Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999244616 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940064)
  • known disease mutation: rs11979 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49455325C>TN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000546031
Genbank transcript ID N/A
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.668G>A
cDNA.860G>A
g.4862G>A
AA changes R223H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 223
frameshift no
known variant Reference ID: rs121964985
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC099

known disease mutation: rs11979 (pathogenic for Non-ketotic hyperglycinemia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940064)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940064)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940064)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.1381
5.1891
(flanking)2.9021
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased4863wt: 0.25 / mu: 0.48wt: AGGCGTGTGGGGTTG
mu: AGGCATGTGGGGTTG		 GCGT|gtgg
Donor increased4858wt: 0.80 / mu: 0.99wt: AGCGGAGGCGTGTGG
mu: AGCGGAGGCATGTGG		 CGGA|ggcg
distance from splice site 75
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      223VPQLKGRVQRRRVGLMCEGAPMRA
mutated  not conserved    223VPQLKGRVQRRHVGLMCEGAPMR
Ptroglodytes  all identical  ENSPTRG00000014924  320VPQLKGKVQRRRVGLMCEGAPMR
Mmulatta  all identical  ENSMMUG00000005452  320VPQLKGKVQRRRVGLMCEGAPMR
Fcatus  all identical  ENSFCAG00000009856  320LPQLKGKVQRRRVGLMCEGAPMR
Mmusculus  all identical  ENSMUSG00000032607  320VPQLKGEVQRRRVGLICEGAPVR
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  330IPQIKAKTARKRVGLVSTGPPVR
Drerio  all identical  ENSDARG00000010862  327VPQIKAKTPRKRVGLISTGPPVR
Dmelanogaster  all identical  FBgn0032287  318LGQLKEGVSRRRVGLQMLGTKPPP
Celegans  all identical  F25B4.1  316VKQLKEKSWPKRRVGLLAPAGRCPR
Xtropicalis  all identical  ENSXETG00000005937  320VPQIKGKVKHKRVGLTSTGPPVR
protein features
start (aa)end (aa)featuredetails 
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 921 / 921
position (AA) of stopcodon in wt / mu AA sequence 307 / 307
position of stopcodon in wt / mu cDNA 1113 / 1113
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 193 / 193
chromosome 3
strand -1
last intron/exon boundary 935
theoretical NMD boundary in CDS 692
length of CDS 921
coding sequence (CDS) position 668
cDNA position
(for ins/del: last normal base / first normal base)		 860
gDNA position
(for ins/del: last normal base / first normal base)		 4862
chromosomal position
(for ins/del: last normal base / first normal base)		 49455325
original gDNA sequence snippet GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG
altered gDNA sequence snippet GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG
original cDNA sequence snippet GGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGG
altered cDNA sequence snippet GGGCAGGGTGCAGCGGAGGCATGTGGGGTTGATGTGTGAGG
wildtype AA sequence MESLVVGDIA ELRPNQGTLS LFTNEAGGIL DDLIVTNTSE GHLYVVSNAG CWEKDLALMQ
DKVRELQNQG RDVGLEVLDN ALLALQGPTA AQVLQAGVAD DLRKLPFMTS AVMEVFGVSG
CRVTRCGYTG EDGVEISVPV AGAVHLATAI LKNPEVKLAG LAARDSLRLE AGLCLYGNDI
DEHTTPVEGS LSWTLGKRRR AAMDFPGAKV IVPQLKGRVQ RRRVGLMCEG APMRAHSPIL
NMEGTKIGTV TSGCPSPSLK KNVAMGYVPC EYSRPGTMLL VEVRRKQQMA VVSKMPFVPT
NYYTLK*
mutated AA sequence MESLVVGDIA ELRPNQGTLS LFTNEAGGIL DDLIVTNTSE GHLYVVSNAG CWEKDLALMQ
DKVRELQNQG RDVGLEVLDN ALLALQGPTA AQVLQAGVAD DLRKLPFMTS AVMEVFGVSG
CRVTRCGYTG EDGVEISVPV AGAVHLATAI LKNPEVKLAG LAARDSLRLE AGLCLYGNDI
DEHTTPVEGS LSWTLGKRRR AAMDFPGAKV IVPQLKGRVQ RRHVGLMCEG APMRAHSPIL
NMEGTKIGTV TSGCPSPSLK KNVAMGYVPC EYSRPGTMLL VEVRRKQQMA VVSKMPFVPT
NYYTLK*
speed 0.70 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