Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999896809134182      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM116828)
  • protein features (might be) affected
  • splice site changes
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:17313359A>CN/A show variant in all transcripts   IGV
HGNC symbol ATP13A2
Ensembl transcript ID ENST00000326735
Genbank transcript ID NM_022089
UniProt peptide Q9NQ11
alteration type single base exchange
alteration region CDS
DNA changes c.3176T>G
cDNA.3210T>G
g.25065T>G
AA changes L1059R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1059
frameshift no
known variant Reference ID: rs137853967
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM116828)

known disease mutation at this position, please check HGMD for details (HGMD ID CM116828)
known disease mutation at this position, please check HGMD for details (HGMD ID CM116828)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
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)4.6591
3.8691
(flanking)1.8411
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 increased25056wt: 0.2909 / mu: 0.2990 (marginal change - not scored)wt: GGTCTTCTCTCTGTCCAGCTTCCAGTACCTCATCCTGGCTG
mu: GGTCTTCTCTCTGTCCAGCTTCCAGTACCGCATCCTGGCTG		 gctt|CCAG
Acc increased25058wt: 0.61 / mu: 0.70wt: TCTTCTCTCTGTCCAGCTTCCAGTACCTCATCCTGGCTGCA
mu: TCTTCTCTCTGTCCAGCTTCCAGTACCGCATCCTGGCTGCA		 ttcc|AGTA
Acc marginally increased25059wt: 0.9520 / mu: 0.9576 (marginal change - not scored)wt: CTTCTCTCTGTCCAGCTTCCAGTACCTCATCCTGGCTGCAG
mu: CTTCTCTCTGTCCAGCTTCCAGTACCGCATCCTGGCTGCAG		 tcca|GTAC
Acc increased25061wt: 0.42 / mu: 0.49wt: TCTCTCTGTCCAGCTTCCAGTACCTCATCCTGGCTGCAGCC
mu: TCTCTCTGTCCAGCTTCCAGTACCGCATCCTGGCTGCAGCC		 cagt|ACCT
Donor gained250590.90mu: CTTCCAGTACCGCAT TCCA|gtac
distance from splice site 60
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1059TVVFSLSSFQYLILAAAVSKGAPF
mutated  not conserved    1059TVVFSLSSFQYRILAAAVSKGAP
Ptroglodytes  all identical  ENSPTRG00000000241  964FQYLILAAAMSKGAP
Mmulatta  all identical  ENSMMUG00000001610  1058TVVFSLSSFQYLILAAAVSKGAP
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000036622  1048TVVFSLSGFQYLILAAAVSKGAP
Ggallus  no alignment  ENSGALG00000003774  n/a
Trubripes  no homologue    
Drerio  all conserved  ENSDARG00000061890  1038TSVFAVSGFQYIIMSVVITKGFP
Dmelanogaster  all conserved  FBgn0052000  1294YTMFCISSFQYIIL
Celegans  all conserved  W08D2.5  1061TALFCVSMFQYIILALVYSKGPP
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
10471066TRANSMEMHelical; (Potential).lost
10671079TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10801097TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10981113TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
11141134TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
11351180TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3543 / 3543
position (AA) of stopcodon in wt / mu AA sequence 1181 / 1181
position of stopcodon in wt / mu cDNA 3577 / 3577
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 35 / 35
chromosome 1
strand -1
last intron/exon boundary 3440
theoretical NMD boundary in CDS 3355
length of CDS 3543
coding sequence (CDS) position 3176
cDNA position
(for ins/del: last normal base / first normal base)		 3210
gDNA position
(for ins/del: last normal base / first normal base)		 25065
chromosomal position
(for ins/del: last normal base / first normal base)		 17313359
original gDNA sequence snippet TCTGTCCAGCTTCCAGTACCTCATCCTGGCTGCAGCCGTGT
altered gDNA sequence snippet TCTGTCCAGCTTCCAGTACCGCATCCTGGCTGCAGCCGTGT
original cDNA sequence snippet TCTGTCCAGCTTCCAGTACCTCATCCTGGCTGCAGCCGTGT
altered cDNA sequence snippet TCTGTCCAGCTTCCAGTACCGCATCCTGGCTGCAGCCGTGT
wildtype AA sequence MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI
PLLLFRWKPL WGVRLRLRPC NLAHAETLVI EIRDKEDSSW QLFTVQVQTE AIGEGSLEPS
PQSQAEDGRS QAAVGAVPEG AWKDTAQLHK SEEAVSVGQK RVLRYYLFQG QRYIWIETQQ
AFYQVSLLDH GRSCDDVHRS RHGLSLQDQM VRKAIYGPNV ISIPVKSYPQ LLVDEALNPY
YGFQAFSIAL WLADHYYWYA LCIFLISSIS ICLSLYKTRK QSQTLRDMVK LSMRVCVCRP
GGEEEWVDSS ELVPGDCLVL PQEGGLMPCD AALVAGECMV NESSLTGESI PVLKTALPEG
LGPYCAETHR RHTLFCGTLI LQARAYVGPH VLAVVTRTGF CTAKGGLVSS ILHPRPINFK
FYKHSMKFVA ALSVLALLGT IYSIFILYRN RVPLNEIVIR ALDLVTVVVP PALPAAMTVC
TLYAQSRLRR QGIFCIHPLR INLGGKLQLV CFDKTGTLTE DGLDVMGVVP LKGQAFLPLV
PEPRRLPVGP LLRALATCHA LSRLQDTPVG DPMDLKMVES TGWVLEEEPA ADSAFGTQVL
AVMRPPLWEP QLQAMEEPPV PVSVLHRFPF SSALQRMSVV VAWPGATQPE AYVKGSPELV
AGLCNPETVP TDFAQMLQSY TAAGYRVVAL ASKPLPTVPS LEAAQQLTRD TVEGDLSLLG
LLVMRNLLKP QTTPVIQALR RTRIRAVMVT GDNLQTAVTV ARGCGMVAPQ EHLIIVHATH
PERGQPASLE FLPMESPTAV NGVKDPDQAA SYTVEPDPRS RHLALSGPTF GIIVKHFPKL
LPKVLVQGTV FARMAPEQKT ELVCELQKLQ YCVGMCGDGA NDCGALKAAD VGISLSQAEA
SVVSPFTSSM ASIECVPMVI REGRCSLDTS FSVFKYMALY SLTQFISVLI LYTINTNLGD
LQFLAIDLVI TTTVAVLMSR TGPALVLGRV RPPGALLSVP VLSSLLLQMV LVTGVQLGGY
FLTLAQPWFV PLNRTVAAPD NLPNYENTVV FSLSSFQYLI LAAAVSKGAP FRRPLYTNVP
FLVALALLSS VLVGLVLVPG LLQGPLALRN ITDTGFKLLL LGLVTLNFVG AFMLESVLDQ
CLPACLRRLR PKRASKKRFK QLERELAEQP WPPLPAGPLR *
mutated AA sequence MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI
PLLLFRWKPL WGVRLRLRPC NLAHAETLVI EIRDKEDSSW QLFTVQVQTE AIGEGSLEPS
PQSQAEDGRS QAAVGAVPEG AWKDTAQLHK SEEAVSVGQK RVLRYYLFQG QRYIWIETQQ
AFYQVSLLDH GRSCDDVHRS RHGLSLQDQM VRKAIYGPNV ISIPVKSYPQ LLVDEALNPY
YGFQAFSIAL WLADHYYWYA LCIFLISSIS ICLSLYKTRK QSQTLRDMVK LSMRVCVCRP
GGEEEWVDSS ELVPGDCLVL PQEGGLMPCD AALVAGECMV NESSLTGESI PVLKTALPEG
LGPYCAETHR RHTLFCGTLI LQARAYVGPH VLAVVTRTGF CTAKGGLVSS ILHPRPINFK
FYKHSMKFVA ALSVLALLGT IYSIFILYRN RVPLNEIVIR ALDLVTVVVP PALPAAMTVC
TLYAQSRLRR QGIFCIHPLR INLGGKLQLV CFDKTGTLTE DGLDVMGVVP LKGQAFLPLV
PEPRRLPVGP LLRALATCHA LSRLQDTPVG DPMDLKMVES TGWVLEEEPA ADSAFGTQVL
AVMRPPLWEP QLQAMEEPPV PVSVLHRFPF SSALQRMSVV VAWPGATQPE AYVKGSPELV
AGLCNPETVP TDFAQMLQSY TAAGYRVVAL ASKPLPTVPS LEAAQQLTRD TVEGDLSLLG
LLVMRNLLKP QTTPVIQALR RTRIRAVMVT GDNLQTAVTV ARGCGMVAPQ EHLIIVHATH
PERGQPASLE FLPMESPTAV NGVKDPDQAA SYTVEPDPRS RHLALSGPTF GIIVKHFPKL
LPKVLVQGTV FARMAPEQKT ELVCELQKLQ YCVGMCGDGA NDCGALKAAD VGISLSQAEA
SVVSPFTSSM ASIECVPMVI REGRCSLDTS FSVFKYMALY SLTQFISVLI LYTINTNLGD
LQFLAIDLVI TTTVAVLMSR TGPALVLGRV RPPGALLSVP VLSSLLLQMV LVTGVQLGGY
FLTLAQPWFV PLNRTVAAPD NLPNYENTVV FSLSSFQYRI LAAAVSKGAP FRRPLYTNVP
FLVALALLSS VLVGLVLVPG LLQGPLALRN ITDTGFKLLL LGLVTLNFVG AFMLESVLDQ
CLPACLRRLR PKRASKKRFK QLERELAEQP WPPLPAGPLR *
speed 0.52 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