Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999787386 (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 ENST00000409155
Genbank transcript ID NM_000031
UniProt peptide P13716
alteration type single base exchange
alteration region CDS
DNA changes c.823G>A
cDNA.1020G>A
g.12249G>A
AA changes V275M Score: 21 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 275
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      275VKDKHPDLPLAVYHVSGEFAMLWH
mutated  all conserved    275VKDKHPDLPLAMYHVSGEFAMLW
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000031965  304DLPLAVYHVSGEFAMLW
Fcatus  all identical  ENSFCAG00000009244  291ELPLAVYHVSGEFAMLW
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 
273277STRANDlost
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 993 / 993
position (AA) of stopcodon in wt / mu AA sequence 331 / 331
position of stopcodon in wt / mu cDNA 1190 / 1190
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 198 / 198
chromosome 9
strand -1
last intron/exon boundary 1129
theoretical NMD boundary in CDS 881
length of CDS 993
coding sequence (CDS) position 823
cDNA position
(for ins/del: last normal base / first normal base)		 1020
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 LIYPIFVTDV PDDIQPITSL PGVARYGVKR
LEEMLRPLVE EGLRCVLIFG VPSRVPKDER GSAADSEESP AIEAIHLLRK TFPNLLVACD
VCLCPYTSHG HCGLLSENGA FRAEESRQRL AEVALAYAKA GCQVVAPSDM MDGRVEAIKE
ALMAHGLGNR VSVMSYSAKF ASCFYGPFRD AAKSSPAFGD RRCYQLPPGA RGLALRAVDR
DVREGADMLM VKPGMPYLDI VREVKDKHPD LPLAVYHVSG EFAMLWHGAQ AGAFDLKAAV
LEAMTAFRRA GADIIITYYT PQLLQWLKEE *
mutated AA sequence MQPQSVLHSG YFHPLLRAWQ TATTTLNASN LIYPIFVTDV PDDIQPITSL PGVARYGVKR
LEEMLRPLVE EGLRCVLIFG VPSRVPKDER GSAADSEESP AIEAIHLLRK TFPNLLVACD
VCLCPYTSHG HCGLLSENGA FRAEESRQRL AEVALAYAKA GCQVVAPSDM MDGRVEAIKE
ALMAHGLGNR VSVMSYSAKF ASCFYGPFRD AAKSSPAFGD RRCYQLPPGA RGLALRAVDR
DVREGADMLM VKPGMPYLDI VREVKDKHPD LPLAMYHVSG EFAMLWHGAQ AGAFDLKAAV
LEAMTAFRRA GADIIITYYT PQLLQWLKEE *
speed 0.75 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