Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999993574      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs11978 (probable pathogenic)
  • known disease mutation at this position (HGMD CM983428)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:49456455C>GN/A show variant in all transcripts   IGV
HGNC symbol AMT
Ensembl transcript ID ENST00000538581
Genbank transcript ID NM_001164711
UniProt peptide P48728
alteration type single base exchange
alteration region CDS
DNA changes c.658G>C
cDNA.886G>C
g.3732G>C
AA changes D220H Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 220
frameshift no
known variant Reference ID: rs121964984
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known as potential disease variant: rs11978 (probable pathogenic for Non-ketotic hyperglycinemia) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)

known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
known disease mutation at this position, please check HGMD for details (HGMD ID CM983428)
regulatory features Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
CTCF, Transcription Factor, CCCTC-binding factor
Cfos, Transcription Factor, Cfos TF binding
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)4.4961
5.4411
(flanking)0.0310.991
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 increased3727wt: 0.7803 / mu: 0.8233 (marginal change - not scored)wt: GGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACA
mu: GGCAGGCCTCTGCCTGTATGGGAATCACATTGATGAACACA		 atgg|GAAT
Donor marginally increased3725wt: 0.9342 / mu: 0.9539 (marginal change - not scored)wt: CTGTATGGGAATGAC
mu: CTGTATGGGAATCAC		 GTAT|ggga
distance from splice site 52
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      220RLEAGLCLYGNDIDEHTTPVEGSL
mutated  not conserved    220RLEAGLCLYGNHIDEHTTPVEGS
Ptroglodytes  all identical  ENSPTRG00000014924  276LEAGLCLYGNDIDEHTTPVEGS
Mmulatta  all identical  ENSMMUG00000005452  276LEAGLCLYGNDIDEHTTPVEGS
Fcatus  all identical  ENSFCAG00000009856  276LEAGLCLYGSDIDEHTTPVEGS
Mmusculus  all identical  ENSMUSG00000032607  276LEAGLCLYGNDIDEHTTPVEGS
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000008892  286LEAGLCLYGNDIDETTTPVEAT
Drerio  all identical  ENSDARG00000010862  283LEAGLCLYGNDIDETTTPVEAT
Dmelanogaster  all identical  FBgn0032287  274RLEAGLCLYGSDIDSKTTPVEAA
Celegans  all identical  F25B4.1  272RLEAGLCLYGSDIEENTTPIEAG
Xtropicalis  all identical  ENSXETG00000005937  276LEAGLCLYGNDIDETTSPVEAS
protein features
start (aa)end (aa)featuredetails 
215222STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1044 / 1044
position (AA) of stopcodon in wt / mu AA sequence 348 / 348
position of stopcodon in wt / mu cDNA 1272 / 1272
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 229 / 229
chromosome 3
strand -1
last intron/exon boundary 1094
theoretical NMD boundary in CDS 815
length of CDS 1044
coding sequence (CDS) position 658
cDNA position
(for ins/del: last normal base / first normal base)		 886
gDNA position
(for ins/del: last normal base / first normal base)		 3732
chromosomal position
(for ins/del: last normal base / first normal base)		 49456455
original gDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered gDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
original cDNA sequence snippet GCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACA
altered cDNA sequence snippet GCCTCTGCCTGTATGGGAATCACATTGATGAACACACTACA
wildtype AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ TKILGSDRVK LMESLVVGDI AELRPNQGTL
SLFTNEAGGI LDDLIVTNTS EGHLYVVSNA GCWEKDLALM QDKVRELQNQ GRDVGLEVLD
NALLALQGPT AAQVLQAGVA DDLRKLPFMT SAVMEVFGVS GCRVTRCGYT GEDGVEISVP
VAGAVHLATA ILKNPEVKLA GLAARDSLRL EAGLCLYGND IDEHTTPVEG SLSWTLGKRR
RAAMDFPGAK VIVPQLKGRV QRRRVGLMCE GAPMRAHSPI LNMEGTKIGT VTSGCPSPSL
KKNVAMGYVP CEYSRPGTML LVEVRRKQQM AVVSKMPFVP TNYYTLK*
mutated AA sequence MQRAVSVVAR LGFRLQAFPP ALCRPLSCAQ TKILGSDRVK LMESLVVGDI AELRPNQGTL
SLFTNEAGGI LDDLIVTNTS EGHLYVVSNA GCWEKDLALM QDKVRELQNQ GRDVGLEVLD
NALLALQGPT AAQVLQAGVA DDLRKLPFMT SAVMEVFGVS GCRVTRCGYT GEDGVEISVP
VAGAVHLATA ILKNPEVKLA GLAARDSLRL EAGLCLYGNH IDEHTTPVEG SLSWTLGKRR
RAAMDFPGAK VIVPQLKGRV QRRRVGLMCE GAPMRAHSPI LNMEGTKIGT VTSGCPSPSL
KKNVAMGYVP CEYSRPGTML LVEVRRKQQM AVVSKMPFVP TNYYTLK*
speed 1.07 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