Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.998536363239899 (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) chr19:871135A>GN/A show variant in all transcripts   IGV
HGNC symbol MED16
Ensembl transcript ID ENST00000269814
Genbank transcript ID N/A
UniProt peptide Q9Y2X0
alteration type single base exchange
alteration region CDS
DNA changes c.2024T>C
cDNA.2157T>C
g.22084T>C
AA changes L675S Score: 145 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 675
frameshift no
known variant Reference ID: rs1683569
databasehomozygous (G/G)heterozygousallele carriers
1000G2618041065
ExAC61829643582
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)2.3911
1.061
(flanking)1.651
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased22085wt: 0.23 / mu: 0.37wt: TGGTTAGCCGCCTGC
mu: TGGTCAGCCGCCTGC		 GTTA|gccg
distance from splice site 99
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      675AWTGCQPATAWLAACSPSSPFVCS
mutated  not conserved    675AWTGCQPATAWSAACSPSSPFVC
Ptroglodytes  no alignment  ENSPTRG00000010168  n/a
Mmulatta  no alignment  ENSMMUG00000009677  n/a
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  not conserved  FBgn0034707  62AGDGSLPGAGLAVGASNSHVYVC
Celegans  no homologue    
Xtropicalis  no alignment  ENSXETG00000021641  n/a
protein features
start (aa)end (aa)featuredetails 
634675REPEATWD 4.lost
790829REPEATWD 5.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2256 / 2256
position (AA) of stopcodon in wt / mu AA sequence 752 / 752
position of stopcodon in wt / mu cDNA 2389 / 2389
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 134 / 134
chromosome 19
strand -1
last intron/exon boundary 2340
theoretical NMD boundary in CDS 2156
length of CDS 2256
coding sequence (CDS) position 2024
cDNA position
(for ins/del: last normal base / first normal base)		 2157
gDNA position
(for ins/del: last normal base / first normal base)		 22084
chromosomal position
(for ins/del: last normal base / first normal base)		 871135
original gDNA sequence snippet CCAGCCAGCGACGGCCTGGTTAGCCGCCTGCAGCCCAAGCA
altered gDNA sequence snippet CCAGCCAGCGACGGCCTGGTCAGCCGCCTGCAGCCCAAGCA
original cDNA sequence snippet CCAGCCAGCGACGGCCTGGTTAGCCGCCTGCAGCCCAAGCA
altered cDNA sequence snippet CCAGCCAGCGACGGCCTGGTCAGCCGCCTGCAGCCCAAGCA
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 SLPNQVAMRA QRASRTRRWW MNAACCPASC
LSPAWTGCQP ATAWLAACSP SSPFVCSLAG RPRCLAVLPP CSSTASPGPQ ASPRSTTCGG
CTLALAPRRN ARPAPGAAVS PCSSRPTEPR R*
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 SLPNQVAMRA QRASRTRRWW MNAACCPASC
LSPAWTGCQP ATAWSAACSP SSPFVCSLAG RPRCLAVLPP CSSTASPGPQ ASPRSTTCGG
CTLALAPRRN ARPAPGAAVS PCSSRPTEPR R*
speed 0.73 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