Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999869264390185 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM067474)
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:121435427G>AN/A show variant in all transcripts   IGV
HGNC symbol HNF1A
Ensembl transcript ID ENST00000535125
Genbank transcript ID N/A
UniProt peptide P20823
alteration type single base exchange
alteration region CDS
DNA changes c.1136G>A
cDNA.1279G>A
g.19082G>A
AA changes S379N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 379
frameshift no
known variant Reference ID: rs2464196
databasehomozygous (A/A)heterozygousallele carriers
1000G2979971294
ExAC67891918925978

known disease mutation at this position, please check HGMD for details (HGMD ID CM067474)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PolII, Polymerase, RNA Polymerase II
phyloP / phastCons
PhyloPPhastCons
(flanking)0.8010.98
0.9210.943
(flanking)-0.5440.863
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased19091wt: 0.3963 / mu: 0.4425 (marginal change - not scored)wt: TGTGACCCAGAGCCCCTTCATGGCCACCATGGCTCAGCTGC
mu: TGTGACCCAGAACCCCTTCATGGCCACCATGGCTCAGCTGC		 tcat|GGCC
Donor increased19086wt: 0.42 / mu: 0.74wt: AGCCCCTTCATGGCC
mu: AACCCCTTCATGGCC		 CCCC|ttca
distance from splice site 42
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      379LMPPVQSHVTQSPFMATMAQLQSP
mutated  all conserved    379LMPPVQSHVTQNPFMATMAQLQS
Ptroglodytes  not conserved  ENSPTRG00000005551  411IMASLPGVMTIGPGEPA
Mmulatta  no homologue    
Fcatus  all conserved  ENSFCAG00000009638  370LEPSHSLLSTEAKLVSATGGPLPPVSTLTA
Mmusculus  not conserved  ENSMUSG00000029556  369LEPSSLLSTEAKLVSATGGPLPPVSTLTA
Ggallus  all identical  ENSGALG00000006968  491NQSPFMATMAQIQN
Trubripes  not conserved  ENSTRUG00000016222  344------KQVSGGGPLPPVSTLTS
Drerio  all identical  ENSDARG00000009470  437IAQQLQSHIAPSSFMATMAQL--
Dmelanogaster  no homologue    
Celegans  all conserved  F54A5.1  237LIRMLESFFTQTPFPDLPRRVEIANAC
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1572 / 1572
position (AA) of stopcodon in wt / mu AA sequence 524 / 524
position of stopcodon in wt / mu cDNA 1715 / 1715
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 144 / 144
chromosome 12
strand 1
last intron/exon boundary 1588
theoretical NMD boundary in CDS 1394
length of CDS 1572
coding sequence (CDS) position 1136
cDNA position
(for ins/del: last normal base / first normal base)		 1279
gDNA position
(for ins/del: last normal base / first normal base)		 19082
chromosomal position
(for ins/del: last normal base / first normal base)		 121435427
original gDNA sequence snippet GCAGAGCCATGTGACCCAGAGCCCCTTCATGGCCACCATGG
altered gDNA sequence snippet GCAGAGCCATGTGACCCAGAACCCCTTCATGGCCACCATGG
original cDNA sequence snippet GCAGAGCCATGTGACCCAGAGCCCCTTCATGGCCACCATGG
altered cDNA sequence snippet GCAGAGCCATGTGACCCAGAACCCCTTCATGGCCACCATGG
wildtype AA sequence MVSKLSQLQT ELLAALLESG LSKEALIQAL GEPGPYLLAG EGPLDKGESC GGGRGELAEL
PNGLGETRGS EDETDDDGED FTPPILKELE NLSPEEAAHQ KAVVETLLQE DPWRVAKMVK
SYLQQHNIPQ REVVDTTGLN QSHLSQHLNK GTPMKTQKRA ALYTWYVRKQ REVAQQFTHA
GQGGLIEEPT GDELPTKKGR RNRFKWGPAS QQILFQAYER QKNPSKEERE TLVEECNRAE
CIQRGVSPSQ AQGLGSNLVT EVSAAGGPLP PVSTLTALHS LEQTSPGLNQ QPQNLIMASL
PGVMTIGPGE PASLGPTFTN TGASTLVIGL ASTQAQSVPV INSMGSSLTT LQPVQFSQPL
HPSYQQPLMP PVQSHVTQSP FMATMAQLQS PHALYSHKPE VAQYTHTGLL PQTMLITDTT
NLSALASLTP TKQVFTSDTE ASSESGLHTP ASQATTLHVP SQDPASIQHL QPAHRLSASP
TVSSSSLVLY QSSDSSNGQS HLLPSNHSVI ETFISTQMAS SSQ*
mutated AA sequence MVSKLSQLQT ELLAALLESG LSKEALIQAL GEPGPYLLAG EGPLDKGESC GGGRGELAEL
PNGLGETRGS EDETDDDGED FTPPILKELE NLSPEEAAHQ KAVVETLLQE DPWRVAKMVK
SYLQQHNIPQ REVVDTTGLN QSHLSQHLNK GTPMKTQKRA ALYTWYVRKQ REVAQQFTHA
GQGGLIEEPT GDELPTKKGR RNRFKWGPAS QQILFQAYER QKNPSKEERE TLVEECNRAE
CIQRGVSPSQ AQGLGSNLVT EVSAAGGPLP PVSTLTALHS LEQTSPGLNQ QPQNLIMASL
PGVMTIGPGE PASLGPTFTN TGASTLVIGL ASTQAQSVPV INSMGSSLTT LQPVQFSQPL
HPSYQQPLMP PVQSHVTQNP FMATMAQLQS PHALYSHKPE VAQYTHTGLL PQTMLITDTT
NLSALASLTP TKQVFTSDTE ASSESGLHTP ASQATTLHVP SQDPASIQHL QPAHRLSASP
TVSSSSLVLY QSSDSSNGQS HLLPSNHSVI ETFISTQMAS SSQ*
speed 0.58 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