Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993431438 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042307)
  • known disease mutation: rs12913 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:42474620A>GN/A show variant in all transcripts   IGV
HGNC symbol ATP1A3
Ensembl transcript ID ENST00000545399
Genbank transcript ID NM_001256214
UniProt peptide P13637
alteration type single base exchange
alteration region CDS
DNA changes c.2377T>C
cDNA.2531T>C
g.23765T>C
AA changes F793L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 793
frameshift no
known variant Reference ID: rs80356536
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs12913 (pathogenic for Dystonia 12) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042307)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042307)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042307)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.9911
3.9911
(flanking)1.4181
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 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      793TLTSNIPEITPFLLFIMANIPLPL
mutated  not conserved    793TLTSNIPEITPLLLFIMANIPLP
Ptroglodytes  no alignment  ENSPTRG00000011041  n/a
Mmulatta  all identical  ENSMMUG00000017427  780TLTSNIPEITPFLL
Fcatus  all identical  ENSFCAG00000012729  680TLTSNIPEITPFLLFIMANIPLP
Mmusculus  all identical  ENSMUSG00000040907  780TLTSNIPEITPFLL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008243  787TSNIPEITPFLFFIIVNIPLP
Drerio  all identical  ENSDARG00000018259  790TLTSNIPEITPFLFFILVNIPLP
Dmelanogaster  all identical  FBgn0002921  808TLTSNIPEISPFLAFILCDIPLP
Celegans  all identical  B0365.3  763TLTSNIPEISPFLTYILFGIPLP
Xtropicalis  all identical  ENSXETG00000023811  792TSNIPEITPFLLFIMANIPLP
protein features
start (aa)end (aa)featuredetails 
793813TRANSMEMHelical; (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3081 / 3081
position (AA) of stopcodon in wt / mu AA sequence 1027 / 1027
position of stopcodon in wt / mu cDNA 3235 / 3235
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 155 / 155
chromosome 19
strand -1
last intron/exon boundary 3207
theoretical NMD boundary in CDS 3002
length of CDS 3081
coding sequence (CDS) position 2377
cDNA position
(for ins/del: last normal base / first normal base)		 2531
gDNA position
(for ins/del: last normal base / first normal base)		 23765
chromosomal position
(for ins/del: last normal base / first normal base)		 42474620
original gDNA sequence snippet ATATCCCGGAGATCACGCCCTTCCTGCTGTTCATCATGGCC
altered gDNA sequence snippet ATATCCCGGAGATCACGCCCCTCCTGCTGTTCATCATGGCC
original cDNA sequence snippet ATATCCCGGAGATCACGCCCTTCCTGCTGTTCATCATGGCC
altered cDNA sequence snippet ATATCCCGGAGATCACGCCCCTCCTGCTGTTCATCATGGCC
wildtype AA sequence MGSGGSDSYR IATSQDKKDD KDSPKKNKGK ERRDLDDLKK EVAMTEHKMS VEEVCRKYNT
DCVQGLTHSK AQEILARDGP NALTPPPTTP EWVKFCRQLF GGFSILLWIG AILCFLAYGI
QAGTEDDPSG DNLYLGIVLA AVVIITGCFS YYQEAKSSKI MESFKNMVPQ QALVIREGEK
MQVNAEEVVV GDLVEIKGGD RVPADLRIIS AHGCKVDNSS LTGESEPQTR SPDCTHDNPL
ETRNITFFST NCVEGTARGV VVATGDRTVM GRIATLASGL EVGKTPIAIE IEHFIQLITG
VAVFLGVSFF ILSLILGYTW LEAVIFLIGI IVANVPEGLL ATVTVCLTLT AKRMARKNCL
VKNLEAVETL GSTSTICSDK TGTLTQNRMT VAHMWFDNQI HEADTTEDQS GTSFDKSSHT
WVALSHIAGL CNRAVFKGGQ DNIPVLKRDV AGDASESALL KCIELSSGSV KLMRERNKKV
AEIPFNSTNK YQLSIHETED PNDNRYLLVM KGAPERILDR CSTILLQGKE QPLDEEMKEA
FQNAYLELGG LGERVLGFCH YYLPEEQFPK GFAFDCDDVN FTTDNLCFVG LMSMIDPPRA
AVPDAVGKCR SAGIKVIMVT GDHPITAKAI AKGVGIISEG NETVEDIAAR LNIPVSQVNP
RDAKACVIHG TDLKDFTSEQ IDEILQNHTE IVFARTSPQQ KLIIVEGCQR QGAIVAVTGD
GVNDSPALKK ADIGVAMGIA GSDVSKQAAD MILLDDNFAS IVTGVEEGRL IFDNLKKSIA
YTLTSNIPEI TPFLLFIMAN IPLPLGTITI LCIDLGTDMV PAISLAYEAA ESDIMKRQPR
NPRTDKLVNE RLISMAYGQI GMIQALGGFF SYFVILAENG FLPGNLVGIR LNWDDRTVND
LEDSYGQQWT YEQRKVVEFT CHTAFFVSIV VVQWADLIIC KTRRNSVFQQ GMKNKILIFG
LFEETALAAF LSYCPGMDVA LRMYPLKPSW WFCAFPYSFL IFVYDEIRKL ILRRNPGGWV
EKETYY*
mutated AA sequence MGSGGSDSYR IATSQDKKDD KDSPKKNKGK ERRDLDDLKK EVAMTEHKMS VEEVCRKYNT
DCVQGLTHSK AQEILARDGP NALTPPPTTP EWVKFCRQLF GGFSILLWIG AILCFLAYGI
QAGTEDDPSG DNLYLGIVLA AVVIITGCFS YYQEAKSSKI MESFKNMVPQ QALVIREGEK
MQVNAEEVVV GDLVEIKGGD RVPADLRIIS AHGCKVDNSS LTGESEPQTR SPDCTHDNPL
ETRNITFFST NCVEGTARGV VVATGDRTVM GRIATLASGL EVGKTPIAIE IEHFIQLITG
VAVFLGVSFF ILSLILGYTW LEAVIFLIGI IVANVPEGLL ATVTVCLTLT AKRMARKNCL
VKNLEAVETL GSTSTICSDK TGTLTQNRMT VAHMWFDNQI HEADTTEDQS GTSFDKSSHT
WVALSHIAGL CNRAVFKGGQ DNIPVLKRDV AGDASESALL KCIELSSGSV KLMRERNKKV
AEIPFNSTNK YQLSIHETED PNDNRYLLVM KGAPERILDR CSTILLQGKE QPLDEEMKEA
FQNAYLELGG LGERVLGFCH YYLPEEQFPK GFAFDCDDVN FTTDNLCFVG LMSMIDPPRA
AVPDAVGKCR SAGIKVIMVT GDHPITAKAI AKGVGIISEG NETVEDIAAR LNIPVSQVNP
RDAKACVIHG TDLKDFTSEQ IDEILQNHTE IVFARTSPQQ KLIIVEGCQR QGAIVAVTGD
GVNDSPALKK ADIGVAMGIA GSDVSKQAAD MILLDDNFAS IVTGVEEGRL IFDNLKKSIA
YTLTSNIPEI TPLLLFIMAN IPLPLGTITI LCIDLGTDMV PAISLAYEAA ESDIMKRQPR
NPRTDKLVNE RLISMAYGQI GMIQALGGFF SYFVILAENG FLPGNLVGIR LNWDDRTVND
LEDSYGQQWT YEQRKVVEFT CHTAFFVSIV VVQWADLIIC KTRRNSVFQQ GMKNKILIFG
LFEETALAAF LSYCPGMDVA LRMYPLKPSW WFCAFPYSFL IFVYDEIRKL ILRRNPGGWV
EKETYY*
speed 0.59 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