Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999919139 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM164207)
  • known disease mutation at this position (HGMD CM990235)
  • known disease mutation: rs17793 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:110765530G>TN/A show variant in all transcripts   IGV
HGNC symbol ATP2A2
Ensembl transcript ID ENST00000308664
Genbank transcript ID NM_001681
UniProt peptide P16615
alteration type single base exchange
alteration region CDS
DNA changes c.803G>T
cDNA.1477G>T
g.46970G>T
AA changes C268F Score: 205 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 268
frameshift no
known variant Reference ID: rs121912733
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs17793 (pathogenic for Darier disease, acral hemorrhagic type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM164207)

known disease mutation at this position, please check HGMD for details (HGMD ID CM164207)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990235)

known disease mutation at this position, please check HGMD for details (HGMD ID CM164207)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990235)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990235)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.11
6.1761
(flanking)2.6991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased46974wt: 0.28 / mu: 0.85wt: GTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATAT
mu: GTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATAT		 catt|GCAG
Acc marginally increased46970wt: 0.7551 / mu: 0.7912 (marginal change - not scored)wt: CAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAA
mu: CAAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAA		 tttg|CATT
Acc marginally increased46967wt: 0.8006 / mu: 0.8527 (marginal change - not scored)wt: TTCCAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCA
mu: TTCCAAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCA		 ttat|TTGC
Acc increased46978wt: 0.54 / mu: 0.88wt: TCTCCCTTATTTGCATTGCAGTCTGGATCATAAATATTGGG
mu: TCTCCCTTATTTTCATTGCAGTCTGGATCATAAATATTGGG		 gcag|TCTG
Acc marginally increased46976wt: 0.9204 / mu: 0.9796 (marginal change - not scored)wt: CATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATATTG
mu: CATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATATTG		 ttgc|AGTC
Acc marginally increased46971wt: 0.9122 / mu: 0.9204 (marginal change - not scored)wt: AAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAA
mu: AAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAA		 ttgc|ATTG
Donor increased46972wt: 0.28 / mu: 0.67wt: TTTGCATTGCAGTCT
mu: TTTTCATTGCAGTCT		 TGCA|ttgc
Acc gained469750.83mu: TCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATATT attg|CAGT
Acc gained469720.85mu: AAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAAT ttca|TTGC
distance from splice site 173
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      268GEQLSKVISLICIAVWIINIGHFN
mutated  not conserved    268GEQLSKVISLIFIAVWIINIGHF
Ptroglodytes  all identical  ENSPTRG00000005437  268GEQLSKVISLICIAVWIINIGHF
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000029467  268GEQLSKVISLICIAVWIINIGHF
Ggallus  all identical  ENSGALG00000003835  268GEQLSKVISLICIAVWIINIGHF
Trubripes  all identical  ENSTRUG00000015616  269GEQLSKVISLICIAVWIINIGHF
Drerio  all identical  ENSDARG00000029439  268GEQLSKVISLICIAVWIINIGHF
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000002512  281GEQLSKVISLICIAVWIINIGHF
protein features
start (aa)end (aa)featuredetails 
254273TRANSMEMHelical; Name=3; (By similarity).lost
274295TOPO_DOMLumenal (By similarity).might get lost (downstream of altered splice site)
294294MOD_RESNitrated tyrosine.might get lost (downstream of altered splice site)
295295MOD_RESNitrated tyrosine.might get lost (downstream of altered splice site)
296313TRANSMEMHelical; Name=4; (By similarity).might get lost (downstream of altered splice site)
304304METALCalcium 2; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
305305METALCalcium 2; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
307307METALCalcium 2; via carbonyl oxygen (By similarity).might get lost (downstream of altered splice site)
309309METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
314756TOPO_DOMCytoplasmic (By similarity).might get lost (downstream of altered splice site)
351351ACT_SITE4-aspartylphosphate intermediate (By similarity).might get lost (downstream of altered splice site)
370400REGIONInteracts with phospholamban 1 (By similarity).might get lost (downstream of altered splice site)
464464MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
537537MOD_RESPhosphothreonine (By similarity).might get lost (downstream of altered splice site)
575594REGIONInteracts with HAX1.might get lost (downstream of altered splice site)
663663MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
702702METALMagnesium (By similarity).might get lost (downstream of altered splice site)
706706METALMagnesium (By similarity).might get lost (downstream of altered splice site)
757776TRANSMEMHelical; Name=5; (By similarity).might get lost (downstream of altered splice site)
767767METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
770770METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
777786TOPO_DOMLumenal (By similarity).might get lost (downstream of altered splice site)
787807TRANSMEMHelical; Name=6; (By similarity).might get lost (downstream of altered splice site)
787807REGIONInteracts with phospholamban 2 (By similarity).might get lost (downstream of altered splice site)
795795METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
798798METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
799799METALCalcium 2 (By similarity).might get lost (downstream of altered splice site)
799799METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
808827TOPO_DOMCytoplasmic (By similarity).might get lost (downstream of altered splice site)
828850TRANSMEMHelical; Name=7; (By similarity).might get lost (downstream of altered splice site)
851896TOPO_DOMLumenal (By similarity).might get lost (downstream of altered splice site)
897916TRANSMEMHelical; Name=8; (By similarity).might get lost (downstream of altered splice site)
907907METALCalcium 1 (By similarity).might get lost (downstream of altered splice site)
917929TOPO_DOMCytoplasmic (By similarity).might get lost (downstream of altered splice site)
930948TRANSMEMHelical; Name=9; (By similarity).might get lost (downstream of altered splice site)
949963TOPO_DOMLumenal (By similarity).might get lost (downstream of altered splice site)
964984TRANSMEMHelical; Name=10; (By similarity).might get lost (downstream of altered splice site)
9851042TOPO_DOMCytoplasmic (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2994 / 2994
position (AA) of stopcodon in wt / mu AA sequence 998 / 998
position of stopcodon in wt / mu cDNA 3668 / 3668
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 675 / 675
chromosome 12
strand 1
last intron/exon boundary 3655
theoretical NMD boundary in CDS 2930
length of CDS 2994
coding sequence (CDS) position 803
cDNA position
(for ins/del: last normal base / first normal base)		 1477
gDNA position
(for ins/del: last normal base / first normal base)		 46970
chromosomal position
(for ins/del: last normal base / first normal base)		 110765530
original gDNA sequence snippet CAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAA
altered gDNA sequence snippet CAAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAA
original cDNA sequence snippet CAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAA
altered cDNA sequence snippet CAAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAA
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 LEPAILE*
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 SKVISLIFIA 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 LEPAILE*
speed 1.07 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