Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999917 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CI991972)
  • known disease mutation at this position (HGMD CM990244)
  • known disease mutation: rs17794 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:110777443T>CN/A show variant in all transcripts   IGV
HGNC symbol ATP2A2
Ensembl transcript ID ENST00000539276
Genbank transcript ID NM_170665
UniProt peptide P16615
alteration type single base exchange
alteration region CDS
DNA changes c.1678T>C
cDNA.1787T>C
g.58883T>C
AA changes C560R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 560
frameshift no
known variant Reference ID: rs121912734
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs17794 (pathogenic for Keratosis follicularis) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990244)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990244)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991972)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990244)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991972)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991972)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990244)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991972)
known disease mutation at this position, please check HGMD for details (HGMD ID CI991972)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990244)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4340.901
5.1711
(flanking)6.2621
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased58878wt: 0.9945 / mu: 0.9964 (marginal change - not scored)wt: CACACTGCGATGCCT
mu: CACACTGCGACGCCT		 CACT|gcga
distance from splice site 84
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      560REWGSGSDTLRCLALATHDNPLRR
mutated  not conserved    560REWGSGSDTLRRLALATHDNPLR
Ptroglodytes  all identical  ENSPTRG00000005437  560REWGSGSDTLRCLALATHDNPLR
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000029467  560REWGSGSDTLRCLALATHDNPLK
Ggallus  all identical  ENSGALG00000003835  560REWGTGRDTLRCLALATHDNPPR
Trubripes  all identical  ENSTRUG00000015616  558REYGTGNDTLRCLALATRDNPPK
Drerio  all identical  ENSDARG00000029439  559REYGTGRDTLRCLALATRDNPLK
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000002512  576REWGTGRDTLRCLALATHDNPPR
protein features
start (aa)end (aa)featuredetails 
314756TOPO_DOMCytoplasmic (By similarity).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3129 / 3129
position (AA) of stopcodon in wt / mu AA sequence 1043 / 1043
position of stopcodon in wt / mu cDNA 3238 / 3238
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 110 / 110
chromosome 12
strand 1
last intron/exon boundary 2969
theoretical NMD boundary in CDS 2809
length of CDS 3129
coding sequence (CDS) position 1678
cDNA position
(for ins/del: last normal base / first normal base)		 1787
gDNA position
(for ins/del: last normal base / first normal base)		 58883
chromosomal position
(for ins/del: last normal base / first normal base)		 110777443
original gDNA sequence snippet GTGGCAGCGACACACTGCGATGCCTGGCCCTGGCCACTCAT
altered gDNA sequence snippet GTGGCAGCGACACACTGCGACGCCTGGCCCTGGCCACTCAT
original cDNA sequence snippet GTGGCAGCGACACACTGCGATGCCTGGCCCTGGCCACTCAT
altered cDNA sequence snippet GTGGCAGCGACACACTGCGACGCCTGGCCCTGGCCACTCAT
wildtype AA sequence MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILVA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RQDRKSVQRI KAKDIVPGDI VEIAVGDKVP ADIRLTSIKS TTLRVDQSIL
TGESVSVIKH TDPVPDPRAV NQDKKNMLFS GTNIAAGKAM GVVVATGVNT EIGKIRDEMV
ATEQERTPLQ QKLDEFGEQL SKVISLICIA VWIINIGHFN DPVHGGSWIR GAIYYFKIAV
ALAVAAIPEG LPAVITTCLA LGTRRMAKKN AIVRSLPSVE TLGCTSVICS DKTGTLTTNQ
MSVCRMFILD RVEGDTCSLN EFTITGSTYA PIGEVHKDDK PVNCHQYDGL VELATICALC
NDSALDYNEA KGVYEKVGEA TETALTCLVE KMNVFDTELK GLSKIERANA CNSVIKQLMK
KEFTLEFSRD RKSMSVYCTP NKPSRTSMSK MFVKGAPEGV IDRCTHIRVG STKVPMTSGV
KQKIMSVIRE WGSGSDTLRC LALATHDNPL RREEMHLEDS ANFIKYETNL TFVGCVGMLD
PPRIEVASSV KLCRQAGIRV IMITGDNKGT AVAICRRIGI FGQDEDVTSK AFTGREFDEL
NPSAQRDACL NARCFARVEP SHKSKIVEFL QSFDEITAMT GDGVNDAPAL KKAEIGIAMG
SGTAVAKTAS EMVLADDNFS TIVAAVEEGR AIYNNMKQFI RYLISSNVGE VVCIFLTAAL
GFPEALIPVQ LLWVNLVTDG LPATALGFNP PDLDIMNKPP RNPKEPLISG WLFFRYLAIG
CYVGAATVGA AAWWFIAADG GPRVSFYQLS HFLQCKEDNP DFEGVDCAIF ESPYPMTMAL
SVLVTIEMCN ALNSLSENQS LLRMPPWENI WLVGSICLSM SLHFLILYVE PLPLIFQITP
LNVTQWLMVL KISLPVILMD ETLKFVARNY LEPGKECVQP ATKSCSFSAC TDGISWPFVL
LIMPLVIWVY STDTNFSDMF WS*
mutated AA sequence MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILVA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RQDRKSVQRI KAKDIVPGDI VEIAVGDKVP ADIRLTSIKS TTLRVDQSIL
TGESVSVIKH TDPVPDPRAV NQDKKNMLFS GTNIAAGKAM GVVVATGVNT EIGKIRDEMV
ATEQERTPLQ QKLDEFGEQL SKVISLICIA VWIINIGHFN DPVHGGSWIR GAIYYFKIAV
ALAVAAIPEG LPAVITTCLA LGTRRMAKKN AIVRSLPSVE TLGCTSVICS DKTGTLTTNQ
MSVCRMFILD RVEGDTCSLN EFTITGSTYA PIGEVHKDDK PVNCHQYDGL VELATICALC
NDSALDYNEA KGVYEKVGEA TETALTCLVE KMNVFDTELK GLSKIERANA CNSVIKQLMK
KEFTLEFSRD RKSMSVYCTP NKPSRTSMSK MFVKGAPEGV IDRCTHIRVG STKVPMTSGV
KQKIMSVIRE WGSGSDTLRR LALATHDNPL RREEMHLEDS ANFIKYETNL TFVGCVGMLD
PPRIEVASSV KLCRQAGIRV IMITGDNKGT AVAICRRIGI FGQDEDVTSK AFTGREFDEL
NPSAQRDACL NARCFARVEP SHKSKIVEFL QSFDEITAMT GDGVNDAPAL KKAEIGIAMG
SGTAVAKTAS EMVLADDNFS TIVAAVEEGR AIYNNMKQFI RYLISSNVGE VVCIFLTAAL
GFPEALIPVQ LLWVNLVTDG LPATALGFNP PDLDIMNKPP RNPKEPLISG WLFFRYLAIG
CYVGAATVGA AAWWFIAADG GPRVSFYQLS HFLQCKEDNP DFEGVDCAIF ESPYPMTMAL
SVLVTIEMCN ALNSLSENQS LLRMPPWENI WLVGSICLSM SLHFLILYVE PLPLIFQITP
LNVTQWLMVL KISLPVILMD ETLKFVARNY LEPGKECVQP ATKSCSFSAC TDGISWPFVL
LIMPLVIWVY STDTNFSDMF WS*
speed 1.01 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