Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.915520404861349 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM071564)
  • known disease mutation: rs1221 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:17322503C>GN/A show variant in all transcripts   IGV
HGNC symbol ATP13A2
Ensembl transcript ID ENST00000452699
Genbank transcript ID NM_001141973
UniProt peptide Q9NQ11
alteration type single base exchange
alteration region CDS
DNA changes c.1495G>C
cDNA.1685G>C
g.15921G>C
AA changes G499R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 499
frameshift no
known variant Reference ID: rs121918227
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs1221 (pathogenic for Kufor-Rakeb syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM071564)

known disease mutation at this position, please check HGMD for details (HGMD ID CM071564)
known disease mutation at this position, please check HGMD for details (HGMD ID CM071564)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.6280.999
1.9051
(flanking)0.651
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased15916wt: 0.21 / mu: 0.48wt: CATCAACCTGGGGGG
mu: CATCAACCTGCGGGG		 TCAA|cctg
Donor increased15912wt: 0.23 / mu: 0.29wt: TGCGCATCAACCTGG
mu: TGCGCATCAACCTGC		 CGCA|tcaa
Donor marginally increased15923wt: 0.9773 / mu: 0.9937 (marginal change - not scored)wt: CTGGGGGGCAAGCTG
mu: CTGCGGGGCAAGCTG		 GGGG|ggca
Donor increased15919wt: 0.34 / mu: 0.74wt: CAACCTGGGGGGCAA
mu: CAACCTGCGGGGCAA		 ACCT|gggg
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      499IFCIHPLRINLGGKLQLVCFDKTG
mutated  not conserved    499IFCIHPLRINLRGKLQLVCFDKT
Ptroglodytes  all identical  ENSPTRG00000000241  409IFCIHPLRINLGGKLQLVCFDKT
Mmulatta  all identical  ENSMMUG00000001610  503IFCIHPLRINLGGKLQLVCFDKT
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000036622  499IFCIHPLRINLGGKLRLVCFDKT
Ggallus  no alignment  ENSGALG00000003774  n/a
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000061890  483VFCISPPRINICGKISLF
Dmelanogaster  not conserved  FBgn0052000  624IFCISPRSINVAGSINCCCFDKT
Celegans  not conserved  W08D2.5  456CISPSTINTCGAINVVCFDKT
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
481932TOPO_DOMCytoplasmic (Potential).lost
513513ACT_SITE4-aspartylphosphate intermediate (By similarity).might get lost (downstream of altered splice site)
855858CONFLICTAPEQ -> IPRA (in Ref. 8; CAA08912).might get lost (downstream of altered splice site)
861861CONFLICTE -> V (in Ref. 8; CAA08912).might get lost (downstream of altered splice site)
878878METALMagnesium (By similarity).might get lost (downstream of altered splice site)
882882METALMagnesium (By similarity).might get lost (downstream of altered splice site)
933952TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
953963TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
964981TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
982997TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
9981018TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10191046TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
10471066TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
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 3528 / 3528
position (AA) of stopcodon in wt / mu AA sequence 1176 / 1176
position of stopcodon in wt / mu cDNA 3718 / 3718
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 191 / 191
chromosome 1
strand -1
last intron/exon boundary 3581
theoretical NMD boundary in CDS 3340
length of CDS 3528
coding sequence (CDS) position 1495
cDNA position
(for ins/del: last normal base / first normal base)		 1685
gDNA position
(for ins/del: last normal base / first normal base)		 15921
chromosomal position
(for ins/del: last normal base / first normal base)		 17322503
original gDNA sequence snippet ACCCACTGCGCATCAACCTGGGGGGCAAGCTGCAGCTGGTG
altered gDNA sequence snippet ACCCACTGCGCATCAACCTGCGGGGCAAGCTGCAGCTGGTG
original cDNA sequence snippet ACCCACTGCGCATCAACCTGGGGGGCAAGCTGCAGCTGGTG
altered cDNA sequence snippet ACCCACTGCGCATCAACCTGCGGGGCAAGCTGCAGCTGGTG
wildtype AA sequence MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI
PLLLFRWKPL WGVRLRLRPC NLAHAETLVI EIRDKEDSSW QLFTVQVQTE AIGEGSLEPS
PQSQAEDGRS QAAVGAVPEG AWKDTAQLHK SEEAKRVLRY YLFQGQRYIW IETQQAFYQV
SLLDHGRSCD DVHRSRHGLS LQDQMVRKAI YGPNVISIPV KSYPQLLVDE ALNPYYGFQA
FSIALWLADH YYWYALCIFL ISSISICLSL YKTRKQSQTL RDMVKLSMRV CVCRPGGEEE
WVDSSELVPG DCLVLPQEGG LMPCDAALVA GECMVNESSL TGESIPVLKT ALPEGLGPYC
AETHRRHTLF CGTLILQARA YVGPHVLAVV TRTGFCTAKG GLVSSILHPR PINFKFYKHS
MKFVAALSVL ALLGTIYSIF ILYRNRVPLN EIVIRALDLV TVVVPPALPA AMTVCTLYAQ
SRLRRQGIFC IHPLRINLGG KLQLVCFDKT GTLTEDGLDV MGVVPLKGQA FLPLVPEPRR
LPVGPLLRAL ATCHALSRLQ DTPVGDPMDL KMVESTGWVL EEEPAADSAF GTQVLAVMRP
PLWEPQLQAM EEPPVPVSVL HRFPFSSALQ RMSVVVAWPG ATQPEAYVKG SPELVAGLCN
PETVPTDFAQ MLQSYTAAGY RVVALASKPL PTVPSLEAAQ QLTRDTVEGD LSLLGLLVMR
NLLKPQTTPV IQALRRTRIR AVMVTGDNLQ TAVTVARGCG MVAPQEHLII VHATHPERGQ
PASLEFLPME SPTAVNGVKD PDQAASYTVE PDPRSRHLAL SGPTFGIIVK HFPKLLPKVL
VQGTVFARMA PEQKTELVCE LQKLQYCVGM CGDGANDCGA LKAADVGISL SQAEASVVSP
FTSSMASIEC VPMVIREGRC SLDTSFSVFK YMALYSLTQF ISVLILYTIN TNLGDLQFLA
IDLVITTTVA VLMSRTGPAL VLGRVRPPGA LLSVPVLSSL LLQMVLVTGV QLGGYFLTLA
QPWFVPLNRT VAAPDNLPNY ENTVVFSLSS FQYLILAAAV SKGAPFRRPL YTNVPFLVAL
ALLSSVLVGL VLVPGLLQGP LALRNITDTG FKLLLLGLVT LNFVGAFMLE SVLDQCLPAC
LRRLRPKRAS KKRFKQLERE LAEQPWPPLP AGPLR*
mutated AA sequence MSADSSPLVG STPTGYGTLT IGTSIDPLSS SVSSVRLSGY CGSPWRVIGY HVVVWMMAGI
PLLLFRWKPL WGVRLRLRPC NLAHAETLVI EIRDKEDSSW QLFTVQVQTE AIGEGSLEPS
PQSQAEDGRS QAAVGAVPEG AWKDTAQLHK SEEAKRVLRY YLFQGQRYIW IETQQAFYQV
SLLDHGRSCD DVHRSRHGLS LQDQMVRKAI YGPNVISIPV KSYPQLLVDE ALNPYYGFQA
FSIALWLADH YYWYALCIFL ISSISICLSL YKTRKQSQTL RDMVKLSMRV CVCRPGGEEE
WVDSSELVPG DCLVLPQEGG LMPCDAALVA GECMVNESSL TGESIPVLKT ALPEGLGPYC
AETHRRHTLF CGTLILQARA YVGPHVLAVV TRTGFCTAKG GLVSSILHPR PINFKFYKHS
MKFVAALSVL ALLGTIYSIF ILYRNRVPLN EIVIRALDLV TVVVPPALPA AMTVCTLYAQ
SRLRRQGIFC IHPLRINLRG KLQLVCFDKT GTLTEDGLDV MGVVPLKGQA FLPLVPEPRR
LPVGPLLRAL ATCHALSRLQ DTPVGDPMDL KMVESTGWVL EEEPAADSAF GTQVLAVMRP
PLWEPQLQAM EEPPVPVSVL HRFPFSSALQ RMSVVVAWPG ATQPEAYVKG SPELVAGLCN
PETVPTDFAQ MLQSYTAAGY RVVALASKPL PTVPSLEAAQ QLTRDTVEGD LSLLGLLVMR
NLLKPQTTPV IQALRRTRIR AVMVTGDNLQ TAVTVARGCG MVAPQEHLII VHATHPERGQ
PASLEFLPME SPTAVNGVKD PDQAASYTVE PDPRSRHLAL SGPTFGIIVK HFPKLLPKVL
VQGTVFARMA PEQKTELVCE LQKLQYCVGM CGDGANDCGA LKAADVGISL SQAEASVVSP
FTSSMASIEC VPMVIREGRC SLDTSFSVFK YMALYSLTQF ISVLILYTIN TNLGDLQFLA
IDLVITTTVA VLMSRTGPAL VLGRVRPPGA LLSVPVLSSL LLQMVLVTGV QLGGYFLTLA
QPWFVPLNRT VAAPDNLPNY ENTVVFSLSS FQYLILAAAV SKGAPFRRPL YTNVPFLVAL
ALLSSVLVGL VLVPGLLQGP LALRNITDTG FKLLLLGLVT LNFVGAFMLE SVLDQCLPAC
LRRLRPKRAS KKRFKQLERE LAEQPWPPLP AGPLR*
speed 1.05 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