Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999584695955329 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:151090424G>AN/A show variant in all transcripts   IGV
HGNC symbol MED12L
Ensembl transcript ID ENST00000273432
Genbank transcript ID N/A
UniProt peptide Q86YW9
alteration type single base exchange
alteration region CDS
DNA changes c.3209G>A
cDNA.3242G>A
g.286941G>A
AA changes R1070Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1070
frameshift no
known variant Reference ID: rs3732765
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC62952017726472
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.4740.42
1.9710.409
(flanking)-1.820.058
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased286943wt: 0.8962 / mu: 0.9810 (marginal change - not scored)wt: TGCGATGTGATGGGA
mu: TGCAATGTGATGGGA		 CGAT|gtga
Donor marginally increased286938wt: 0.9167 / mu: 0.9281 (marginal change - not scored)wt: AGGTTTGCGATGTGA
mu: AGGTTTGCAATGTGA		 GTTT|gcga
distance from splice site 70
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1070LKNDDFTMRGLRCDGNADDIWTAS
mutated  all conserved    1070LKNDDFTMRGLQCDGNADDIWT
Ptroglodytes  all identical  ENSPTRG00000015534  1210LKNDDFTMRGLRCDGNADDIWTA
Mmulatta  all identical  ENSMMUG00000017239  1209LKNDDFTMRGLRCDGNADDIWTA
Fcatus  all identical  ENSFCAG00000010395  1177GLRRDGNADDIWTA
Mmusculus  all identical  ENSMUSG00000056476  1245MKNEDFGMRGLRRDGNAEDAWAT
Ggallus  not conserved  ENSGALG00000010370  1178VKNEELPVRGLLDEIAEDEMWAS
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0001324  1349SGTSSGGLGGAFGSGKRSGFNTPVHP
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 5430 / 5430
position (AA) of stopcodon in wt / mu AA sequence 1810 / 1810
position of stopcodon in wt / mu cDNA 5463 / 5463
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 34 / 34
chromosome 3
strand 1
last intron/exon boundary 5411
theoretical NMD boundary in CDS 5327
length of CDS 5430
coding sequence (CDS) position 3209
cDNA position
(for ins/del: last normal base / first normal base)		 3242
gDNA position
(for ins/del: last normal base / first normal base)		 286941
chromosomal position
(for ins/del: last normal base / first normal base)		 151090424
original gDNA sequence snippet CTTCACCATGAGAGGTTTGCGATGTGATGGGAATGCTGATG
altered gDNA sequence snippet CTTCACCATGAGAGGTTTGCAATGTGATGGGAATGCTGATG
original cDNA sequence snippet CTTCACCATGAGAGGTTTGCGATGTGATGGGAATGCTGATG
altered cDNA sequence snippet CTTCACCATGAGAGGTTTGCAATGTGATGGGAATGCTGATG
wildtype AA sequence MAAFGLLSYE QRPLKRPRLG PPDVYPQDPK QKEDELTAVN VKQGFNNQPA FTGDEHGSAR
NIVINPSKIG AYFSSILAEK LKLNTFQDTG KKKPQVNAKD NYWLVTARSQ SAIHSWFSDL
AGNKPLSILA KKVPILSKKE DVFAYLAKYS VPMVRATWLI KMTCAYYSAI SEAKIKKRQA
PDPNLEWTQI STRYLREQLA KISDFYHMAS STGDGPVPVP PEVEQAMKQW EYNEKLAFHM
FQEGMLEKHE YLTWILDVLE KIRPMDDDLL KLLLPLMLQV RARIYEVEQQ IKQRGRAVEV
RWSFDKCQES TAGVTISRVL HTLEVLDRHC FDRTDSSNSM ETLYHKIFWA NQNKDNQEVA
PNDEAVVTLL CEWAVSCKRS GKHRAMAVAK LLEKRQAEIE AERCGESEVL DEKESISSSS
LAGSSLPVFQ NVLLRFLDTQ APSLSDPNSE CEKVEFVNLV LLFCEFIRHD VFSHDAYMCT
LISRGDLSVT ASTRPRSPVG ENADEHYSKD HDVKMEIFSP MPGESCENAN TSLGRRMSVN
CEKLVKREKP RELIFPSNYD LLRHLQYATH FPIPLDESSS HECNQRTILL YGVGKERDEA
RHQLKKITKD ILKILNKKST TETGVGDEGQ KARKNKQETF PTLETVFTKL QLLSYFDQHQ
VTSQISNNVL EQITSFASGT SYHLPLAHHI QLIFDLMEPA LNINGLIDFA IQLLNELSVV
EAELLLKSSS LAGSYTTGLC VCIVAVLRRY HSCLILNPDQ TAQVFEGLCG VVKHVVNPSE
CSSPERCILA YLYDLYVSCS HLRSKFGDLF SSACSKVKQT IYNNVMPANS NLRWDPDFMM
DFIENPSARS INYSMLGKIL SDNAANRYSF VCNTLMNVCM GHQDAGRIND IANFSSELTA
CCTVLSSEWL GVLKALCCSS NHVWGFNDVL CTVDVSDLSF HDSLATFIAI LIARQCFSLE
DVVQHVALPS LLAAACGDAD AEPGARMTCR LLLHLFRAPQ ACFLPQATGK PFPGIRSSCD
RHLLAAAHNS IEVGAVFAVL KAIMMLGDAK IGNNSVSSLK NDDFTMRGLR CDGNADDIWT
ASQNPKSCGK SISIETANLR EYARYVLRTI CQQEWVGEHC LKEPERLCTD KELILDPVLS
NMQAQKLLQL ICYPHGIKEC TEGDNLQRQH IKRILQNLEQ WTLRQSWLEL QLMIKQCLKD
PGSGSVAEMN NLLDNIAKAT IEVFQQSADL NNSSNSGMSL FNPNSIGSAD TSSTRQNGIK
TFLSSSERRG VWLVAPLIAR LPTSVQGRVL KAAGEELEKG QHLGSSSKKE RDRQKQKSMS
LLSQQPFLSL VLTCLKGQDE QREGLLTSLQ NQVNQILSNW REERYQDDIK ARQMMHEALQ
LRLNLVGGMF DTVQRSTQWT TDWALLLLQI ITSGTVDMHT NNELFTTVLD MLGVLINGTL
ASDLSNASPG GSEENKRAYM NLVKKLKKEL GDKRSESIDK VRQLLPLPKQ TCDVITCEPM
GSLIDTKGNK IAGFDSIDKK QGLQVSTKQK VSPWDLFEGQ KNPAPLSWAW FGTVRVDRRV
IKYEEQHHLL LYHTHPMPKP RSYYLQPLPL PPEEEEEEPT SPVSQEPERK SAELSDQGKT
TTDEEKKTKG RKRKTKSSSR VDEYPQSNIY RVPPNYSPIS SQMMHHPQST LWGYNLVGQP
QQPGFFLQNQ SLTPGGSRLD PAGSFVPTNT KQALSNMLQR RSGAMMQPPS LHAITSQQQL
IQMKLLQQQQ QQRLLRQAQT RPFQQFPRQG LQQTQQQQQT AALVRQLQKQ LSSNQPQQGV
TPYGHPSHF*
mutated AA sequence MAAFGLLSYE QRPLKRPRLG PPDVYPQDPK QKEDELTAVN VKQGFNNQPA FTGDEHGSAR
NIVINPSKIG AYFSSILAEK LKLNTFQDTG KKKPQVNAKD NYWLVTARSQ SAIHSWFSDL
AGNKPLSILA KKVPILSKKE DVFAYLAKYS VPMVRATWLI KMTCAYYSAI SEAKIKKRQA
PDPNLEWTQI STRYLREQLA KISDFYHMAS STGDGPVPVP PEVEQAMKQW EYNEKLAFHM
FQEGMLEKHE YLTWILDVLE KIRPMDDDLL KLLLPLMLQV RARIYEVEQQ IKQRGRAVEV
RWSFDKCQES TAGVTISRVL HTLEVLDRHC FDRTDSSNSM ETLYHKIFWA NQNKDNQEVA
PNDEAVVTLL CEWAVSCKRS GKHRAMAVAK LLEKRQAEIE AERCGESEVL DEKESISSSS
LAGSSLPVFQ NVLLRFLDTQ APSLSDPNSE CEKVEFVNLV LLFCEFIRHD VFSHDAYMCT
LISRGDLSVT ASTRPRSPVG ENADEHYSKD HDVKMEIFSP MPGESCENAN TSLGRRMSVN
CEKLVKREKP RELIFPSNYD LLRHLQYATH FPIPLDESSS HECNQRTILL YGVGKERDEA
RHQLKKITKD ILKILNKKST TETGVGDEGQ KARKNKQETF PTLETVFTKL QLLSYFDQHQ
VTSQISNNVL EQITSFASGT SYHLPLAHHI QLIFDLMEPA LNINGLIDFA IQLLNELSVV
EAELLLKSSS LAGSYTTGLC VCIVAVLRRY HSCLILNPDQ TAQVFEGLCG VVKHVVNPSE
CSSPERCILA YLYDLYVSCS HLRSKFGDLF SSACSKVKQT IYNNVMPANS NLRWDPDFMM
DFIENPSARS INYSMLGKIL SDNAANRYSF VCNTLMNVCM GHQDAGRIND IANFSSELTA
CCTVLSSEWL GVLKALCCSS NHVWGFNDVL CTVDVSDLSF HDSLATFIAI LIARQCFSLE
DVVQHVALPS LLAAACGDAD AEPGARMTCR LLLHLFRAPQ ACFLPQATGK PFPGIRSSCD
RHLLAAAHNS IEVGAVFAVL KAIMMLGDAK IGNNSVSSLK NDDFTMRGLQ CDGNADDIWT
ASQNPKSCGK SISIETANLR EYARYVLRTI CQQEWVGEHC LKEPERLCTD KELILDPVLS
NMQAQKLLQL ICYPHGIKEC TEGDNLQRQH IKRILQNLEQ WTLRQSWLEL QLMIKQCLKD
PGSGSVAEMN NLLDNIAKAT IEVFQQSADL NNSSNSGMSL FNPNSIGSAD TSSTRQNGIK
TFLSSSERRG VWLVAPLIAR LPTSVQGRVL KAAGEELEKG QHLGSSSKKE RDRQKQKSMS
LLSQQPFLSL VLTCLKGQDE QREGLLTSLQ NQVNQILSNW REERYQDDIK ARQMMHEALQ
LRLNLVGGMF DTVQRSTQWT TDWALLLLQI ITSGTVDMHT NNELFTTVLD MLGVLINGTL
ASDLSNASPG GSEENKRAYM NLVKKLKKEL GDKRSESIDK VRQLLPLPKQ TCDVITCEPM
GSLIDTKGNK IAGFDSIDKK QGLQVSTKQK VSPWDLFEGQ KNPAPLSWAW FGTVRVDRRV
IKYEEQHHLL LYHTHPMPKP RSYYLQPLPL PPEEEEEEPT SPVSQEPERK SAELSDQGKT
TTDEEKKTKG RKRKTKSSSR VDEYPQSNIY RVPPNYSPIS SQMMHHPQST LWGYNLVGQP
QQPGFFLQNQ SLTPGGSRLD PAGSFVPTNT KQALSNMLQR RSGAMMQPPS LHAITSQQQL
IQMKLLQQQQ QQRLLRQAQT RPFQQFPRQG LQQTQQQQQT AALVRQLQKQ LSSNQPQQGV
TPYGHPSHF*
speed 1.14 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