Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.20694511901203 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM920008)
  • known disease mutation: rs2461 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:40761004T>CN/A show variant in all transcripts   IGV
HGNC symbol ADSL
Ensembl transcript ID ENST00000216194
Genbank transcript ID NM_000026
UniProt peptide P30566
alteration type single base exchange
alteration region CDS
DNA changes c.1312T>C
cDNA.1368T>C
g.18498T>C
AA changes S438P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 438
frameshift no
known variant Reference ID: rs119450940
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs2461 (pathogenic for Adenylosuccinate lyase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM920008)

known disease mutation at this position, please check HGMD for details (HGMD ID CM920008)
known disease mutation at this position, please check HGMD for details (HGMD ID CM920008)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.0120.938
1.2460.952
(flanking)1.5860.952
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased18495wt: 0.77 / mu: 0.86wt: ATGCCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTA
mu: ATGCCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTA		 attc|ACTC
Acc marginally increased18499wt: 0.5057 / mu: 0.5123 (marginal change - not scored)wt: CTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTGG
mu: CTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTGG		 actc|CCAG
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      438IQVDAYFSPIHSQLDHLLDPSSFT
mutated  not conserved    438IQVDAYFSPIHPQLDHLLDPSSF
Ptroglodytes  all identical  ENSPTRG00000014407  438IQADAYFSPIHSQLDHLLDPSSF
Mmulatta  all identical  ENSMMUG00000005341  317IQADAYFSPIHSQLDRLLDPSSF
Fcatus  all identical  ENSFCAG00000004798  438IQADAYFSPIHSQLDRLLDPSSF
Mmusculus  all identical  ENSMUSG00000022407  438IRADAYFSPIHSQLEHLLDPSSF
Ggallus  not conserved  ENSGALG00000012034  439FSPIHEHLDSLLDPSSF
Trubripes  not conserved  ENSTRUG00000001024  454FAPILGQLDAILEPKTF
Drerio  not conserved  ENSDARG00000017049  436FAPILGELDALLDPKTF
Dmelanogaster  not conserved  FBgn0038467  433PYFSPILEQLDTILDAKTF
Celegans  not conserved  R06C7.5  431TMADPFFDSVRDRVVGLVNNPINF
Xtropicalis  all conserved  ENSXETG00000006328  457FAPIHAHLEQLLDPKSF
protein features
start (aa)end (aa)featuredetails 
434437HELIXmight get lost (downstream of altered splice site)
440443HELIXmight get lost (downstream of altered splice site)
446449HELIXmight get lost (downstream of altered splice site)
453463HELIXmight get lost (downstream of altered splice site)
465469HELIXmight get lost (downstream of altered splice site)
470472HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1455 / 1455
position (AA) of stopcodon in wt / mu AA sequence 485 / 485
position of stopcodon in wt / mu cDNA 1511 / 1511
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 57 / 57
chromosome 22
strand 1
last intron/exon boundary 1425
theoretical NMD boundary in CDS 1318
length of CDS 1455
coding sequence (CDS) position 1312
cDNA position
(for ins/del: last normal base / first normal base)		 1368
gDNA position
(for ins/del: last normal base / first normal base)		 18498
chromosomal position
(for ins/del: last normal base / first normal base)		 40761004
original gDNA sequence snippet CCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTG
altered gDNA sequence snippet CCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTG
original cDNA sequence snippet CCTACTTCAGTCCCATTCACTCCCAGTTGGATCATTTACTG
altered cDNA sequence snippet CCTACTTCAGTCCCATTCACCCCCAGTTGGATCATTTACTG
wildtype AA sequence MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCP KAAGIIHLGA TSCYVGDNTD
LIILRNALDL LLPKLARVIS RLADFAKERA SLPTLGFTHF QPAQLTTVGK RCCLWIQDLC
MDLQNLKRVR DDLRFRGVKG TTGTQASFLQ LFEGDDHKVE QLDKMVTEKA GFKRAFIITG
QTYTRKVDIE VLSVLASLGA SVHKICTDIR LLANLKEMEE PFEKQQIGSS AMPYKRNPMR
SERCCSLARH LMTLVMDPLQ TASVQWFERT LDDSANRRIC LAEAFLTADT ILNTLQNISE
GLVVYPKVIE RRIRQELPFM ATENIIMAMV KAGGSRQDCH EKIRVLSQQA ASVVKQEGGD
NDLIERIQVD AYFSPIHSQL DHLLDPSSFT GRASQQVQRF LEEEVYPLLK PYESVMKVKA
ELCL*
mutated AA sequence MAAGGDHGSP DSYRSPLASR YASPEMCFVF SDRYKFRTWR QLWLWLAEAE QTLGLPITDE
QIQEMKSNLE NIDFKMAAEE EKRLRHDVMA HVHTFGHCCP KAAGIIHLGA TSCYVGDNTD
LIILRNALDL LLPKLARVIS RLADFAKERA SLPTLGFTHF QPAQLTTVGK RCCLWIQDLC
MDLQNLKRVR DDLRFRGVKG TTGTQASFLQ LFEGDDHKVE QLDKMVTEKA GFKRAFIITG
QTYTRKVDIE VLSVLASLGA SVHKICTDIR LLANLKEMEE PFEKQQIGSS AMPYKRNPMR
SERCCSLARH LMTLVMDPLQ TASVQWFERT LDDSANRRIC LAEAFLTADT ILNTLQNISE
GLVVYPKVIE RRIRQELPFM ATENIIMAMV KAGGSRQDCH EKIRVLSQQA ASVVKQEGGD
NDLIERIQVD AYFSPIHPQL DHLLDPSSFT GRASQQVQRF LEEEVYPLLK PYESVMKVKA
ELCL*
speed 0.54 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