Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999841998 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM910020)
  • known disease mutation: rs16863 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:116151365C>TN/A show variant in all transcripts   IGV
HGNC symbol ALAD
Ensembl transcript ID ENST00000277315
Genbank transcript ID N/A
UniProt peptide P13716
alteration type single base exchange
alteration region CDS
DNA changes c.772G>A
cDNA.1034G>A
g.12249G>A
AA changes V258M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 258
frameshift no
known variant Reference ID: rs121912981
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs16863 (pathogenic for Porphobilinogen synthase deficiency) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM910020)

known disease mutation at this position, please check HGMD for details (HGMD ID CM910020)
known disease mutation at this position, please check HGMD for details (HGMD ID CM910020)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.5111
5.4451
(flanking)-1.0810.735
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 increased12249wt: 0.7534 / mu: 0.7762 (marginal change - not scored)wt: ACCCTGACCTCCCTCTCGCCGTGTACCACGTCTCTGGAGAG
mu: ACCCTGACCTCCCTCTCGCCATGTACCACGTCTCTGGAGAG		 gccg|TGTA
Acc marginally increased12252wt: 0.9286 / mu: 0.9696 (marginal change - not scored)wt: CTGACCTCCCTCTCGCCGTGTACCACGTCTCTGGAGAGTTT
mu: CTGACCTCCCTCTCGCCATGTACCACGTCTCTGGAGAGTTT		 gtgt|ACCA
Acc marginally increased12246wt: 0.6164 / mu: 0.6346 (marginal change - not scored)wt: AGCACCCTGACCTCCCTCTCGCCGTGTACCACGTCTCTGGA
mu: AGCACCCTGACCTCCCTCTCGCCATGTACCACGTCTCTGGA		 ctcg|CCGT
Donor increased12252wt: 0.44 / mu: 0.68wt: CCGTGTACCACGTCT
mu: CCATGTACCACGTCT		 GTGT|acca
Donor marginally increased12245wt: 0.9316 / mu: 0.9855 (marginal change - not scored)wt: CCTCTCGCCGTGTAC
mu: CCTCTCGCCATGTAC		 TCTC|gccg
distance from splice site 22
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      258VKDKHPDLPLAVYHVSGEFAMLWH
mutated  all conserved    258VKDKHPDLPLAMYHVSGEFAMLW
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000031965  304VKDKHPDLPLAVYHVSGEFAMLW
Fcatus  all identical  ENSFCAG00000009244  291VKDKHPELPLAVYHVSGEFAMLW
Mmusculus  all identical  ENSMUSG00000028393  275VKDKHPELPLAVYQVSGEFAMLW
Ggallus  all identical  ENSGALG00000008869  282AKERHPTHPLAVYHVSGEFAMLW
Trubripes  all identical  ENSTRUG00000010590  284VKDKFPNHPLAVYNVSGEFAMMW
Drerio  all identical  ENSDARG00000052815  277VKNKHPTHPLAVYNVSGEFAMLW
Dmelanogaster  all identical  FBgn0036271  271TKDSYPYHTLYVYQVSGEFAMLY
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000023474  221VKEKHPALPLAVYHVSGEYAMLW
protein features
start (aa)end (aa)featuredetails 
258267HELIXlost
273277STRANDmight get lost (downstream of altered splice site)
279279BINDINGSubstrate 2.might get lost (downstream of altered splice site)
279290HELIXmight get lost (downstream of altered splice site)
296310HELIXmight get lost (downstream of altered splice site)
313317STRANDmight get lost (downstream of altered splice site)
318318BINDINGSubstrate 2.might get lost (downstream of altered splice site)
320326HELIXmight get lost (downstream of altered splice site)
327329TURNmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 942 / 942
position (AA) of stopcodon in wt / mu AA sequence 314 / 314
position of stopcodon in wt / mu cDNA 1204 / 1204
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 263 / 263
chromosome 9
strand -1
last intron/exon boundary 1143
theoretical NMD boundary in CDS 830
length of CDS 942
coding sequence (CDS) position 772
cDNA position
(for ins/del: last normal base / first normal base)		 1034
gDNA position
(for ins/del: last normal base / first normal base)		 12249
chromosomal position
(for ins/del: last normal base / first normal base)		 116151365
original gDNA sequence snippet ACCCTGACCTCCCTCTCGCCGTGTACCACGTCTCTGGAGAG
altered gDNA sequence snippet ACCCTGACCTCCCTCTCGCCATGTACCACGTCTCTGGAGAG
original cDNA sequence snippet ACCCTGACCTCCCTCTCGCCGTGTACCACGTCTCTGGAGAG
altered cDNA sequence snippet ACCCTGACCTCCCTCTCGCCATGTACCACGTCTCTGGAGAG
wildtype AA sequence MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTYG VKRLEEMLRP LVEEGLRCVL
IFGVPSRVPK DERGSAADSE ESPAIEAIHL LRKTFPNLLV ACDVCLCPYT SHGHCGLLSE
NGAFRAEESR QRLAEVALAY AKAGCQVVAP SDMMDGRVEA IKEALMAHGL GNRVSVMSYS
AKFASCFYGP FRDAAKSSPA FGDRRCYQLP PGARGLALRA VDRDVREGAD MLMVKPGMPY
LDIVREVKDK HPDLPLAVYH VSGEFAMLWH GAQAGAFDLK AAVLEAMTAF RRAGADIIIT
YYTPQLLQWL KEE*
mutated AA sequence MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTYG VKRLEEMLRP LVEEGLRCVL
IFGVPSRVPK DERGSAADSE ESPAIEAIHL LRKTFPNLLV ACDVCLCPYT SHGHCGLLSE
NGAFRAEESR QRLAEVALAY AKAGCQVVAP SDMMDGRVEA IKEALMAHGL GNRVSVMSYS
AKFASCFYGP FRDAAKSSPA FGDRRCYQLP PGARGLALRA VDRDVREGAD MLMVKPGMPY
LDIVREVKDK HPDLPLAMYH VSGEFAMLWH GAQAGAFDLK AAVLEAMTAF RRAGADIIIT
YYTPQLLQWL KEE*
speed 1.03 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