Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000308664
Querying Taster for transcript #2: ENST00000539276
Querying Taster for transcript #3: ENST00000395494
MT speed 4.05 s - this script 7.92336 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ATP2A2disease_causing_automatic0.999999999857627simple_aaeaffected0C241Fsingle base exchangers121912733show file
ATP2A2disease_causing_automatic0.999999999919139simple_aaeaffected0C268Fsingle base exchangers121912733show file
ATP2A2disease_causing_automatic0.999999999919139simple_aaeaffected0C268Fsingle base exchangers121912733show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999857627 (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 ENST00000395494
Genbank transcript ID N/A
UniProt peptide P16615
alteration type single base exchange
alteration region CDS
DNA changes c.722G>T
cDNA.1285G>T
g.46970G>T
AA changes C241F Score: 205 explain score(s)
position(s) of altered AA
if AA alteration in CDS
241
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 marginally increased46971wt: 0.9122 / mu: 0.9204 (marginal change - not scored)wt: AAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAA
mu: AAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAA
 ttgc|ATTG
Acc marginally increased46970wt: 0.7551 / mu: 0.7912 (marginal change - not scored)wt: CAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAA
mu: CAAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAA
 tttg|CATT
Acc increased46974wt: 0.28 / mu: 0.85wt: GTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATAT
mu: GTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATAT
 catt|GCAG
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
Donor increased46972wt: 0.28 / mu: 0.67wt: TTTGCATTGCAGTCT
mu: TTTTCATTGCAGTCT
 TGCA|ttgc
Acc gained469720.85mu: AAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAAT ttca|TTGC
Acc gained469750.83mu: TCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATATT attg|CAGT
distance from splice site 173
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      241GEQLSKVISLICIAVWIINIGHFN
mutated  not conserved    241FIAVWIINIGHF
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 
111253TOPO_DOMCytoplasmic (By similarity).lost
254273TRANSMEMHelical; Name=3; (By similarity).might get lost (downstream of altered splice site)
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)
787807REGIONInteracts with phospholamban 2 (By similarity).might get lost (downstream of altered splice site)
787807TRANSMEMHelical; Name=6; (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 1 (By similarity).might get lost (downstream of altered splice site)
799799METALCalcium 2 (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 3048 / 3048
position (AA) of stopcodon in wt / mu AA sequence 1016 / 1016
position of stopcodon in wt / mu cDNA 3611 / 3611
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 564 / 564
chromosome 12
strand 1
last intron/exon boundary 3342
theoretical NMD boundary in CDS 2728
length of CDS 3048
coding sequence (CDS) position 722
cDNA position
(for ins/del: last normal base / first normal base)
1285
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 VEIAGESVSV IKHTDPVPDP RAVNQDKKNM
LFSGTNIAAG KAMGVVVATG VNTEIGKIRD EMVATEQERT PLQQKLDEFG EQLSKVISLI
CIAVWIINIG HFNDPVHGGS WIRGAIYYFK IAVALAVAAI PEGLPAVITT CLALGTRRMA
KKNAIVRSLP SVETLGCTSV ICSDKTGTLT TNQMSVCRMF ILDRVEGDTC SLNEFTITGS
TYAPIGEVHK DDKPVNCHQY DGLVELATIC ALCNDSALDY NEAKGVYEKV GEATETALTC
LVEKMNVFDT ELKGLSKIER ANACNSVIKQ LMKKEFTLEF SRDRKSMSVY CTPNKPSRTS
MSKMFVKGAP EGVIDRCTHI RVGSTKVPMT SGVKQKIMSV IREWGSGSDT LRCLALATHD
NPLRREEMHL EDSANFIKYE TNLTFVGCVG MLDPPRIEVA SSVKLCRQAG IRVIMITGDN
KGTAVAICRR IGIFGQDEDV TSKAFTGREF DELNPSAQRD ACLNARCFAR VEPSHKSKIV
EFLQSFDEIT AMTGDGVNDA PALKKAEIGI AMGSGTAVAK TASEMVLADD NFSTIVAAVE
EGRAIYNNMK QFIRYLISSN VGEVVCIFLT AALGFPEALI PVQLLWVNLV TDGLPATALG
FNPPDLDIMN KPPRNPKEPL ISGWLFFRYL AIGCYVGAAT VGAAAWWFIA ADGGPRVSFY
QLSHFLQCKE DNPDFEGVDC AIFESPYPMT MALSVLVTIE MCNALNSLSE NQSLLRMPPW
ENIWLVGSIC LSMSLHFLIL YVEPLPLIFQ ITPLNVTQWL MVLKISLPVI LMDETLKFVA
RNYLEPGKEC VQPATKSCSF SACTDGISWP FVLLIMPLVI WVYSTDTNFS DMFWS*
mutated AA sequence MENAHTKTVE EVLGHFGVNE STGLSLEQVK KLKERWGSNE LPAEEGKTLL ELVIEQFEDL
LVRILLLAAC ISFVLAWFEE GEETITAFVE PFVILLILVA NAIVGVWQER NAENAIEALK
EYEPEMGKVY RQDRKSVQRI KAKDIVPGDI VEIAGESVSV IKHTDPVPDP RAVNQDKKNM
LFSGTNIAAG KAMGVVVATG VNTEIGKIRD EMVATEQERT PLQQKLDEFG EQLSKVISLI
FIAVWIINIG HFNDPVHGGS WIRGAIYYFK IAVALAVAAI PEGLPAVITT CLALGTRRMA
KKNAIVRSLP SVETLGCTSV ICSDKTGTLT TNQMSVCRMF ILDRVEGDTC SLNEFTITGS
TYAPIGEVHK DDKPVNCHQY DGLVELATIC ALCNDSALDY NEAKGVYEKV GEATETALTC
LVEKMNVFDT ELKGLSKIER ANACNSVIKQ LMKKEFTLEF SRDRKSMSVY CTPNKPSRTS
MSKMFVKGAP EGVIDRCTHI RVGSTKVPMT SGVKQKIMSV IREWGSGSDT LRCLALATHD
NPLRREEMHL EDSANFIKYE TNLTFVGCVG MLDPPRIEVA SSVKLCRQAG IRVIMITGDN
KGTAVAICRR IGIFGQDEDV TSKAFTGREF DELNPSAQRD ACLNARCFAR VEPSHKSKIV
EFLQSFDEIT AMTGDGVNDA PALKKAEIGI AMGSGTAVAK TASEMVLADD NFSTIVAAVE
EGRAIYNNMK QFIRYLISSN VGEVVCIFLT AALGFPEALI PVQLLWVNLV TDGLPATALG
FNPPDLDIMN KPPRNPKEPL ISGWLFFRYL AIGCYVGAAT VGAAAWWFIA ADGGPRVSFY
QLSHFLQCKE DNPDFEGVDC AIFESPYPMT MALSVLVTIE MCNALNSLSE NQSLLRMPPW
ENIWLVGSIC LSMSLHFLIL YVEPLPLIFQ ITPLNVTQWL MVLKISLPVI LMDETLKFVA
RNYLEPGKEC VQPATKSCSF SACTDGISWP FVLLIMPLVI WVYSTDTNFS DMFWS*
speed 1.45 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
back to results table
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 marginally increased46971wt: 0.9122 / mu: 0.9204 (marginal change - not scored)wt: AAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAA
mu: AAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAA
 ttgc|ATTG
Acc marginally increased46970wt: 0.7551 / mu: 0.7912 (marginal change - not scored)wt: CAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAA
mu: CAAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAA
 tttg|CATT
Acc increased46974wt: 0.28 / mu: 0.85wt: GTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATAT
mu: GTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATAT
 catt|GCAG
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
Donor increased46972wt: 0.28 / mu: 0.67wt: TTTGCATTGCAGTCT
mu: TTTTCATTGCAGTCT
 TGCA|ttgc
Acc gained469720.85mu: AAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAAT ttca|TTGC
Acc gained469750.83mu: TCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATATT attg|CAGT
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 1.36 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
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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 ENST00000539276
Genbank transcript ID NM_170665
UniProt peptide P16615
alteration type single base exchange
alteration region CDS
DNA changes c.803G>T
cDNA.912G>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 marginally increased46971wt: 0.9122 / mu: 0.9204 (marginal change - not scored)wt: AAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAA
mu: AAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAA
 ttgc|ATTG
Acc marginally increased46970wt: 0.7551 / mu: 0.7912 (marginal change - not scored)wt: CAAAGTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAA
mu: CAAAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAA
 tttg|CATT
Acc increased46974wt: 0.28 / mu: 0.85wt: GTCATCTCCCTTATTTGCATTGCAGTCTGGATCATAAATAT
mu: GTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATAT
 catt|GCAG
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
Donor increased46972wt: 0.28 / mu: 0.67wt: TTTGCATTGCAGTCT
mu: TTTTCATTGCAGTCT
 TGCA|ttgc
Acc gained469720.85mu: AAGTCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAAT ttca|TTGC
Acc gained469750.83mu: TCATCTCCCTTATTTTCATTGCAGTCTGGATCATAAATATT attg|CAGT
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 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 803
cDNA position
(for ins/del: last normal base / first normal base)
912
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 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 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 LEPGKECVQP ATKSCSFSAC TDGISWPFVL
LIMPLVIWVY STDTNFSDMF WS*
speed 1.24 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
back to results table

Problems