Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.996995149890714 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960120)
  • known disease mutation at this position (HGMD CM960121)
  • known disease mutation: rs156281 (pathogenic)
  • protein features (might be) affected
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analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:52532674C>TN/A show variant in all transcripts   IGV
HGNC symbol ATP7B
Ensembl transcript ID ENST00000542656
Genbank transcript ID N/A
UniProt peptide P35670
alteration type single base exchange
alteration region CDS
DNA changes c.1454G>A
cDNA.1499G>A
g.52957G>A
AA changes R485Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 485
frameshift no
known variant Reference ID: rs137853285
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs156281 (pathogenic for Wilson disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960121)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960121)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960121)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960120)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960121)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.0280.993
6.0280.999
(flanking)-0.4930.82
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 increased52957wt: 0.9808 / mu: 0.9847 (marginal change - not scored)wt: TCCTTGTCTTTCAGCTCCTCGGTGGGTGGTACTTCTACGTT
mu: TCCTTGTCTTTCAGCTCCTCAGTGGGTGGTACTTCTACGTT		 ctcg|GTGG
Acc marginally increased52951wt: 0.4235 / mu: 0.4439 (marginal change - not scored)wt: TCACTGTCCTTGTCTTTCAGCTCCTCGGTGGGTGGTACTTC
mu: TCACTGTCCTTGTCTTTCAGCTCCTCAGTGGGTGGTACTTC		 cagc|TCCT
Acc marginally increased52954wt: 0.5381 / mu: 0.5590 (marginal change - not scored)wt: CTGTCCTTGTCTTTCAGCTCCTCGGTGGGTGGTACTTCTAC
mu: CTGTCCTTGTCTTTCAGCTCCTCAGTGGGTGGTACTTCTAC		 ctcc|TCGG
distance from splice site 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      485IERNLQKEAAPRWVVLLRSGLQIS
mutated  all conserved    485EAAPQWVVLLRSGLQI
Ptroglodytes  no alignment  ENSPTRG00000005897  n/a
Mmulatta  no alignment  ENSMMUG00000016520  n/a
Fcatus  all identical  ENSFCAG00000003710  374IEGLLSRREGVRRV
Mmusculus  no alignment  ENSMUSG00000006567  n/a
Ggallus  no alignment  ENSGALG00000017021  n/a
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no alignment  FBgn0030343  n/a
Celegans  no alignment  Y76A2A.2  n/a
Xtropicalis  no alignment  ENSXETG00000020713  n/a
protein features
start (aa)end (aa)featuredetails 
1653TOPO_DOMCytoplasmic (Potential).lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1587 / 1587
position (AA) of stopcodon in wt / mu AA sequence 529 / 529
position of stopcodon in wt / mu cDNA 1632 / 1632
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 46 / 46
chromosome 13
strand -1
last intron/exon boundary 1493
theoretical NMD boundary in CDS 1397
length of CDS 1587
coding sequence (CDS) position 1454
cDNA position
(for ins/del: last normal base / first normal base)		 1499
gDNA position
(for ins/del: last normal base / first normal base)		 52957
chromosomal position
(for ins/del: last normal base / first normal base)		 52532674
original gDNA sequence snippet TCCTTGTCTTTCAGCTCCTCGGTGGGTGGTACTTCTACGTT
altered gDNA sequence snippet TCCTTGTCTTTCAGCTCCTCAGTGGGTGGTACTTCTACGTT
original cDNA sequence snippet GCAGAAAGAAGCTGCTCCTCGGTGGGTGGTACTTCTACGTT
altered cDNA sequence snippet GCAGAAAGAAGCTGCTCCTCAGTGGGTGGTACTTCTACGTT
wildtype AA sequence MKKSFAFDNV GYEGGLDGLG PSSQVATSTV RILGMTCQSC VKSIEDRISN LKGIISMKVS
LEQGSATVKY VPSVVCLQQV CHQIGDMGFE ASIAEGKAAS WPSRSLPAQE AVVKLRVEGM
TCQSCVSSIE GKVRKLQGVV RVKVSLSNQE AVITYQPYLI QPEDLRDHVN DMGFEAAIKS
KVAPLSLGPI DIERLQSTNP KRPLSSANQN FNNSETLGHQ GSHVVTLQLR IDGMHCKSCV
LNIEENIGQL LGVQSIQVSL ENKTAQVKYD PSCTSPVALQ RAIEALPPGN FKVSLPDGAE
GSGTDHRSSS SHSPGSPPRN QVQGTCSTTL IAIAGMTCAS CVHSIEGMIS QLEGVQQISV
SLAEGTATVL YNPSVISPEE LRAAIEDMGF EASVVSESCS TNPLGNHSAG NSMVQTTDGT
PTSVQEVAPH TGRLPANHAP DILAKSPQST RAVAPQKCFL QIKGMTCASC VSNIERNLQK
EAAPRWVVLL RSGLQISETQ VSQHGRAHRP GHKHCLCLFS GHPGGCCG*
mutated AA sequence MKKSFAFDNV GYEGGLDGLG PSSQVATSTV RILGMTCQSC VKSIEDRISN LKGIISMKVS
LEQGSATVKY VPSVVCLQQV CHQIGDMGFE ASIAEGKAAS WPSRSLPAQE AVVKLRVEGM
TCQSCVSSIE GKVRKLQGVV RVKVSLSNQE AVITYQPYLI QPEDLRDHVN DMGFEAAIKS
KVAPLSLGPI DIERLQSTNP KRPLSSANQN FNNSETLGHQ GSHVVTLQLR IDGMHCKSCV
LNIEENIGQL LGVQSIQVSL ENKTAQVKYD PSCTSPVALQ RAIEALPPGN FKVSLPDGAE
GSGTDHRSSS SHSPGSPPRN QVQGTCSTTL IAIAGMTCAS CVHSIEGMIS QLEGVQQISV
SLAEGTATVL YNPSVISPEE LRAAIEDMGF EASVVSESCS TNPLGNHSAG NSMVQTTDGT
PTSVQEVAPH TGRLPANHAP DILAKSPQST RAVAPQKCFL QIKGMTCASC VSNIERNLQK
EAAPQWVVLL RSGLQISETQ VSQHGRAHRP GHKHCLCLFS GHPGGCCG*
speed 0.89 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