Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999953032 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM060825)
  • known disease mutation at this position (HGMD CM940062)
  • known disease mutation: rs11975 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49459656C>TN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000273588
Genbank transcript ID NM_000481
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.139G>A
cDNA.442G>A
g.531G>A
AA changes G47R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 47
frameshift no
known variant Reference ID: rs121964982
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs11975 (pathogenic for Non-ketotic hyperglycinemia|Inborn genetic diseases) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060825)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940062)
regulatory features CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2AZ, Histone, Histone 2A variant Z
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
PolII, Polymerase, RNA Polymerase II
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)3.761
5.4121
(flanking)-1.7650.355
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 increased532wt: 0.4473 / mu: 0.4763 (marginal change - not scored)wt: CTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCGG
mu: CTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCGG		 gcgg|GAAA
Acc marginally increased522wt: 0.2275 / mu: 0.2275 (marginal change - not scored)wt: CGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTG
mu: CGCTCTATGACTTCCACCTGGCCCACGGCAGGAAAATGGTG		 ctgg|CCCA
Donor increased532wt: 0.43 / mu: 0.87wt: CGGCGGGAAAATGGT
mu: CGGCAGGAAAATGGT		 GCGG|gaaa
Donor increased531wt: 0.66 / mu: 0.97wt: ACGGCGGGAAAATGG
mu: ACGGCAGGAAAATGG		 GGCG|ggaa
Donor gained5270.69mu: GCCCACGGCAGGAAA CCAC|ggca
distance from splice site 49
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      47TPLYDFHLAHGGKMVAFAGWSLPV
mutated  not conserved    47TPLYDFHLAHGRKMVAFAGWSLP
Ptroglodytes  all identical  ENSPTRG00000014924  47TPLYDFHLAHGGKMVAFAGWSLP
Mmulatta  all identical  ENSMMUG00000005452  47TPLYDFHLAHGGKMVAFAGWSLP
Fcatus  all identical  ENSFCAG00000009856  47TPLYDFHLAHGGKMVAFAGWSLP
Mmusculus  all identical  ENSMUSG00000032607  47TPLYDFHLAHGGKMVAFAGWSLP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  57TPLFDFHRAHGGKMVEFAGWSMP
Drerio  all identical  ENSDARG00000010862  54TPLYDFHRAHGGKMVEFAGWSMP
Dmelanogaster  all identical  FBgn0032287  40TALYDFHVQKGGKIVNFGGYALP
Celegans  all identical  F25B4.1  39TCLIETHKKHGGKLVEFAGYDMP
Xtropicalis  all identical  ENSXETG00000005937  47TPLYDFHREHGGKMVEFAGWKLP
protein features
start (aa)end (aa)featuredetails 
4852STRANDmight get lost (downstream of altered splice site)
5560STRANDmight get lost (downstream of altered splice site)
6574HELIXmight get lost (downstream of altered splice site)
7580STRANDmight get lost (downstream of altered splice site)
8491STRANDmight get lost (downstream of altered splice site)
94101HELIXmight get lost (downstream of altered splice site)
9595CONFLICTV -> C (in Ref. 2; BAA03512).might get lost (downstream of altered splice site)
102104STRANDmight get lost (downstream of altered splice site)
113120STRANDmight get lost (downstream of altered splice site)
126134STRANDmight get lost (downstream of altered splice site)
138144STRANDmight get lost (downstream of altered splice site)
146148HELIXmight get lost (downstream of altered splice site)
149165HELIXmight get lost (downstream of altered splice site)
171174STRANDmight get lost (downstream of altered splice site)
178184STRANDmight get lost (downstream of altered splice site)
187192HELIXmight get lost (downstream of altered splice site)
199201HELIXmight get lost (downstream of altered splice site)
206212STRANDmight get lost (downstream of altered splice site)
215222STRANDmight get lost (downstream of altered splice site)
225235STRANDmight get lost (downstream of altered splice site)
232232BINDINGSubstrate.might get lost (downstream of altered splice site)
237248HELIXmight get lost (downstream of altered splice site)
253255STRANDmight get lost (downstream of altered splice site)
258267HELIXmight get lost (downstream of altered splice site)
261261BINDINGSubstrate.might get lost (downstream of altered splice site)
273275TURNmight get lost (downstream of altered splice site)
283287TURNmight get lost (downstream of altered splice site)
289291HELIXmight get lost (downstream of altered splice site)
294299HELIXmight get lost (downstream of altered splice site)
305312HELIXmight get lost (downstream of altered splice site)
319328STRANDmight get lost (downstream of altered splice site)
335337STRANDmight get lost (downstream of altered splice site)
343353STRANDmight get lost (downstream of altered splice site)
354357TURNmight get lost (downstream of altered splice site)
358365STRANDmight get lost (downstream of altered splice site)
367369HELIXmight get lost (downstream of altered splice site)
375380STRANDmight get lost (downstream of altered splice site)
383390STRANDmight get lost (downstream of altered splice site)
399399BINDINGSubstrate.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1212 / 1212
position (AA) of stopcodon in wt / mu AA sequence 404 / 404
position of stopcodon in wt / mu cDNA 1515 / 1515
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 304 / 304
chromosome 3
strand -1
last intron/exon boundary 1337
theoretical NMD boundary in CDS 983
length of CDS 1212
coding sequence (CDS) position 139
cDNA position
(for ins/del: last normal base / first normal base)		 442
gDNA position
(for ins/del: last normal base / first normal base)		 531
chromosomal position
(for ins/del: last normal base / first normal base)		 49459656
original gDNA sequence snippet ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG
altered gDNA sequence snippet ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG
original cDNA sequence snippet ACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCGTTTGCG
altered cDNA sequence snippet ACTTCCACCTGGCCCACGGCAGGAAAATGGTGGCGTTTGCG
wildtype AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNDIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRR VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEV RRKQQMAVVS KMPFVPTNYY TLK*
mutated AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGRKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQGTLSLFT
NEAGGILDDL IVTNTSEGHL YVVSNAGCWE KDLALMQDKV RELQNQGRDV GLEVLDNALL
ALQGPTAAQV LQAGVADDLR KLPFMTSAVM EVFGVSGCRV TRCGYTGEDG VEISVPVAGA
VHLATAILKN PEVKLAGLAA RDSLRLEAGL CLYGNDIDEH TTPVEGSLSW TLGKRRRAAM
DFPGAKVIVP QLKGRVQRRR VGLMCEGAPM RAHSPILNME GTKIGTVTSG CPSPSLKKNV
AMGYVPCEYS RPGTMLLVEV RRKQQMAVVS KMPFVPTNYY TLK*
speed 1.19 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