Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999945707936 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM074064)
  • known disease mutation: rs8297 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:127834262C>AN/A show variant in all transcripts   IGV
HGNC symbol BIN1
Ensembl transcript ID ENST00000393041
Genbank transcript ID NM_139349
UniProt peptide O00499
alteration type single base exchange
alteration region CDS
DNA changes c.105G>T
cDNA.450G>T
g.30670G>T
AA changes K35N Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 35
frameshift no
known variant Reference ID: rs121909273
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8297 (pathogenic for Myopathy, centronuclear, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM074064)

known disease mutation at this position, please check HGMD for details (HGMD ID CM074064)
known disease mutation at this position, please check HGMD for details (HGMD ID CM074064)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.5671
0.711
(flanking)3.0851
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased30665wt: 0.43 / mu: 0.74wt: AGCTGGGGAAGGCAG
mu: AGCTGGGGAATGCAG		 CTGG|ggaa
Donor marginally increased30673wt: 0.9866 / mu: 0.9918 (marginal change - not scored)wt: AAGGCAGATGAGACC
mu: AATGCAGATGAGACC		 GGCA|gatg
Donor gained306630.36mu: GAAGCTGGGGAATGC AGCT|gggg
distance from splice site 21
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      35RAQEKVLQKLGKADETKDEQFEQC
mutated  not conserved    35RAQEKVLQKLGNADETKDEQFEQ
Ptroglodytes  all identical  ENSPTRG00000012423  35RAQEKVLQKLGKADETKDEQFEQ
Mmulatta  no homologue    
Fcatus  all identical  ENSFCAG00000000531  7VLQKLGKADETKDEQFEQ
Mmusculus  all identical  ENSMUSG00000024381  35RAQEKVLQKLGKADETKDEQFEQ
Ggallus  all identical  ENSGALG00000011541  35RAQEKVLQKLGKADETKDEQFEQ
Trubripes  all identical  ENSTRUG00000013580  35RAQEKVLQKLGKADETKDAAFEE
Drerio  all identical  ENSDARG00000042114  35RAQEKVMQKLGKADETKDLAFEE
Dmelanogaster  all identical  FBgn0027356  30RAKEKILQNLGKVDRTADEIFDD
Celegans  all identical  F58G6.1  26RTKEKLLEGIGKAKATQDEVFDQ
Xtropicalis  all identical  ENSXETG00000000473  7VLQKLGKADETKDEQFEQ
protein features
start (aa)end (aa)featuredetails 
1122REGIONInteraction with BIN2.lost
833HELIXmight get lost (downstream of altered splice site)
1542COILEDPotential.lost
29276DOMAINBAR.lost
4389HELIXmight get lost (downstream of altered splice site)
97121HELIXmight get lost (downstream of altered splice site)
123131HELIXmight get lost (downstream of altered splice site)
133161HELIXmight get lost (downstream of altered splice site)
193267COILEDPotential.might get lost (downstream of altered splice site)
205268HELIXmight get lost (downstream of altered splice site)
296296MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
298298MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
303303MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
307307MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
323323MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
331331MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
378421REGIONClathrin-binding.might get lost (downstream of altered splice site)
474474CONFLICTA -> P (in Ref. 2; AAB63263).might get lost (downstream of altered splice site)
481481CONFLICTA -> S (in Ref. 10; AAC24126/AAC23750/ AAC23751).might get lost (downstream of altered splice site)
510510CONFLICTS -> C (in Ref. 7; AAC23440/AAC23441).might get lost (downstream of altered splice site)
520592DOMAINSH3.might get lost (downstream of altered splice site)
523527STRANDmight get lost (downstream of altered splice site)
528528CONFLICTQ -> H (in Ref. 7; AAC23440/AAC23441).might get lost (downstream of altered splice site)
535537STRANDmight get lost (downstream of altered splice site)
546549STRANDmight get lost (downstream of altered splice site)
555557HELIXmight get lost (downstream of altered splice site)
562567STRANDmight get lost (downstream of altered splice site)
568572HELIXmight get lost (downstream of altered splice site)
573579HELIXmight get lost (downstream of altered splice site)
576576CONFLICTE -> K (in Ref. 7; AAC23440/AAC23441).might get lost (downstream of altered splice site)
582585STRANDmight get lost (downstream of altered splice site)
586588HELIXmight get lost (downstream of altered splice site)
589591STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1428 / 1428
position (AA) of stopcodon in wt / mu AA sequence 476 / 476
position of stopcodon in wt / mu cDNA 1773 / 1773
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 346 / 346
chromosome 2
strand -1
last intron/exon boundary 1666
theoretical NMD boundary in CDS 1270
length of CDS 1428
coding sequence (CDS) position 105
cDNA position
(for ins/del: last normal base / first normal base)		 450
gDNA position
(for ins/del: last normal base / first normal base)		 30670
chromosomal position
(for ins/del: last normal base / first normal base)		 127834262
original gDNA sequence snippet GTTCTCCAGAAGCTGGGGAAGGCAGATGAGACCAAGGATGA
altered gDNA sequence snippet GTTCTCCAGAAGCTGGGGAATGCAGATGAGACCAAGGATGA
original cDNA sequence snippet GTTCTCCAGAAGCTGGGGAAGGCAGATGAGACCAAGGATGA
altered cDNA sequence snippet GTTCTCCAGAAGCTGGGGAATGCAGATGAGACCAAGGATGA
wildtype AA sequence MAEMGSKGVT AGKIASNVQK KLTRAQEKVL QKLGKADETK DEQFEQCVQN FNKQLTEGTR
LQKDLRTYLA SVKAMHEASK KLNECLQEVY EPDWPGRDEA NKIAENNDLL WMDYHQKLVD
QALLTMDTYL GQFPDIKSRI AKRGRKLVDY DSARHHYESL QTAKKKDEAK IAKAEEELIK
AQKVFEEMNV DLQEELPSLW NSRVGFYVNT FQSIAGLEEN FHKEMSKLNQ NLNDVLVGLE
KQHGSNTFTV KAQPSDNAPA KGNKSPSPPD GSPAATPEIR VNHEPEPAGG ATPGATLPKS
PSQPTESPAG SLPSGEPSAA EGTFAVSWPS QTAEPGPAQP AEASEVAGGT QPAAGAQEPG
ETAASEAASS SLPAVVVETF PATVNGTVEG GSGAGRLDLP PGFMFKVQAQ HDYTATDTDE
LQLKAGDVVL VIPFQNPEEQ DEGWLMGVKE SDWNQHKELE KCRGVFPENF TERVP*
mutated AA sequence MAEMGSKGVT AGKIASNVQK KLTRAQEKVL QKLGNADETK DEQFEQCVQN FNKQLTEGTR
LQKDLRTYLA SVKAMHEASK KLNECLQEVY EPDWPGRDEA NKIAENNDLL WMDYHQKLVD
QALLTMDTYL GQFPDIKSRI AKRGRKLVDY DSARHHYESL QTAKKKDEAK IAKAEEELIK
AQKVFEEMNV DLQEELPSLW NSRVGFYVNT FQSIAGLEEN FHKEMSKLNQ NLNDVLVGLE
KQHGSNTFTV KAQPSDNAPA KGNKSPSPPD GSPAATPEIR VNHEPEPAGG ATPGATLPKS
PSQPTESPAG SLPSGEPSAA EGTFAVSWPS QTAEPGPAQP AEASEVAGGT QPAAGAQEPG
ETAASEAASS SLPAVVVETF PATVNGTVEG GSGAGRLDLP PGFMFKVQAQ HDYTATDTDE
LQLKAGDVVL VIPFQNPEEQ DEGWLMGVKE SDWNQHKELE KCRGVFPENF TERVP*
speed 0.97 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