Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999989902 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000426324
Genbank transcript ID NM_001030018
UniProt peptide P07741
alteration type single base exchange
alteration region CDS
DNA changes c.194A>T
cDNA.220A>T
g.1395A>T
AA changes D65V Score: 152 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 65
frameshift no
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 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      65HGGRIDYIAGLDSRGFLFGPSLAQ
mutated  not conserved    65IAGLVSRGFLFGPSLA
Ptroglodytes  all identical  ENSPTRG00000008466  65IAGLDSRGFLFGPSLA
Mmulatta  not conserved  ENSMMUG00000013824  65IAGEYSRGFLFGPSLA
Fcatus  no alignment  ENSFCAG00000018452  n/a
Mmusculus  all identical  ENSMUSG00000006589  65IAGLDSRGFLFGPSLA
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000005211  65GLDARGFLFGPLLA
Drerio  all identical  ENSDARG00000003519  63IVGLDARGFLFGPLLA
Dmelanogaster  all identical  FBgn0000109  69VGLDSRGFLFNLLIA
Celegans  all conserved  T19B4.3  69VG-HVDSVAGLEARG
Xtropicalis  all identical  ENSXETG00000027084  65VIAGLDSRGFLFGPSLA
protein features
start (aa)end (aa)featuredetails 
6567TURNlost
6879HELIXmight get lost (downstream of altered splice site)
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 normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 405 / 405
position (AA) of stopcodon in wt / mu AA sequence 135 / 135
position of stopcodon in wt / mu cDNA 431 / 431
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 194
cDNA position
(for ins/del: last normal base / first normal base)		 220
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 CGACTACATCGCAGGCCTAGACTCCCGAGGCTTCCTCTTTG
altered cDNA sequence snippet CGACTACATCGCAGGCCTAGTCTCCCGAGGCTTCCTCTTTG
wildtype AA sequence MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGLDSRGFL FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG
QRVVVVDDLL ATGV*
mutated AA sequence MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGLVSRGFL FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG
QRVVVVDDLL ATGV*
speed 0.96 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