Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: without_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • known disease mutation at this position (HGMD CM880009)
  • known disease mutation: rs18296 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88876242A>GN/A show variant in all transcripts   IGV
HGNC symbol APRT
Ensembl transcript ID ENST00000426324
Genbank transcript ID NM_001030018
UniProt peptide P07741
alteration type single base exchange
alteration region intron
DNA changes g.2111T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs28999113
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs18296 (pathogenic for Adenine phosphoribosyltransferase deficiency|APRT deficiency, Japanese type) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM880009)

known disease mutation at this position, please check HGMD for details (HGMD ID CM880009)
known disease mutation at this position, please check HGMD for details (HGMD ID CM880009)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)5.2691
4.3641
(flanking)2.8221
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 increased2103wt: 0.9114 / mu: 0.9248 (marginal change - not scored)wt: GACCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTG
mu: GACCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTG		 ccca|GGAA
Acc marginally increased2105wt: 0.2583 / mu: 0.3307 (marginal change - not scored)wt: CCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTGTG
mu: CCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTGTG		 cagg|AACC
Acc marginally increased2104wt: 0.8036 / mu: 0.8236 (marginal change - not scored)wt: ACCTCACCCTCCCATCCCCAGGAACCATGAACGCTGCCTGT
mu: ACCTCACCCTCCCATCCCCAGGAACCACGAACGCTGCCTGT		 ccag|GAAC
Donor marginally increased2103wt: 0.8481 / mu: 0.8970 (marginal change - not scored)wt: TCCCCAGGAACCATG
mu: TCCCCAGGAACCACG		 CCCA|ggaa
Donor increased2110wt: 0.71 / mu: 0.82wt: GAACCATGAACGCTG
mu: GAACCACGAACGCTG		 ACCA|tgaa
Donor increased2106wt: 0.47 / mu: 0.70wt: CCAGGAACCATGAAC
mu: CCAGGAACCACGAAC		 AGGA|acca
distance from splice site 128
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
134145HELIXmight get lost (downstream of altered splice site)
135135MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
149159STRANDmight get lost (downstream of altered splice site)
160162HELIXmight get lost (downstream of altered splice site)
164168HELIXmight get lost (downstream of altered splice site)
173179STRANDmight get lost (downstream of altered splice site)
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 27 / 27
chromosome 16
strand -1
last intron/exon boundary 427
theoretical NMD boundary in CDS 350
length of CDS 405
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 2111
chromosomal position
(for ins/del: last normal base / first normal base)		 88876242
original gDNA sequence snippet CCTCCCATCCCCAGGAACCATGAACGCTGCCTGTGAGCTGC
altered gDNA sequence snippet CCTCCCATCCCCAGGAACCACGAACGCTGCCTGTGAGCTGC
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGLDSRGFL FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG
QRVVVVDDLL ATGV*
mutated AA sequence N/A
speed 0.60 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