Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999971309494 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM161467)
  • known disease mutation at this position (HGMD CM930060)
  • known disease mutation at this position (HGMD CM994116)
  • known disease mutation: rs3859 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:52511706T>CN/A show variant in all transcripts   IGV
HGNC symbol ATP7B
Ensembl transcript ID ENST00000417240
Genbank transcript ID N/A
UniProt peptide P35670
alteration type single base exchange
alteration region CDS
DNA changes c.1442A>G
cDNA.1584A>G
g.73925A>G
AA changes N481S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 481
frameshift no
known variant Reference ID: rs121907990
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC01818

known disease mutation: rs3859 (pathogenic for Wilson disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)

known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)

known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994116)

known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)

known disease mutation at this position, please check HGMD for details (HGMD ID CM161467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994116)
known disease mutation at this position, please check HGMD for details (HGMD ID CM930060)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994116)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4990.82
4.8180.998
(flanking)4.8180.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained739240.89mu: GGGTCAGTGACTCCC GTCA|gtga
distance from splice site 95
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      481GKKVAMVGDGVNDSPALAQADMGV
mutated  all conserved    481SDSPALAQADMG
Ptroglodytes  all identical  ENSPTRG00000005897  1218VNDSPALAQADMG
Mmulatta  all identical  ENSMMUG00000016520  1229VNDSPALAQADMG
Fcatus  all identical  ENSFCAG00000003710  1258VNDSPALARADVG
Mmusculus  all identical  ENSMUSG00000006567  1267VNDSPALAQADVG
Ggallus  all identical  ENSGALG00000017021  1248GVNDSPALAKADIG
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0030343  1040GIRVAMVGDGVNDSPALAQADVG
Celegans  all identical  Y76A2A.2  1044KNKVAMVGDGVNDSPALAEANVG
Xtropicalis  all identical  ENSXETG00000020713  1214NKRVAMVGDGVNDSPALA
protein features
start (aa)end (aa)featuredetails 
1653TOPO_DOMCytoplasmic (Potential).lost
488488CONFLICTQ -> G (in Ref. 8; AAA16173).might get lost (downstream of altered splice site)
488495STRANDmight get lost (downstream of altered splice site)
489555DOMAINHMA 5.might get lost (downstream of altered splice site)
499501STRANDmight get lost (downstream of altered splice site)
502511HELIXmight get lost (downstream of altered splice site)
519522STRANDmight get lost (downstream of altered splice site)
523526TURNmight get lost (downstream of altered splice site)
527532STRANDmight get lost (downstream of altered splice site)
534536TURNmight get lost (downstream of altered splice site)
539549HELIXmight get lost (downstream of altered splice site)
552555STRANDmight get lost (downstream of altered splice site)
562572STRANDmight get lost (downstream of altered splice site)
565631DOMAINHMA 6.might get lost (downstream of altered splice site)
576588HELIXmight get lost (downstream of altered splice site)
589591STRANDmight get lost (downstream of altered splice site)
594598STRANDmight get lost (downstream of altered splice site)
599602TURNmight get lost (downstream of altered splice site)
603607STRANDmight get lost (downstream of altered splice site)
610612TURNmight get lost (downstream of altered splice site)
615625HELIXmight get lost (downstream of altered splice site)
628630STRANDmight get lost (downstream of altered splice site)
635635CONFLICTN -> T (in Ref. 8; AAA16173).might get lost (downstream of altered splice site)
654675TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
676697TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
698717TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
718724TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
725745TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
746764TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
765785TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
767767CONFLICTP -> L (in Ref. 8; AAA16173).might get lost (downstream of altered splice site)
786919TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
837837CONFLICTG -> A (in Ref. 8; AAA16173).might get lost (downstream of altered splice site)
920942TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
943972TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
973994TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
9951322TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
10271027ACT_SITE4-aspartylphosphate intermediate (By similarity).might get lost (downstream of altered splice site)
10391044STRANDmight get lost (downstream of altered splice site)
10481050TURNmight get lost (downstream of altered splice site)
10531064HELIXmight get lost (downstream of altered splice site)
10721083HELIXmight get lost (downstream of altered splice site)
10911097STRANDmight get lost (downstream of altered splice site)
10981100TURNmight get lost (downstream of altered splice site)
11011107STRANDmight get lost (downstream of altered splice site)
11091113HELIXmight get lost (downstream of altered splice site)
11271130STRANDmight get lost (downstream of altered splice site)
11431149STRANDmight get lost (downstream of altered splice site)
11511158HELIXmight get lost (downstream of altered splice site)
11631173HELIXmight get lost (downstream of altered splice site)
11741176TURNmight get lost (downstream of altered splice site)
11771184STRANDmight get lost (downstream of altered splice site)
11871194STRANDmight get lost (downstream of altered splice site)
12671267METALMagnesium (By similarity).might get lost (downstream of altered splice site)
12711271METALMagnesium (By similarity).might get lost (downstream of altered splice site)
13231340TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
13411351TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
13521371TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
13721465TOPO_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 2031 / 2031
position (AA) of stopcodon in wt / mu AA sequence 677 / 677
position of stopcodon in wt / mu cDNA 2173 / 2173
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 143 / 143
chromosome 13
strand -1
last intron/exon boundary 1900
theoretical NMD boundary in CDS 1707
length of CDS 2031
coding sequence (CDS) position 1442
cDNA position
(for ins/del: last normal base / first normal base)		 1584
gDNA position
(for ins/del: last normal base / first normal base)		 73925
chromosomal position
(for ins/del: last normal base / first normal base)		 52511706
original gDNA sequence snippet CATGGTGGGGGATGGGGTCAATGACTCCCCGGCCTTGGCCC
altered gDNA sequence snippet CATGGTGGGGGATGGGGTCAGTGACTCCCCGGCCTTGGCCC
original cDNA sequence snippet CATGGTGGGGGATGGGGTCAATGACTCCCCGGCCTTGGCCC
altered cDNA sequence snippet CATGGTGGGGGATGGGGTCAGTGACTCCCCGGCCTTGGCCC
wildtype AA sequence MDVLIVLATS IAYVYSLVIL VVAVAEKAER SPVTFFDTPP MLFVFIALGR WLEHLAKSKT
SEALAKLMSL QATEATVVTL GEDNLIIREE QVPMELVQRG DIVKVVPGGK FPVDGKVLEG
NTMADESLIT GEAMPVTKKP GSTVIAGSIN AHGSVLIKAT HVGNDTTLAQ IVKLVEEAQM
SKAPIQQLAD RFSGYFVPFI IIMSTLTLVV WIVIGFIDFG VVQRYFPNPN KHISQTEVII
RFAFQTSITV LCIACPCSLG LATPTAVMVG TGVAAQNGIL IKGGKPLEMA HKELGTETLG
YCTDFQAVPG CGIGCKVSNV EGILAHSERP LSAPASHLNE AGSLPAEKDA VPQTFSVLIG
NREWLRRNGL TISSDVSDAM TDHEMKGQTA ILVAIDGVLC GMIAIADAVK QEAALAVHTL
QSMGVDVVLI TGDNRKTARA IATQVGINKV FAEVLPSHKV AKVQELQNKG KKVAMVGDGV
NDSPALAQAD MGVAIGTGTD VAIEAADVVL IRNDLLDVVA SIHLSKRTVR RIRINLVLAL
IYNLVGIPIA AGVFMPIGIV LQPWMGSAAM AASSVSVVLS SLQLKCYKKP DLERYEAQAH
GHMKPLTASQ VSVHIGMDDR WRDSPRATPW DQVSYVSQVS LSSLTSDKPS RHSAAADDDG
DKWSLLLNGR DEEQYI*
mutated AA sequence MDVLIVLATS IAYVYSLVIL VVAVAEKAER SPVTFFDTPP MLFVFIALGR WLEHLAKSKT
SEALAKLMSL QATEATVVTL GEDNLIIREE QVPMELVQRG DIVKVVPGGK FPVDGKVLEG
NTMADESLIT GEAMPVTKKP GSTVIAGSIN AHGSVLIKAT HVGNDTTLAQ IVKLVEEAQM
SKAPIQQLAD RFSGYFVPFI IIMSTLTLVV WIVIGFIDFG VVQRYFPNPN KHISQTEVII
RFAFQTSITV LCIACPCSLG LATPTAVMVG TGVAAQNGIL IKGGKPLEMA HKELGTETLG
YCTDFQAVPG CGIGCKVSNV EGILAHSERP LSAPASHLNE AGSLPAEKDA VPQTFSVLIG
NREWLRRNGL TISSDVSDAM TDHEMKGQTA ILVAIDGVLC GMIAIADAVK QEAALAVHTL
QSMGVDVVLI TGDNRKTARA IATQVGINKV FAEVLPSHKV AKVQELQNKG KKVAMVGDGV
SDSPALAQAD MGVAIGTGTD VAIEAADVVL IRNDLLDVVA SIHLSKRTVR RIRINLVLAL
IYNLVGIPIA AGVFMPIGIV LQPWMGSAAM AASSVSVVLS SLQLKCYKKP DLERYEAQAH
GHMKPLTASQ VSVHIGMDDR WRDSPRATPW DQVSYVSQVS LSSLTSDKPS RHSAAADDDG
DKWSLLLNGR DEEQYI*
speed 1.50 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