Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999987294 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM001614)
  • known disease mutation: rs17806 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:28913549C>TN/A show variant in all transcripts   IGV
HGNC symbol ATP2A1
Ensembl transcript ID ENST00000536376
Genbank transcript ID N/A
UniProt peptide O14983
alteration type single base exchange
alteration region CDS
DNA changes c.1991C>T
cDNA.2189C>T
g.23824C>T
AA changes P664L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 664
frameshift no
known variant Reference ID: rs121918115
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17806 (pathogenic for Brody myopathy) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001614)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001614)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001614)
regulatory features PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5811
5.5811
(flanking)-1.6110.026
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 45
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      664TAALGLPEALIPVQLLWVNLVTDG
mutated  not conserved    664ALILVQLLWVNLVTD
Ptroglodytes  all identical  ENSPTRG00000007941  742TAALGLPEALIPVQLLWVNLVTD
Mmulatta  all identical  ENSMMUG00000023526  70ALGLPEALIPVQLLWVNLVTD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000030730  789ALIPVQLLWVNLVTD
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006333  786ALIPVQLLWVNLVTD
Drerio  all identical  ENSDARG00000020574  789ALIPVQLLWVNLVTD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000009695  789ALIPVQLLWVNLVTD
protein features
start (aa)end (aa)featuredetails 
314757TOPO_DOMCytoplasmic (By similarity).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2610 / 2610
position (AA) of stopcodon in wt / mu AA sequence 870 / 870
position of stopcodon in wt / mu cDNA 2808 / 2808
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 199 / 199
chromosome 16
strand 1
last intron/exon boundary 2846
theoretical NMD boundary in CDS 2597
length of CDS 2610
coding sequence (CDS) position 1991
cDNA position
(for ins/del: last normal base / first normal base)		 2189
gDNA position
(for ins/del: last normal base / first normal base)		 23824
chromosomal position
(for ins/del: last normal base / first normal base)		 28913549
original gDNA sequence snippet GCTGCCTGAGGCCCTGATCCCGGTGCAGCTGCTATGGGTGA
altered gDNA sequence snippet GCTGCCTGAGGCCCTGATCCTGGTGCAGCTGCTATGGGTGA
original cDNA sequence snippet GCTGCCTGAGGCCCTGATCCCGGTGCAGCTGCTATGGGTGA
altered cDNA sequence snippet GCTGCCTGAGGCCCTGATCCTGGTGCAGCTGCTATGGGTGA
wildtype AA sequence MGKVYRADRK SVQRIKARDI VPGDIVEVAV GDKVPADIRI LAIKSTTLRV DQSILTGESV
SVIKHTEPVP DPRAVNQDKK NMLFSGTNIA AGKALGIVAT TGVGTEIGKI RDQMAATEQD
KTPLQQKLDE FGEQLSKVIS LICVAVWLIN IGHFNDPVHG GSWFRGAIYY FKIAVALAVA
AIPEGLPAVI TTCLALGTRR MAKKNAIVRS LPSVETLGCT SVICSDKTGT LTTNQMSVCK
MFIIDKVDGD ICLLNEFSIT GSTYAPEGEV LKNDKPVRPG QYDGLVELAT ICALCNDSSL
DFNEAKGVYE KVGEATETAL TTLVEKMNVF NTDVRSLSKV ERANACNSVI RQLMKKEFTL
EFSRDRKSMS VYCSPAKSSR AAVGNKMFVK GAPEGVIDRC NYVRVGTTRV PLTGPVKEKI
MAVIKEWGTG RDTLRCLALA TRDTPPKREE MVLDDSARFL EYETDLTFVG VVGMLDPPRK
EVTGSIQLCR DAGIRVIMIT GDNKGTAIAI CRRIGIFGEN EEVADRAYTG REFDDLPLAE
QREACRRACC FARVEPSHKS KIVEYLQSYD EITAMTGDGV NDAPALKKAE IGIAMGSGTA
VAKTASEMVL ADDNFSTIVA AVEEGRAIYN NMKQFIRYLI SSNVGEVVCI FLTAALGLPE
ALIPVQLLWV NLVTDGLPAT ALGFNPPDLD IMDRPPRSPK EPLISGWLFF RYMAIGGYVG
AATVGAAAWW FLYAEDGPHV NYSQLTHFMQ CTEDNTHFEG IDCEVFEAPE PMTMALSVLV
TIEMCNALNS LSENQSLLRM PPWVNIWLLG SICLSMSLHF LILYVDPLPM IFKLRALDLT
QWLMVLKISL PVIGLDEILK FVARNYLEG*
mutated AA sequence MGKVYRADRK SVQRIKARDI VPGDIVEVAV GDKVPADIRI LAIKSTTLRV DQSILTGESV
SVIKHTEPVP DPRAVNQDKK NMLFSGTNIA AGKALGIVAT TGVGTEIGKI RDQMAATEQD
KTPLQQKLDE FGEQLSKVIS LICVAVWLIN IGHFNDPVHG GSWFRGAIYY FKIAVALAVA
AIPEGLPAVI TTCLALGTRR MAKKNAIVRS LPSVETLGCT SVICSDKTGT LTTNQMSVCK
MFIIDKVDGD ICLLNEFSIT GSTYAPEGEV LKNDKPVRPG QYDGLVELAT ICALCNDSSL
DFNEAKGVYE KVGEATETAL TTLVEKMNVF NTDVRSLSKV ERANACNSVI RQLMKKEFTL
EFSRDRKSMS VYCSPAKSSR AAVGNKMFVK GAPEGVIDRC NYVRVGTTRV PLTGPVKEKI
MAVIKEWGTG RDTLRCLALA TRDTPPKREE MVLDDSARFL EYETDLTFVG VVGMLDPPRK
EVTGSIQLCR DAGIRVIMIT GDNKGTAIAI CRRIGIFGEN EEVADRAYTG REFDDLPLAE
QREACRRACC FARVEPSHKS KIVEYLQSYD EITAMTGDGV NDAPALKKAE IGIAMGSGTA
VAKTASEMVL ADDNFSTIVA AVEEGRAIYN NMKQFIRYLI SSNVGEVVCI FLTAALGLPE
ALILVQLLWV NLVTDGLPAT ALGFNPPDLD IMDRPPRSPK EPLISGWLFF RYMAIGGYVG
AATVGAAAWW FLYAEDGPHV NYSQLTHFMQ CTEDNTHFEG IDCEVFEAPE PMTMALSVLV
TIEMCNALNS LSENQSLLRM PPWVNIWLLG SICLSMSLHF LILYVDPLPM IFKLRALDLT
QWLMVLKISL PVIGLDEILK FVARNYLEG*
speed 0.64 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