Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999572344634 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • 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 ENST00000563655
Genbank transcript ID N/A
UniProt peptide P07741
alteration type single base exchange
alteration region CDS
DNA changes c.326T>C
cDNA.347T>C
g.2111T>C
AA changes M109T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 109
frameshift no
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 7
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      109VVDDLLATGGTMNAACELLGRLQA
mutated  not conserved    109VVDDLLATGGTTNAACELLGRLQ
Ptroglodytes  all identical  ENSPTRG00000008466  136VVDDLLATGGTMNAACELLGRLQ
Mmulatta  all identical  ENSMMUG00000013824  136VVDDLLATGGTMHAACELLGHLQ
Fcatus  all identical  ENSFCAG00000018452  109TMHAACELLGQLR
Mmusculus  all identical  ENSMUSG00000006589  136IVDDLLATGGTMFAACDLLHQLR
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000005211  136IIDDLLATGGTLYAACELLKTLQ
Drerio  all conserved  ENSDARG00000003519  134IIDDLLATGGTLYAAIELIKQQK
Dmelanogaster  all conserved  FBgn0000109  140VVDDLLATGGSLVAATELIGKVG
Celegans  all conserved  T19B4.3  139LLATGGTLRAATDLVVKAG
Xtropicalis  all identical  ENSXETG00000027084  136LIDDLLATGGTMNAACELVKRRN
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 462 / 462
position (AA) of stopcodon in wt / mu AA sequence 154 / 154
position of stopcodon in wt / mu cDNA 483 / 483
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 326
cDNA position
(for ins/del: last normal base / first normal base)		 347
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 GCTGGCCACTGGTGGAACCATGAACGCTGCCTGTGAGCTGC
altered cDNA sequence snippet GCTGGCCACTGGTGGAACCACGAACGCTGCCTGTGAGCTGC
wildtype AA sequence MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGECPVAAS RALPPLRAPR AELEIQKDAL EPGQRVVVVD DLLATGGTMN AACELLGRLQ
AEVLECVSLV ELTSLKGREK LAPVPFFSLL QYE*
mutated AA sequence MADSELQLVE QRIRSFPDFP TPGVVFRDIS PVLKDPASFR AAIGLLARHL KATHGGRIDY
IAGECPVAAS RALPPLRAPR AELEIQKDAL EPGQRVVVVD DLLATGGTTN AACELLGRLQ
AEVLECVSLV ELTSLKGREK LAPVPFFSLL QYE*
speed 1.00 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