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 ENST00000474524
Genbank transcript ID NM_053002
UniProt peptide Q86YW9
alteration type single base exchange
alteration region CDS
DNA changes c.3629G>A
cDNA.3667G>A
g.286941G>A
AA changes R1210Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1210
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      1210LKNDDFTMRGLRCDGNADDIWTAS
mutated  all conserved    1210NDDFTMRGLQCDGNADDIWTA
Ptroglodytes  all identical  ENSPTRG00000015534  1210NDDFTMRGLRCDGNADDIWTA
Mmulatta  all identical  ENSMMUG00000017239  1209NDDFTMRGLRCDGNADDIWTA
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 6438 / 6438
position (AA) of stopcodon in wt / mu AA sequence 2146 / 2146
position of stopcodon in wt / mu cDNA 6476 / 6476
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 39 / 39
chromosome 3
strand 1
last intron/exon boundary 6424
theoretical NMD boundary in CDS 6335
length of CDS 6438
coding sequence (CDS) position 3629
cDNA position
(for ins/del: last normal base / first normal base)		 3667
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 KLLLPLMLQY SDEFVQSAYL SRRLAYFCAR
RLSLLLSDSP NLLAAHSPHM MIGPNNSSIG APSPGPPGPG MSPVQLAFSD FLSCAQHGPL
VYGLSCMLQT VTLCCPSALV WNYSTNENKS ANPGSPLDLL QVAPSSLPMP GGNTAFNQQV
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 RPFQQGQPGD QAALFAAQAR
PSPQLPQYPG LQQAQTMPQG YTMYGTQMPL QQTSQQQAGS VVLSPSYNSR AYPAAHSNPV
LMERLRQIQQ QPSGYVQQQA SPYLQPLTGS QRLNHQALQQ SPLVGGGIDA VLTSAHPNLP
SVPLPQDPMR PRQPQVRQQQ RLLQMQQPQQ PQPQQPPQPQ QSSQSQSQTL GLQAMQPQQP
LFPRQGLQQT QQQQQTAALV RQLQKQLSSN QPQQGVTPYG HPSHF*
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 KLLLPLMLQY SDEFVQSAYL SRRLAYFCAR
RLSLLLSDSP NLLAAHSPHM MIGPNNSSIG APSPGPPGPG MSPVQLAFSD FLSCAQHGPL
VYGLSCMLQT VTLCCPSALV WNYSTNENKS ANPGSPLDLL QVAPSSLPMP GGNTAFNQQV
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 RPFQQGQPGD QAALFAAQAR
PSPQLPQYPG LQQAQTMPQG YTMYGTQMPL QQTSQQQAGS VVLSPSYNSR AYPAAHSNPV
LMERLRQIQQ QPSGYVQQQA SPYLQPLTGS QRLNHQALQQ SPLVGGGIDA VLTSAHPNLP
SVPLPQDPMR PRQPQVRQQQ RLLQMQQPQQ PQPQQPPQPQ QSSQSQSQTL GLQAMQPQQP
LFPRQGLQQT QQQQQTAALV RQLQKQLSSN QPQQGVTPYG HPSHF*
speed 1.08 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