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 CM910042)
  • known disease mutation: rs18297 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88876958T>AN/A show variant in all transcripts   IGV
HGNC symbol APRT
Ensembl transcript ID ENST00000563655
Genbank transcript ID N/A
UniProt peptide P07741
alteration type single base exchange
alteration region intron
DNA changes g.1395A>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs104894506
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs18297 (pathogenic for Adenine phosphoribosyltransferase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910042)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910042)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910042)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
EBF, Transcription Factor, EBF Transcription Factor Binding
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-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
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
Max, Transcription Factor, Max TF binding
PolII, Polymerase, RNA Polymerase II
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SP1, Transcription Factor, SP1 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
phyloP / phastCons
PhyloPPhastCons
(flanking)1.6521
3.6841
(flanking)4.6410.999
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 increased1388wt: 0.7682 / mu: 0.7827 (marginal change - not scored)wt: TCCTGTCACTTACCCTGACAGGCCTAGACTCCCGAGGCTTC
mu: TCCTGTCACTTACCCTGACAGGCCTAGTCTCCCGAGGCTTC		 acag|GCCT
Acc marginally increased1385wt: 0.5149 / mu: 0.5191 (marginal change - not scored)wt: CACTCCTGTCACTTACCCTGACAGGCCTAGACTCCCGAGGC
mu: CACTCCTGTCACTTACCCTGACAGGCCTAGTCTCCCGAGGC		 ctga|CAGG
Donor marginally increased1388wt: 0.9562 / mu: 0.9941 (marginal change - not scored)wt: TGACAGGCCTAGACT
mu: TGACAGGCCTAGTCT		 ACAG|gcct
Acc gained14020.31mu: CTGACAGGCCTAGTCTCCCGAGGCTTCCTCTTTGGCCCCTC ccga|GGCT
distance from splice site 402
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
8288STRANDmight get lost (downstream of altered splice site)
94103STRANDmight get lost (downstream of altered splice site)
100100MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
106113STRANDmight get lost (downstream of altered splice site)
114114MOD_RESN6-acetyllysine.might get lost (downstream of altered splice site)
122133STRANDmight get lost (downstream of altered splice site)
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 22 / 22
chromosome 16
strand -1
last intron/exon boundary 341
theoretical NMD boundary in CDS 269
length of CDS 462
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)		 1395
chromosomal position
(for ins/del: last normal base / first normal base)		 88876958
original gDNA sequence snippet ACTTACCCTGACAGGCCTAGACTCCCGAGGCTTCCTCTTTG
altered gDNA sequence snippet ACTTACCCTGACAGGCCTAGTCTCCCGAGGCTTCCTCTTTG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGECPVAAS RALPPLRAPR AELEIQKDAL EPGQRVVVVD DLLATGGTMN AACELLGRLQ
AEVLECVSLV ELTSLKGREK LAPVPFFSLL QYE*
mutated AA sequence N/A
speed 0.09 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