Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.99999999999795 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940063)
  • known disease mutation: rs11974 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49456475C>TN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000458307
Genbank transcript ID NM_001164710
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.674G>A
cDNA.693G>A
g.3712G>A
AA changes G225D Score: 94 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 225
frameshift no
known variant Reference ID: rs121964981
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs11974 (pathogenic for Non-ketotic hyperglycinemia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940063)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940063)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940063)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
DNase1, Open Chromatin, DNase1 Hypersensitive Site
FOSL2, Transcription Factor, FOSL2 Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
Jund, Transcription Factor, Jund TF binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)0.3011
5.4411
(flanking)5.4411
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 72
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      225LAARDSLRLEAGLCLYGNDIDEHT
mutated  not conserved    225LAARDSLRLEADLCLYGNDIDEH
Ptroglodytes  all identical  ENSPTRG00000014924  269LAARDSLRLEAGLCLYGNDIDEH
Mmulatta  all identical  ENSMMUG00000005452  269LAARDSLRLEAGLCLYGNDIDEH
Fcatus  all identical  ENSFCAG00000009856  269LAARDSLRLEAGLCLYGSDIDEH
Mmusculus  all identical  ENSMUSG00000032607  269LAARDSLRLEAGLCLYGNDIDEH
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  279GLCLYGNDIDET
Drerio  all identical  ENSDARG00000010862  276LGARDSLRLEAGLCLYGNDIDET
Dmelanogaster  all identical  FBgn0032287  267LGARDSLRLEAGLCLYGSDIDSK
Celegans  all identical  F25B4.1  265RLEAGLCLYGSDIEEN
Xtropicalis  all identical  ENSXETG00000005937  269LAARDSLRLEAGLCLYGNDIDET
protein features
start (aa)end (aa)featuredetails 
225235STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1080 / 1080
position (AA) of stopcodon in wt / mu AA sequence 360 / 360
position of stopcodon in wt / mu cDNA 1099 / 1099
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 20 / 20
chromosome 3
strand -1
last intron/exon boundary 921
theoretical NMD boundary in CDS 851
length of CDS 1080
coding sequence (CDS) position 674
cDNA position
(for ins/del: last normal base / first normal base)		 693
gDNA position
(for ins/del: last normal base / first normal base)		 3712
chromosomal position
(for ins/del: last normal base / first normal base)		 49456475
original gDNA sequence snippet CAGCCTGCGCCTGGAGGCAGGCCTCTGCCTGTATGGGAATG
altered gDNA sequence snippet CAGCCTGCGCCTGGAGGCAGACCTCTGCCTGTATGGGAATG
original cDNA sequence snippet CAGCCTGCGCCTGGAGGCAGGCCTCTGCCTGTATGGGAATG
altered cDNA sequence snippet CAGCCTGCGCCTGGAGGCAGACCTCTGCCTGTATGGGAATG
wildtype AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQDKVRELQ
NQGRDVGLEV LDNALLALQG PTAAQVLQAG VADDLRKLPF MTSAVMEVFG VSGCRVTRCG
YTGEDGVEIS VPVAGAVHLA TAILKNPEVK LAGLAARDSL RLEAGLCLYG NDIDEHTTPV
EGSLSWTLGK RRRAAMDFPG AKVIVPQLKG RVQRRRVGLM CEGAPMRAHS PILNMEGTKI
GTVTSGCPSP SLKKNVAMGY VPCEYSRPGT MLLVEVRRKQ QMAVVSKMPF VPTNYYTLK*
mutated AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ EVLRRTPLYD FHLAHGGKMV AFAGWSLPVQ
YRDSHTDSHL HTRQHCSLFD VSHMLQTKIL GSDRVKLMES LVVGDIAELR PNQDKVRELQ
NQGRDVGLEV LDNALLALQG PTAAQVLQAG VADDLRKLPF MTSAVMEVFG VSGCRVTRCG
YTGEDGVEIS VPVAGAVHLA TAILKNPEVK LAGLAARDSL RLEADLCLYG NDIDEHTTPV
EGSLSWTLGK RRRAAMDFPG AKVIVPQLKG RVQRRRVGLM CEGAPMRAHS PILNMEGTKI
GTVTSGCPSP SLKKNVAMGY VPCEYSRPGT MLLVEVRRKQ QMAVVSKMPF VPTNYYTLK*
speed 0.50 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