Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.131028066819702 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • heterozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM970138)
  • known disease mutation: rs3862 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:52535985A>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.1601T>G
cDNA.1758T>G
g.49646T>G
AA changes M534R Score: 91 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 534
frameshift no
known variant Reference ID: rs121907998
databasehomozygous (C/C)heterozygousallele carriers
1000G011
ExAC06161

known disease mutation: rs3862 (pathogenic for Wilson disease) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM970138)

known disease mutation at this position, please check HGMD for details (HGMD ID CM970138)
known disease mutation at this position, please check HGMD for details (HGMD ID CM970138)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5421
0.7640.993
(flanking)0.0070.983
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased49650wt: 0.9853 / mu: 0.9938 (marginal change - not scored)wt: ATGGAAATAAAGCAG
mu: AGGGAAATAAAGCAG		 GGAA|ataa
Donor marginally increased49643wt: 0.3505 / mu: 0.4291 (marginal change - not scored)wt: CCACAAGATGGAAAT
mu: CCACAAGAGGGAAAT		 ACAA|gatg
Donor marginally increased49646wt: 0.7999 / mu: 0.8417 (marginal change - not scored)wt: CAAGATGGAAATAAA
mu: CAAGAGGGAAATAAA		 AGAT|ggaa
Donor marginally increased49638wt: 0.8952 / mu: 0.9325 (marginal change - not scored)wt: TTGGACCACAAGATG
mu: TTGGACCACAAGAGG		 GGAC|caca
Donor marginally increased49645wt: 0.9283 / mu: 0.9986 (marginal change - not scored)wt: ACAAGATGGAAATAA
mu: ACAAGAGGGAAATAA		 AAGA|tgga
Donor gained496400.97mu: GGACCACAAGAGGGA ACCA|caag
distance from splice site 13
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      534RNPNAHHLDHKMEIKQWKKSFLCS
mutated  not conserved    534RNPNAHHLDHKREIKQWK
Ptroglodytes  all identical  ENSPTRG00000005897  593RNPNARHLDHKMEIKQWKKSFLC
Mmulatta  all identical  ENSMMUG00000016520  628RIPNAHHLDHKMEIKQWKKSFLC
Fcatus  all conserved  ENSFCAG00000003710  633PNVHHLDHKVEIKQWKKSFLC
Mmusculus  not conserved  ENSMUSG00000006567  647RNPNAHHLDHKTEIKQWKKSFLC
Ggallus  not conserved  ENSGALG00000017021  620RVPNTHNLDHKKEIQQWRKSFLC
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0030343  365RDKMAHNYLEHKEEIRKWRNAFLV
Celegans  not conserved  Y76A2A.2  410RDDQMKRLDHSDDVKKWRNTFFI
Xtropicalis  not conserved  ENSXETG00000020713  600RDPTAHKLDHKEEIKQWRNSFLF
protein features
start (aa)end (aa)featuredetails 
1653TOPO_DOMCytoplasmic (Potential).lost
489555DOMAINHMA 5.lost
527532STRANDmight get lost (downstream of altered splice site)
534536TURNlost
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 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 1601
cDNA position
(for ins/del: last normal base / first normal base)		 1758
gDNA position
(for ins/del: last normal base / first normal base)		 49646
chromosomal position
(for ins/del: last normal base / first normal base)		 52535985
original gDNA sequence snippet TCATCACTTGGACCACAAGATGGAAATAAAGCAGTAGGTAG
altered gDNA sequence snippet TCATCACTTGGACCACAAGAGGGAAATAAAGCAGTAGGTAG
original cDNA sequence snippet TCATCACTTGGACCACAAGATGGAAATAAAGCAGTGGAAGA
altered cDNA sequence snippet TCATCACTTGGACCACAAGAGGGAAATAAAGCAGTGGAAGA
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 DHKREIKQWK
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*
speed 1.26 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