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 ENST00000400366
Genbank transcript ID NM_001243182
UniProt peptide P35670
alteration type single base exchange
alteration region CDS
DNA changes c.3476A>G
cDNA.3633A>G
g.73925A>G
AA changes N1159S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1159
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      1159GKKVAMVGDGVNDSPALAQADMGV
mutated  all conserved    1159GKKVAMVGDGVSDSPALAQADMG
Ptroglodytes  all identical  ENSPTRG00000005897  1218GKKVAMVGDGVNDSPALAQADMG
Mmulatta  all identical  ENSMMUG00000016520  1229DGVNDSPALAQADMG
Fcatus  all identical  ENSFCAG00000003710  1258GKRVAMVGDGVNDSPALARADVG
Mmusculus  all identical  ENSMUSG00000006567  1267GVNDSPALAQADVG
Ggallus  all identical  ENSGALG00000017021  1248RRKVAMVGDGVNDSPALAKADIG
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0030343  1040GIRVAMVGDGVNDSPALA
Celegans  all identical  Y76A2A.2  1044KNKVAMVGDGVNDSPALAEANVG
Xtropicalis  all identical  ENSXETG00000020713  1214AMVGDGVNDSPALARADVG
protein features
start (aa)end (aa)featuredetails 
9951322TOPO_DOMCytoplasmic (Potential).lost
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 4065 / 4065
position (AA) of stopcodon in wt / mu AA sequence 1355 / 1355
position of stopcodon in wt / mu cDNA 4222 / 4222
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 158 / 158
chromosome 13
strand -1
last intron/exon boundary 3949
theoretical NMD boundary in CDS 3741
length of CDS 4065
coding sequence (CDS) position 3476
cDNA position
(for ins/del: last normal base / first normal base)		 3633
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 MPEQERQITA REGASRKILS KLSLPTRAWE PAMKKSFAFD NVGYEGGLDG LGPSSQVATS
TVRILGMTCQ SCVKSIEDRI SNLKGIISMK VSLEQGSATV KYVPSVVCLQ QVCHQIGDMG
FEASIAEGKA ASWPSRSLPA QEAVVKLRVE GMTCQSCVSS IEGKVRKLQG VVRVKVSLSN
QEAVITYQPY LIQPEDLRDH VNDMGFEAAI KSKVAPLSLG PIDIERLQST NPKRPLSSAN
QNFNNSETLG HQGSHVVTLQ LRIDGMHCMI SQLEGVQQIS VSLAEGTATV LYNPSVISPE
ELRAAIEDMG FEASVVSESC STNPLGNHSA GNSMVQTTDG TPTSVQEVAP HTGRLPANHA
PDILAKSPQS TRAVAPQKCF LQIKGMTCAS CVSNIERNLQ KEAGVLSVLV ALMAGKAEIK
YDPEVIQPLE IAQFIQDLGF EAAVMEDYAG SDGNIELTIT GMTCASCVHN IESKLTRTNG
ITYASVALAT SKALVKFDPE IIGPRDIIKI IEEIGFHASL AQRNPNAHHL DHKMEIKQWK
KSFLCSLVFG IPVMALMIYM LIPSNEPHQS MVLDHNIIPG LSILNLIFFI LCTFVQLLGG
WYFYVQAYKS LRHRSANMDV LIVLATSIAY VYSLVILVVA VAEKAERSPV TFFDTPPMLF
VFIALGRWLE HLAKSKTSEA LAKLMSLQAT EATVVTLGED NLIIREEQVP MELVQRGDIV
KVVPGGKFPV DGKVLEGNTM ADESLITGEA MPVTKKPGST VIAGSINAHG SVLIKATHVG
NDTTLAQIVK LVEEAQMSKA PIQQLADRFS GYFVPFIIIM STLTLVVWIV IGFIDFGVVQ
RYFPNPNKHI SQTEVIIRFA FQTSITVLCI ACPCSLGLAT PTAVMVGTGV AAQNGILIKG
GKPLEMAHKI KTVMFDKTGT ITHGVPRVMR VLLLGDVATL PLRKVLAVVG TAEASSEHPL
GVAVTKYCKE ELGTETLGYC TDFQAVPGCG IGCKVSNVEG ILAHSERPLS APASHLNEAG
SLPAEKDAVP QTFSVLIGNR EWLRRNGLTI SSDVSDAMTD HEMKGQTAIL VAIDGVLCGM
IAIADAVKQE AALAVHTLQS MGVDVVLITG DNRKTARAIA TQVGINKVFA EVLPSHKVAK
VQELQNKGKK VAMVGDGVND SPALAQADMG VAIGTGTDVA IEAADVVLIR NDLLDVVASI
HLSKRTVRRI RINLVLALIY NLVGIPIAAG VFMPIGIVLQ PWMGSAAMAA SSVSVVLSSL
QLKCYKKPDL ERYEAQAHGH MKPLTASQVS VHIGMDDRWR DSPRATPWDQ VSYVSQVSLS
SLTSDKPSRH SAAADDDGDK WSLLLNGRDE EQYI*
mutated AA sequence MPEQERQITA REGASRKILS KLSLPTRAWE PAMKKSFAFD NVGYEGGLDG LGPSSQVATS
TVRILGMTCQ SCVKSIEDRI SNLKGIISMK VSLEQGSATV KYVPSVVCLQ QVCHQIGDMG
FEASIAEGKA ASWPSRSLPA QEAVVKLRVE GMTCQSCVSS IEGKVRKLQG VVRVKVSLSN
QEAVITYQPY LIQPEDLRDH VNDMGFEAAI KSKVAPLSLG PIDIERLQST NPKRPLSSAN
QNFNNSETLG HQGSHVVTLQ LRIDGMHCMI SQLEGVQQIS VSLAEGTATV LYNPSVISPE
ELRAAIEDMG FEASVVSESC STNPLGNHSA GNSMVQTTDG TPTSVQEVAP HTGRLPANHA
PDILAKSPQS TRAVAPQKCF LQIKGMTCAS CVSNIERNLQ KEAGVLSVLV ALMAGKAEIK
YDPEVIQPLE IAQFIQDLGF EAAVMEDYAG SDGNIELTIT GMTCASCVHN IESKLTRTNG
ITYASVALAT SKALVKFDPE IIGPRDIIKI IEEIGFHASL AQRNPNAHHL DHKMEIKQWK
KSFLCSLVFG IPVMALMIYM LIPSNEPHQS MVLDHNIIPG LSILNLIFFI LCTFVQLLGG
WYFYVQAYKS LRHRSANMDV LIVLATSIAY VYSLVILVVA VAEKAERSPV TFFDTPPMLF
VFIALGRWLE HLAKSKTSEA LAKLMSLQAT EATVVTLGED NLIIREEQVP MELVQRGDIV
KVVPGGKFPV DGKVLEGNTM ADESLITGEA MPVTKKPGST VIAGSINAHG SVLIKATHVG
NDTTLAQIVK LVEEAQMSKA PIQQLADRFS GYFVPFIIIM STLTLVVWIV IGFIDFGVVQ
RYFPNPNKHI SQTEVIIRFA FQTSITVLCI ACPCSLGLAT PTAVMVGTGV AAQNGILIKG
GKPLEMAHKI KTVMFDKTGT ITHGVPRVMR VLLLGDVATL PLRKVLAVVG TAEASSEHPL
GVAVTKYCKE ELGTETLGYC TDFQAVPGCG IGCKVSNVEG ILAHSERPLS APASHLNEAG
SLPAEKDAVP QTFSVLIGNR EWLRRNGLTI SSDVSDAMTD HEMKGQTAIL VAIDGVLCGM
IAIADAVKQE AALAVHTLQS MGVDVVLITG DNRKTARAIA TQVGINKVFA EVLPSHKVAK
VQELQNKGKK VAMVGDGVSD SPALAQADMG VAIGTGTDVA IEAADVVLIR NDLLDVVASI
HLSKRTVRRI RINLVLALIY NLVGIPIAAG VFMPIGIVLQ PWMGSAAMAA SSVSVVLSSL
QLKCYKKPDL ERYEAQAHGH MKPLTASQVS VHIGMDDRWR DSPRATPWDQ VSYVSQVSLS
SLTSDKPSRH SAAADDDGDK WSLLLNGRDE EQYI*
speed 1.09 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