Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999645756 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960133)
  • known disease mutation: rs35725 (pathogenic)
  • protein features (might be) affected
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:52513227G>AN/A show variant in all transcripts   IGV
HGNC symbol ATP7B
Ensembl transcript ID ENST00000448424
Genbank transcript ID N/A
UniProt peptide P35670
alteration type single base exchange
alteration region CDS
DNA changes c.3425C>T
cDNA.3499C>T
g.72404C>T
AA changes T1142M Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 1142
frameshift no
known variant Reference ID: rs193922107
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs35725 (pathogenic for Wilson disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960133)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960133)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960133)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-4.7310.003
5.961
(flanking)4.9241
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 increased72406wt: 0.6587 / mu: 0.7368 (marginal change - not scored)wt: TGGACGTGGTTCTGATCACGGGGGACAACCGGAAGACAGCC
mu: TGGACGTGGTTCTGATCATGGGGGACAACCGGAAGACAGCC		 acgg|GGGA
distance from splice site 41
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      1142LQSMGVDVVLITGDNRKTARAIAT
mutated  not conserved    1142IMGDNRKTARAIA
Ptroglodytes  all identical  ENSPTRG00000005897  1168LQSMGVDVVLITGDNRKTARAI
Mmulatta  all identical  ENSMMUG00000016520  1179LQSMGVDVVLITGDNRKTARAIA
Fcatus  all identical  ENSFCAG00000003710  1208LKSMGVDVVLITGDNRKTARAIA
Mmusculus  all identical  ENSMUSG00000006567  1217LKSMGVDVALITGDNRKTARAIA
Ggallus  all identical  ENSGALG00000017021  1198LKNMGIDVVLITGDNRKTAKAIA
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  all identical  FBgn0030343  990IDVVLLTGDNKNTAASIA
Celegans  all identical  Y76A2A.2  994LREMGLRVVLLTGDNSKTAESTA
Xtropicalis  all identical  ENSXETG00000020713  1164LKSMGIDVVLITGDNRKTAKAIA
protein features
start (aa)end (aa)featuredetails 
9951322TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4164 / 4164
position (AA) of stopcodon in wt / mu AA sequence 1388 / 1388
position of stopcodon in wt / mu cDNA 4238 / 4238
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 75 / 75
chromosome 13
strand -1
last intron/exon boundary 3965
theoretical NMD boundary in CDS 3840
length of CDS 4164
coding sequence (CDS) position 3425
cDNA position
(for ins/del: last normal base / first normal base)		 3499
gDNA position
(for ins/del: last normal base / first normal base)		 72404
chromosomal position
(for ins/del: last normal base / first normal base)		 52513227
original gDNA sequence snippet TGTGGACGTGGTTCTGATCACGGGGGACAACCGGAAGACAG
altered gDNA sequence snippet TGTGGACGTGGTTCTGATCATGGGGGACAACCGGAAGACAG
original cDNA sequence snippet TGTGGACGTGGTTCTGATCACGGGGGACAACCGGAAGACAG
altered cDNA sequence snippet TGTGGACGTGGTTCTGATCATGGGGGACAACCGGAAGACAG
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 LRIDGMHCKS CVLNIEENIG QLLGVQSIQV SLENKTAQVK
YDPSCTSPVA LQRAIEALPP GNFKVSLPDG AEGSGTDHRS SSSHSPGSPP RNQVQGTCST
TLIAIAGMTC ASCVHSIEGM ISQLEGVQQI SVSLAEGTAT VLYNPSVISP EELRAAIEDM
GFEASVVSES CSTNPLGNHS AGNSMVQTTD GTPTSVQEVA PHTGRLPANH APDILAKSPQ
STRAVAPQKC FLQIKGMTCA SCVSNIERNL QKEAGVLSVL VALMAGKAEI KYDPEVIQPL
EIAQFIQDLG FEAAVMEDYA GSDGNIELTI TGMTCASCVH NIESKLTRTN GITYASVALA
TSKALVKFDP EIIGPRDIIK IIEEIGFHAS LAQRNPNAHH LDHKMEIKQW KKSFLCSLVF
GIPVMALMIY MLIPSNEPHQ SMVLDHNIIP GLSILNLIFF ILCTFVQSKT SEALAKLMSL
QATEATVVTL GEDNLIIREE QVPMELVQRG DIVKVVPGGK FPVDGKVLEG NTMADESLIT
GEAMPVTKKP GSTVIAGSIN AHGSVLIKAT HVGNDTTLAQ IVKLVEEAQM SKAPIQQLAD
RFSGYFVPFI IIMSTLTLVV WIVIGFIDFG VVQRYFPNPN KHISQTEVII RFAFQTSITV
LCIACPCSLG LATPTAVMVG TGVAAQNGIL IKGGKPLEMA HKIKTVMFDK TGTITHGVPR
VMRVLLLGDV ATLPLRKVLA VVGTAEASSE HPLGVAVTKY CKEELGTETL GYCTDFQAVP
GCGIGCKVSN VEGILAHSER PLSAPASHLN EAGSLPAEKD AVPQTFSVLI GNREWLRRNG
LTISSDVSDA MTDHEMKGQT AILVAIDGVL CGMIAIADAV KQEAALAVHT LQSMGVDVVL
ITGDNRKTAR AIATQVGINK VFAEVLPSHK VAKVQELQNK GKKVAMVGDG VNDSPALAQA
DMGVAIGTGT DVAIEAADVV LIRNDLLDVV ASIHLSKRTV RRIRINLVLA LIYNLVGIPI
AAGVFMPIGI VLQPWMGSAA MAASSVSVVL SSLQLKCYKK PDLERYEAQA HGHMKPLTAS
QVSVHIGMDD RWRDSPRATP WDQVSYVSQV SLSSLTSDKP SRHSAAADDD GDKWSLLLNG
RDEEQYI*
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 LRIDGMHCKS CVLNIEENIG QLLGVQSIQV SLENKTAQVK
YDPSCTSPVA LQRAIEALPP GNFKVSLPDG AEGSGTDHRS SSSHSPGSPP RNQVQGTCST
TLIAIAGMTC ASCVHSIEGM ISQLEGVQQI SVSLAEGTAT VLYNPSVISP EELRAAIEDM
GFEASVVSES CSTNPLGNHS AGNSMVQTTD GTPTSVQEVA PHTGRLPANH APDILAKSPQ
STRAVAPQKC FLQIKGMTCA SCVSNIERNL QKEAGVLSVL VALMAGKAEI KYDPEVIQPL
EIAQFIQDLG FEAAVMEDYA GSDGNIELTI TGMTCASCVH NIESKLTRTN GITYASVALA
TSKALVKFDP EIIGPRDIIK IIEEIGFHAS LAQRNPNAHH LDHKMEIKQW KKSFLCSLVF
GIPVMALMIY MLIPSNEPHQ SMVLDHNIIP GLSILNLIFF ILCTFVQSKT SEALAKLMSL
QATEATVVTL GEDNLIIREE QVPMELVQRG DIVKVVPGGK FPVDGKVLEG NTMADESLIT
GEAMPVTKKP GSTVIAGSIN AHGSVLIKAT HVGNDTTLAQ IVKLVEEAQM SKAPIQQLAD
RFSGYFVPFI IIMSTLTLVV WIVIGFIDFG VVQRYFPNPN KHISQTEVII RFAFQTSITV
LCIACPCSLG LATPTAVMVG TGVAAQNGIL IKGGKPLEMA HKIKTVMFDK TGTITHGVPR
VMRVLLLGDV ATLPLRKVLA VVGTAEASSE HPLGVAVTKY CKEELGTETL GYCTDFQAVP
GCGIGCKVSN VEGILAHSER PLSAPASHLN EAGSLPAEKD AVPQTFSVLI GNREWLRRNG
LTISSDVSDA MTDHEMKGQT AILVAIDGVL CGMIAIADAV KQEAALAVHT LQSMGVDVVL
IMGDNRKTAR AIATQVGINK VFAEVLPSHK VAKVQELQNK GKKVAMVGDG VNDSPALAQA
DMGVAIGTGT DVAIEAADVV LIRNDLLDVV ASIHLSKRTV RRIRINLVLA LIYNLVGIPI
AAGVFMPIGI VLQPWMGSAA MAASSVSVVL SSLQLKCYKK PDLERYEAQA HGHMKPLTAS
QVSVHIGMDD RWRDSPRATP WDQVSYVSQV SLSSLTSDKP SRHSAAADDD GDKWSLLLNG
RDEEQYI*
speed 1.25 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