
Drerio  no alignment  ENSDARG00000040779  n/a
Dmelanogaster  no alignment  FBgn0034707  n/a
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000021641  n/a
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2634 / 2634
position (AA) of stopcodon in wt / mu AA sequence 878 / 878
position of stopcodon in wt / mu cDNA 2634 / 2634
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 1 / 1
chromosome 19
strand -1
last intron/exon boundary 2484
theoretical NMD boundary in CDS 2433
length of CDS 2634
coding sequence (CDS) position 2620
cDNA position
(for ins/del: last normal base / first normal base)		 2620
gDNA position
(for ins/del: last normal base / first normal base)		 25104
chromosomal position
(for ins/del: last normal base / first normal base)		 868115
original gDNA sequence snippet CCCTGGACCATCTGCATCCAGAGGACCGTCCGTGACGGCCG
altered gDNA sequence snippet CCCTGGACCATCTGCATCCAAAGGACCGTCCGTGACGGCCG
original cDNA sequence snippet CCCTGGACCATCTGCATCCAGAGGACCGTCCGTGACGGCCG
altered cDNA sequence snippet CCCTGGACCATCTGCATCCAAAGGACCGTCCGTGACGGCCG
wildtype AA sequence MCDLRRPAAG GMMDLAYVCE WEKWSKSTHC PSVPLACAWS CRNLIAFTMD LRSDDQDLTR
MIHILDTEHP WDLHSIPSEH HEAITCLEWD QSGSRLLSAD ADGQIKCWSM ADHLANSWES
SVGSLVEGDP IVALSWLHNG VKLALHVEKS GASSFGEKFS RVKFSPSLTL FGGKPMEGWI
AVTVSGLVTV SLLKPSGQVL TSTESLCRLR GRVALADIAF TGGGNIVVAT ADGSSASPVQ
FYKVCVSVVS EKCRIDTEIL PSLFMRCTTD LNRKDKFPAI THLKFLARDM SEQVLLCASS
QTSSIVECWS LRKEGLPVNN IFQQISPVVG DKQPTILKWR ILSATNDLDR VSAVALPKLP
ISLTNTDLKV ASDTQFYPGL GLALAFHDGS VHIVHRLSLQ TMAVFYSSAA PRPVDEPAMK
RPRTAGPAVH LKAMQLSWTS LALVGIDSHG KLSVLRLSPS MGHPLEVGLA LRHLLFLLEY
CMVTGYDWWD ILLHVQPSMV QSLVEKLHEE YTRQTAALQQ VLSTRILAMK ASLCKLSPCT
VTRVCDYHTK LFLIAISSTL KSLLRPHFLN TPDKSPGDRL TEICTKITDV DIDKVMINLK
TEEFVLDMNT LQALQQLLQW VGDFVLYLLA SLPNQGSLLR PGHSFLRDGT SLGMLRELMV
VIRIWGLLKP SCLPVYTATS DTQDSMSLLF RLLTKLWICC RDEGPASEPD EALVDECCLL
PSQLLIPSLD WLPASDGLVS RLQPKQPLRL QFGRAPTLPG SAATLQLDGL ARAPGQPKID
HLRRLHLGAC PTEECKACTR CGCVTMLKSP NRTTAVKQWE QRWIKNCLAV EGRGPDACVT
SRASEEAPAF VQLGPQSTHH SPRTPRSLDH LHPEDRP*
mutated AA sequence MCDLRRPAAG GMMDLAYVCE WEKWSKSTHC PSVPLACAWS CRNLIAFTMD LRSDDQDLTR
MIHILDTEHP WDLHSIPSEH HEAITCLEWD QSGSRLLSAD ADGQIKCWSM ADHLANSWES
SVGSLVEGDP IVALSWLHNG VKLALHVEKS GASSFGEKFS RVKFSPSLTL FGGKPMEGWI
AVTVSGLVTV SLLKPSGQVL TSTESLCRLR GRVALADIAF TGGGNIVVAT ADGSSASPVQ
FYKVCVSVVS EKCRIDTEIL PSLFMRCTTD LNRKDKFPAI THLKFLARDM SEQVLLCASS
QTSSIVECWS LRKEGLPVNN IFQQISPVVG DKQPTILKWR ILSATNDLDR VSAVALPKLP
ISLTNTDLKV ASDTQFYPGL GLALAFHDGS VHIVHRLSLQ TMAVFYSSAA PRPVDEPAMK
RPRTAGPAVH LKAMQLSWTS LALVGIDSHG KLSVLRLSPS MGHPLEVGLA LRHLLFLLEY
CMVTGYDWWD ILLHVQPSMV QSLVEKLHEE YTRQTAALQQ VLSTRILAMK ASLCKLSPCT
VTRVCDYHTK LFLIAISSTL KSLLRPHFLN TPDKSPGDRL TEICTKITDV DIDKVMINLK
TEEFVLDMNT LQALQQLLQW VGDFVLYLLA SLPNQGSLLR PGHSFLRDGT SLGMLRELMV
VIRIWGLLKP SCLPVYTATS DTQDSMSLLF RLLTKLWICC RDEGPASEPD EALVDECCLL
PSQLLIPSLD WLPASDGLVS RLQPKQPLRL QFGRAPTLPG SAATLQLDGL ARAPGQPKID
HLRRLHLGAC PTEECKACTR CGCVTMLKSP NRTTAVKQWE QRWIKNCLAV EGRGPDACVT
SRASEEAPAF VQLGPQSTHH SPRTPRSLDH LHPKDRP*
speed 0.95 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