Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999947905166 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940079)
  • known disease mutation: rs18300 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr16:88876549A>GN/A show variant in all transcripts   IGV
HGNC symbol APRT
Ensembl transcript ID ENST00000378364
Genbank transcript ID NM_000485
UniProt peptide P07741
alteration type single base exchange
alteration region CDS
DNA changes c.329T>C
cDNA.374T>C
g.1804T>C
AA changes L110P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 110
frameshift no
known variant Reference ID: rs104894508
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs18300 (pathogenic for Adenine phosphoribosyltransferase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940079)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940079)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940079)
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
H3K4me1, Histone, Histone 3 Lysine 4 Mono-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
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)1.0381
1.7171
(flanking)2.2491
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased1801wt: 0.23 / mu: 0.36wt: CCACTTCCCACTCCAGGCTGAGCTGGAGATTCAGAAAGACG
mu: CCACTTCCCACTCCAGGCTGAGCCGGAGATTCAGAAAGACG		 ctga|GCTG
Donor increased1804wt: 0.28 / mu: 0.71wt: TGAGCTGGAGATTCA
mu: TGAGCCGGAGATTCA		 AGCT|ggag
Donor marginally increased1796wt: 0.9832 / mu: 0.9927 (marginal change - not scored)wt: CTCCAGGCTGAGCTG
mu: CTCCAGGCTGAGCCG		 CCAG|gctg
Donor marginally increased1802wt: 0.2540 / mu: 0.2830 (marginal change - not scored)wt: GCTGAGCTGGAGATT
mu: GCTGAGCCGGAGATT		 TGAG|ctgg
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      110ASYSLEYGKAELEIQKDALEPGQR
mutated  not conserved    110ASYSLEYGKAEPEIQKDALEPG
Ptroglodytes  all identical  ENSPTRG00000008466  110ASYSLEYGKAELEIQKDALEPG
Mmulatta  all identical  ENSMMUG00000013824  110ASYALEYGKAELEIQKDALEPG
Fcatus  no alignment  ENSFCAG00000018452  n/a
Mmusculus  all identical  ENSMUSG00000006589  110ASYSLEYGKAELEIQKDALEPG
Ggallus  no homologue    
Trubripes  not conserved  ENSTRUG00000005211  110VAYELEYGKAEAEIQKDAVAPGQ
Drerio  not conserved  ENSDARG00000003519  108VAYSLEYGKAEAEMQEDAVSAG
Dmelanogaster  not conserved  FBgn0000109  114VEYKLEYGIDTFELQKSAIKPGQ
Celegans  all conserved  T19B4.3  113ASYVKEYGEDRVEIQEGAIKNGD
Xtropicalis  all identical  ENSXETG00000027084  110VSYSLEYGKAELEMQYDAVEP
protein features
start (aa)end (aa)featuredetails 
106113STRANDlost
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 543 / 543
position (AA) of stopcodon in wt / mu AA sequence 181 / 181
position of stopcodon in wt / mu cDNA 588 / 588
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 46 / 46
chromosome 16
strand -1
last intron/exon boundary 446
theoretical NMD boundary in CDS 350
length of CDS 543
coding sequence (CDS) position 329
cDNA position
(for ins/del: last normal base / first normal base)		 374
gDNA position
(for ins/del: last normal base / first normal base)		 1804
chromosomal position
(for ins/del: last normal base / first normal base)		 88876549
original gDNA sequence snippet CTTCCCACTCCAGGCTGAGCTGGAGATTCAGAAAGACGCCC
altered gDNA sequence snippet CTTCCCACTCCAGGCTGAGCCGGAGATTCAGAAAGACGCCC
original cDNA sequence snippet GGAGTACGGGAAGGCTGAGCTGGAGATTCAGAAAGACGCCC
altered cDNA sequence snippet GGAGTACGGGAAGGCTGAGCCGGAGATTCAGAAAGACGCCC
wildtype AA sequence MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGLDSRGFL FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEL EIQKDALEPG
QRVVVVDDLL ATGGTMNAAC ELLGRLQAEV LECVSLVELT SLKGREKLAP VPFFSLLQYE
*
mutated AA sequence MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGLDSRGFL FGPSLAQELG LGCVLIRKRG KLPGPTLWAS YSLEYGKAEP EIQKDALEPG
QRVVVVDDLL ATGGTMNAAC ELLGRLQAEV LECVSLVELT SLKGREKLAP VPFFSLLQYE
*
speed 1.09 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