Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999994458 (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 ENST00000395503
Genbank transcript ID NM_004320
UniProt peptide O14983
alteration type single base exchange
alteration region CDS
DNA changes c.2366C>T
cDNA.2550C>T
g.23824C>T
AA changes P789L Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 789
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      789TAALGLPEALIPVQLLWVNLVTDG
mutated  not conserved    789LGLPEALILVQLLWVNLVTD
Ptroglodytes  all identical  ENSPTRG00000007941  742LGLPEALIPVQLLWVNLVTD
Mmulatta  all identical  ENSMMUG00000023526  70ALGLPEALIPVQLLWVNLVTD
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000030730  789LGLPEALIPVQLLWVNLVTD
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000006333  786LGLPEALIPVQLLWVNLVTD
Drerio  all identical  ENSDARG00000020574  789LGLPEALIPVQLLWVNLVTD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000009695  789LGLPEALIPVQLLWVNLVTD
protein features
start (aa)end (aa)featuredetails 
788808TRANSMEMHelical; Name=6; (By similarity).lost
788808REGIONInteracts with phospholamban 2 (By similarity).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2985 / 2985
position (AA) of stopcodon in wt / mu AA sequence 995 / 995
position of stopcodon in wt / mu cDNA 3169 / 3169
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 185 / 185
chromosome 16
strand 1
last intron/exon boundary 3207
theoretical NMD boundary in CDS 2972
length of CDS 2985
coding sequence (CDS) position 2366
cDNA position
(for ins/del: last normal base / first normal base)		 2550
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 MEAAHAKTTE ECLAYFGVSE TTGLTPDQVK RNLEKYGLNE LPAEEGKTLW ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILIA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RADRKSVQRI KARDIVPGDI VEVAVGDKVP ADIRILAIKS TTLRVDQSIL
TGESVSVIKH TEPVPDPRAV NQDKKNMLFS GTNIAAGKAL GIVATTGVGT EIGKIRDQMA
ATEQDKTPLQ QKLDEFGEQL SKVISLICVA VWLINIGHFN DPVHGGSWFR GAIYYFKIAV
ALAVAAIPEG LPAVITTCLA LGTRRMAKKN AIVRSLPSVE TLGCTSVICS DKTGTLTTNQ
MSVCKMFIID KVDGDICLLN EFSITGSTYA PEGEVLKNDK PVRPGQYDGL VELATICALC
NDSSLDFNEA KGVYEKVGEA TETALTTLVE KMNVFNTDVR SLSKVERANA CNSVIRQLMK
KEFTLEFSRD RKSMSVYCSP AKSSRAAVGN KMFVKGAPEG VIDRCNYVRV GTTRVPLTGP
VKEKIMAVIK EWGTGRDTLR CLALATRDTP PKREEMVLDD SARFLEYETD LTFVGVVGML
DPPRKEVTGS IQLCRDAGIR VIMITGDNKG TAIAICRRIG IFGENEEVAD RAYTGREFDD
LPLAEQREAC RRACCFARVE PSHKSKIVEY LQSYDEITAM TGDGVNDAPA LKKAEIGIAM
GSGTAVAKTA SEMVLADDNF STIVAAVEEG RAIYNNMKQF IRYLISSNVG EVVCIFLTAA
LGLPEALIPV QLLWVNLVTD GLPATALGFN PPDLDIMDRP PRSPKEPLIS GWLFFRYMAI
GGYVGAATVG AAAWWFLYAE DGPHVNYSQL THFMQCTEDN THFEGIDCEV FEAPEPMTMA
LSVLVTIEMC NALNSLSENQ SLLRMPPWVN IWLLGSICLS MSLHFLILYV DPLPMIFKLR
ALDLTQWLMV LKISLPVIGL DEILKFVARN YLEG*
mutated AA sequence MEAAHAKTTE ECLAYFGVSE TTGLTPDQVK RNLEKYGLNE LPAEEGKTLW ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILIA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RADRKSVQRI KARDIVPGDI VEVAVGDKVP ADIRILAIKS TTLRVDQSIL
TGESVSVIKH TEPVPDPRAV NQDKKNMLFS GTNIAAGKAL GIVATTGVGT EIGKIRDQMA
ATEQDKTPLQ QKLDEFGEQL SKVISLICVA VWLINIGHFN DPVHGGSWFR GAIYYFKIAV
ALAVAAIPEG LPAVITTCLA LGTRRMAKKN AIVRSLPSVE TLGCTSVICS DKTGTLTTNQ
MSVCKMFIID KVDGDICLLN EFSITGSTYA PEGEVLKNDK PVRPGQYDGL VELATICALC
NDSSLDFNEA KGVYEKVGEA TETALTTLVE KMNVFNTDVR SLSKVERANA CNSVIRQLMK
KEFTLEFSRD RKSMSVYCSP AKSSRAAVGN KMFVKGAPEG VIDRCNYVRV GTTRVPLTGP
VKEKIMAVIK EWGTGRDTLR CLALATRDTP PKREEMVLDD SARFLEYETD LTFVGVVGML
DPPRKEVTGS IQLCRDAGIR VIMITGDNKG TAIAICRRIG IFGENEEVAD RAYTGREFDD
LPLAEQREAC RRACCFARVE PSHKSKIVEY LQSYDEITAM TGDGVNDAPA LKKAEIGIAM
GSGTAVAKTA SEMVLADDNF STIVAAVEEG RAIYNNMKQF IRYLISSNVG EVVCIFLTAA
LGLPEALILV QLLWVNLVTD GLPATALGFN PPDLDIMDRP PRSPKEPLIS GWLFFRYMAI
GGYVGAATVG AAAWWFLYAE DGPHVNYSQL THFMQCTEDN THFEGIDCEV FEAPEPMTMA
LSVLVTIEMC NALNSLSENQ SLLRMPPWVN IWLLGSICLS MSLHFLILYV DPLPMIFKLR
ALDLTQWLMV LKISLPVIGL DEILKFVARN YLEG*
speed 0.76 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