Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999996153683 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042303)
  • known disease mutation at this position (HGMD CM127590)
  • known disease mutation: rs12910 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:42489242A>GN/A show variant in all transcripts   IGV
HGNC symbol ATP1A3
Ensembl transcript ID ENST00000543770
Genbank transcript ID NM_001256213
UniProt peptide P13637
alteration type single base exchange
alteration region CDS
DNA changes c.854T>C
cDNA.890T>C
g.9143T>C
AA changes I285T Score: 89 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 285
frameshift no
known variant Reference ID: rs80356532
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs12910 (pathogenic for Dystonia 12) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042303)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127590)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042303)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127590)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042303)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0410.993
4.1551
(flanking)4.1551
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 97
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      285LASGLEVGKTPIAIEIEHFIQLIT
mutated  not conserved    285LASGLEVGKTPTAIEIEHFIQLI
Ptroglodytes  no alignment  ENSPTRG00000011041  n/a
Mmulatta  all identical  ENSMMUG00000017427  274LASGLEVGKTPIAIEIEHFIQLI
Fcatus  all identical  ENSFCAG00000012729  174IAIEIEHFIQLI
Mmusculus  all identical  ENSMUSG00000040907  274LASGLEVGKTPIAIEIEHFIQLI
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008243  281LTSGLETGKTPIAKEIEHFIHII
Drerio  all identical  ENSDARG00000018259  284LTSGLETGKTPIAKEIEHFIHII
Dmelanogaster  all identical  FBgn0002921  302LASGLDTGETPIAKEIHHFIHLI
Celegans  all identical  B0365.3  262LASGLDTGMTPIAREIEHFIHLI
Xtropicalis  all identical  ENSXETG00000023811  286LASGLEVGKTPIAKEIEHFIHLI
protein features
start (aa)end (aa)featuredetails 
279298TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3075 / 3075
position (AA) of stopcodon in wt / mu AA sequence 1025 / 1025
position of stopcodon in wt / mu cDNA 3111 / 3111
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 37 / 37
chromosome 19
strand -1
last intron/exon boundary 3083
theoretical NMD boundary in CDS 2996
length of CDS 3075
coding sequence (CDS) position 854
cDNA position
(for ins/del: last normal base / first normal base)		 890
gDNA position
(for ins/del: last normal base / first normal base)		 9143
chromosomal position
(for ins/del: last normal base / first normal base)		 42489242
original gDNA sequence snippet GGAGGTGGGCAAGACGCCCATCGCCATCGAGATTGAGCACT
altered gDNA sequence snippet GGAGGTGGGCAAGACGCCCACCGCCATCGAGATTGAGCACT
original cDNA sequence snippet GGAGGTGGGCAAGACGCCCATCGCCATCGAGATTGAGCACT
altered cDNA sequence snippet GGAGGTGGGCAAGACGCCCACCGCCATCGAGATTGAGCACT
wildtype AA sequence MGGWEEERNR RATDKKDDKD SPKKNKGKER RDLDDLKKEV AMTEHKMSVE EVCRKYNTDC
VQGLTHSKAQ EILARDGPNA LTPPPTTPEW VKFCRQLFGG FSILLWIGAI LCFLAYGIQA
GTEDDPSGDN LYLGIVLAAV VIITGCFSYY QEAKSSKIME SFKNMVPQQA LVIREGEKMQ
VNAEEVVVGD LVEIKGGDRV PADLRIISAH GCKVDNSSLT GESEPQTRSP DCTHDNPLET
RNITFFSTNC VEGTARGVVV ATGDRTVMGR IATLASGLEV GKTPIAIEIE HFIQLITGVA
VFLGVSFFIL SLILGYTWLE AVIFLIGIIV ANVPEGLLAT VTVCLTLTAK RMARKNCLVK
NLEAVETLGS TSTICSDKTG TLTQNRMTVA HMWFDNQIHE ADTTEDQSGT SFDKSSHTWV
ALSHIAGLCN RAVFKGGQDN IPVLKRDVAG DASESALLKC IELSSGSVKL MRERNKKVAE
IPFNSTNKYQ LSIHETEDPN DNRYLLVMKG APERILDRCS TILLQGKEQP LDEEMKEAFQ
NAYLELGGLG ERVLGFCHYY LPEEQFPKGF AFDCDDVNFT TDNLCFVGLM SMIDPPRAAV
PDAVGKCRSA GIKVIMVTGD HPITAKAIAK GVGIISEGNE TVEDIAARLN IPVSQVNPRD
AKACVIHGTD LKDFTSEQID EILQNHTEIV FARTSPQQKL IIVEGCQRQG AIVAVTGDGV
NDSPALKKAD IGVAMGIAGS DVSKQAADMI LLDDNFASIV TGVEEGRLIF DNLKKSIAYT
LTSNIPEITP FLLFIMANIP LPLGTITILC IDLGTDMVPA ISLAYEAAES DIMKRQPRNP
RTDKLVNERL ISMAYGQIGM IQALGGFFSY FVILAENGFL PGNLVGIRLN WDDRTVNDLE
DSYGQQWTYE QRKVVEFTCH TAFFVSIVVV QWADLIICKT RRNSVFQQGM KNKILIFGLF
EETALAAFLS YCPGMDVALR MYPLKPSWWF CAFPYSFLIF VYDEIRKLIL RRNPGGWVEK
ETYY*
mutated AA sequence MGGWEEERNR RATDKKDDKD SPKKNKGKER RDLDDLKKEV AMTEHKMSVE EVCRKYNTDC
VQGLTHSKAQ EILARDGPNA LTPPPTTPEW VKFCRQLFGG FSILLWIGAI LCFLAYGIQA
GTEDDPSGDN LYLGIVLAAV VIITGCFSYY QEAKSSKIME SFKNMVPQQA LVIREGEKMQ
VNAEEVVVGD LVEIKGGDRV PADLRIISAH GCKVDNSSLT GESEPQTRSP DCTHDNPLET
RNITFFSTNC VEGTARGVVV ATGDRTVMGR IATLASGLEV GKTPTAIEIE HFIQLITGVA
VFLGVSFFIL SLILGYTWLE AVIFLIGIIV ANVPEGLLAT VTVCLTLTAK RMARKNCLVK
NLEAVETLGS TSTICSDKTG TLTQNRMTVA HMWFDNQIHE ADTTEDQSGT SFDKSSHTWV
ALSHIAGLCN RAVFKGGQDN IPVLKRDVAG DASESALLKC IELSSGSVKL MRERNKKVAE
IPFNSTNKYQ LSIHETEDPN DNRYLLVMKG APERILDRCS TILLQGKEQP LDEEMKEAFQ
NAYLELGGLG ERVLGFCHYY LPEEQFPKGF AFDCDDVNFT TDNLCFVGLM SMIDPPRAAV
PDAVGKCRSA GIKVIMVTGD HPITAKAIAK GVGIISEGNE TVEDIAARLN IPVSQVNPRD
AKACVIHGTD LKDFTSEQID EILQNHTEIV FARTSPQQKL IIVEGCQRQG AIVAVTGDGV
NDSPALKKAD IGVAMGIAGS DVSKQAADMI LLDDNFASIV TGVEEGRLIF DNLKKSIAYT
LTSNIPEITP FLLFIMANIP LPLGTITILC IDLGTDMVPA ISLAYEAAES DIMKRQPRNP
RTDKLVNERL ISMAYGQIGM IQALGGFFSY FVILAENGFL PGNLVGIRLN WDDRTVNDLE
DSYGQQWTYE QRKVVEFTCH TAFFVSIVVV QWADLIICKT RRNSVFQQGM KNKILIFGLF
EETALAAFLS YCPGMDVALR MYPLKPSWWF CAFPYSFLIF VYDEIRKLIL RRNPGGWVEK
ETYY*
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