Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999995060823 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980083)
  • known disease mutation: rs11976 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49459670T>CN/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.125A>G
cDNA.428A>G
g.517A>G
AA changes H42R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 42
frameshift no
known variant Reference ID: rs121964983
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs11976 (pathogenic for Non-ketotic hyperglycinemia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980083)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980083)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980083)
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)3.8861
1.9791
(flanking)5.4821
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 increased520wt: 0.8216 / mu: 0.8374 (marginal change - not scored)wt: ACCGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGG
mu: ACCGCTCTATGACTTCCGCCTGGCCCACGGCGGGAAAATGG		 acct|GGCC
Acc increased516wt: 0.24 / mu: 0.48wt: GGACACCGCTCTATGACTTCCACCTGGCCCACGGCGGGAAA
mu: GGACACCGCTCTATGACTTCCGCCTGGCCCACGGCGGGAAA		 ttcc|ACCT
Acc marginally increased522wt: 0.2275 / mu: 0.2283 (marginal change - not scored)wt: CGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTG
mu: CGCTCTATGACTTCCGCCTGGCCCACGGCGGGAAAATGGTG		 ctgg|CCCA
Acc increased525wt: 0.25 / mu: 0.32wt: TCTATGACTTCCACCTGGCCCACGGCGGGAAAATGGTGGCG
mu: TCTATGACTTCCGCCTGGCCCACGGCGGGAAAATGGTGGCG		 gccc|ACGG
distance from splice site 35
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      42EVLRRTPLYDFHLAHGGKMVAFAG
mutated  not conserved    42EVLRRTPLYDFRLAHGGKMVAFA
Ptroglodytes  all identical  ENSPTRG00000014924  42EVLRRTPLYDFHLAHGGKMVAFA
Mmulatta  all identical  ENSMMUG00000005452  42DVLRRTPLYDFHLAHGGKMVAFA
Fcatus  all identical  ENSFCAG00000009856  42DVLRRTPLYDFHLAHGGKMVAFA
Mmusculus  all identical  ENSMUSG00000032607  42DVLRRTPLYDFHLAHGGKMVAFA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  52AALKKTPLFDFHRAHGGKMVEFA
Drerio  all identical  ENSDARG00000010862  49LRKTPLYDFHRAHGGKMVEFA
Dmelanogaster  all identical  FBgn0032287  35EG-QRTALYDFHVQKGGKIVNFG
Celegans  all identical  F25B4.1  34ASAKQTCLIETHKKHGGKLVEFA
Xtropicalis  all identical  ENSXETG00000005937  42NPPRQTPLYDFHREHGGKMVEFA
protein features
start (aa)end (aa)featuredetails 
3944HELIXlost
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 125
cDNA position
(for ins/del: last normal base / first normal base)		 428
gDNA position
(for ins/del: last normal base / first normal base)		 517
chromosomal position
(for ins/del: last normal base / first normal base)		 49459670
original gDNA sequence snippet GACACCGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAA
altered gDNA sequence snippet GACACCGCTCTATGACTTCCGCCTGGCCCACGGCGGGAAAA
original cDNA sequence snippet GACACCGCTCTATGACTTCCACCTGGCCCACGGCGGGAAAA
altered cDNA sequence snippet GACACCGCTCTATGACTTCCGCCTGGCCCACGGCGGGAAAA
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 FRLAHGGKMV 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 1.11 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