Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999705421 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM042308)
  • known disease mutation at this position (HGMD CM127591)
  • known disease mutation: rs12914 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:42474557C>AN/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.2440G>T
cDNA.2594G>T
g.23828G>T
AA changes D814Y Score: 160 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 814
frameshift no
known variant Reference ID: rs80356537
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs12914 (pathogenic for Dystonia 12) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042308)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042308)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127591)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042308)
known disease mutation at this position, please check HGMD for details (HGMD ID CM127591)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042308)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.9911
4.8311
(flanking)0.231
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 increased23828wt: 0.9329 / mu: 0.9452 (marginal change - not scored)wt: CCATCACCATCCTCTGCATCGATCTGGGCACTGACATGGTG
mu: CCATCACCATCCTCTGCATCTATCTGGGCACTGACATGGTG		 atcg|ATCT
Acc marginally increased23832wt: 0.9066 / mu: 0.9768 (marginal change - not scored)wt: CACCATCCTCTGCATCGATCTGGGCACTGACATGGTGAGCC
mu: CACCATCCTCTGCATCTATCTGGGCACTGACATGGTGAGCC		 atct|GGGC
Acc marginally increased23826wt: 0.9142 / mu: 0.9650 (marginal change - not scored)wt: CACCATCACCATCCTCTGCATCGATCTGGGCACTGACATGG
mu: CACCATCACCATCCTCTGCATCTATCTGGGCACTGACATGG		 gcat|CGAT
Acc increased23834wt: 0.50 / mu: 0.86wt: CCATCCTCTGCATCGATCTGGGCACTGACATGGTGAGCCCT
mu: CCATCCTCTGCATCTATCTGGGCACTGACATGGTGAGCCCT		 ctgg|GCAC
Acc increased23829wt: 0.34 / mu: 0.39wt: CATCACCATCCTCTGCATCGATCTGGGCACTGACATGGTGA
mu: CATCACCATCCTCTGCATCTATCTGGGCACTGACATGGTGA		 tcga|TCTG
Acc gained238330.71mu: ACCATCCTCTGCATCTATCTGGGCACTGACATGGTGAGCCC tctg|GGCA
distance from splice site 18
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      814LPLGTITILCIDLGTDMVPAISLA
mutated  not conserved    814LPLGTITILCIYLGTDMVPAISL
Ptroglodytes  no alignment  ENSPTRG00000011041  n/a
Mmulatta  all identical  ENSMMUG00000017427  801LPLGTITILCIDLGTDMVPAISL
Fcatus  all identical  ENSFCAG00000012729  701LPLGTITILCIDLGTDMVPAISL
Mmusculus  all identical  ENSMUSG00000040907  801LPLGTITILCIDLGTDMVPAISL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008243  808LPLGTITILCIDLGTDMVPAISL
Drerio  all identical  ENSDARG00000018259  811LPLGTITILCIDLGTDMVPAISL
Dmelanogaster  all identical  FBgn0002921  829LPLGTVTILCIDLGTDMVPAISL
Celegans  all identical  B0365.3  784VTILCIDLGTDMVPAISL
Xtropicalis  all identical  ENSXETG00000023811  813LPLGTITILCIDLGTDMVPAISL
protein features
start (aa)end (aa)featuredetails 
814833TOPO_DOMCytoplasmic (Potential).lost
834856TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
857908TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
909928TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
919919CONFLICTV -> A (in Ref. 5; AAA52286).might get lost (downstream of altered splice site)
929941TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
933933MOD_RESPhosphoserine; by PKA (By similarity).might get lost (downstream of altered splice site)
942960TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
944944CONFLICTL -> M (in Ref. 5; AAA52286).might get lost (downstream of altered splice site)
961975TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
976996TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
982982CONFLICTF -> S (in Ref. 2; CAA31390).might get lost (downstream of altered splice site)
9971013TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10061006CONFLICTW -> S (in Ref. 1; AAA51798).might get lost (downstream of altered splice site)
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 2440
cDNA position
(for ins/del: last normal base / first normal base)		 2594
gDNA position
(for ins/del: last normal base / first normal base)		 23828
chromosomal position
(for ins/del: last normal base / first normal base)		 42474557
original gDNA sequence snippet CCATCACCATCCTCTGCATCGATCTGGGCACTGACATGGTG
altered gDNA sequence snippet CCATCACCATCCTCTGCATCTATCTGGGCACTGACATGGTG
original cDNA sequence snippet CCATCACCATCCTCTGCATCGATCTGGGCACTGACATGGTC
altered cDNA sequence snippet CCATCACCATCCTCTGCATCTATCTGGGCACTGACATGGTC
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 TPFLLFIMAN IPLPLGTITI LCIYLGTDMV PAISLAYEAA ESDIMKRQPR
NPRTDKLVNE RLISMAYGQI GMIQALGGFF SYFVILAENG FLPGNLVGIR LNWDDRTVND
LEDSYGQQWT YEQRKVVEFT CHTAFFVSIV VVQWADLIIC KTRRNSVFQQ GMKNKILIFG
LFEETALAAF LSYCPGMDVA LRMYPLKPSW WFCAFPYSFL IFVYDEIRKL ILRRNPGGWV
EKETYY*
speed 0.84 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