Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999994103 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM000002)
  • known disease mutation: rs5567 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr17:6330004A>GN/A show variant in all transcripts   IGV
HGNC symbol AIPL1
Ensembl transcript ID ENST00000575265
Genbank transcript ID N/A
UniProt peptide Q9NZN9
alteration type single base exchange
alteration region CDS
DNA changes c.715T>C
cDNA.732T>C
g.8516T>C
AA changes C239R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 239
frameshift no
known variant Reference ID: rs62637012
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5567 (pathogenic for Leber congenital amaurosis 4|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000002)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000002)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000002)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.361
2.6321
(flanking)0.3931
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased8508wt: 0.21 / mu: 0.33wt: CAATACTCTGATCCTCAACTACTGCCAGTGCCTGCTGAAGA
mu: CAATACTCTGATCCTCAACTACTGCCAGCGCCTGCTGAAGA		 acta|CTGC
distance from splice site 73
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      239MINTLILNYCQCLLKKEEYYEVLE
mutated  not conserved    239MINTLILNYCQRLLKKEEYYEVL
Ptroglodytes  all identical  ENSPTRG00000008640  239MINTLILNYCQCLLKKEEYYEVL
Mmulatta  all identical  ENSMMUG00000017759  239MINTLTLNYCQCLLKKEEYYEVL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000040554  239MINTLILNYCQCLLKKEEYYEVL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016169  239MANTLTLNYCQCLLRME
Drerio  all identical  ENSDARG00000075067  239MANTLTLNYCQCLLRMEEYYEVI
Dmelanogaster  all identical  FBgn0030345  232IKTPLLLNYAQCRLIAG
Celegans  all identical  C56C10.10  252ANMSQCYLNIGDLHEAE
Xtropicalis  all identical  ENSXETG00000006821  239MINTLVLNYCQCLLRMEEYYEVI
protein features
start (aa)end (aa)featuredetails 
230263REPEATTPR 2.lost
244244CONFLICTE -> K (in Ref. 3; CAG17882).might get lost (downstream of altered splice site)
262262MUTAGENG->S: No interaction with NUB1.might get lost (downstream of altered splice site)
264297REPEATTPR 3.might get lost (downstream of altered splice site)
306315CONFLICTRLLENRMAEK -> EAAGEPHGGE (in Ref. 1; AAF26708).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 813 / 813
position (AA) of stopcodon in wt / mu AA sequence 271 / 271
position of stopcodon in wt / mu cDNA 830 / 830
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 18 / 18
chromosome 17
strand -1
last intron/exon boundary 660
theoretical NMD boundary in CDS 592
length of CDS 813
coding sequence (CDS) position 715
cDNA position
(for ins/del: last normal base / first normal base)		 732
gDNA position
(for ins/del: last normal base / first normal base)		 8516
chromosomal position
(for ins/del: last normal base / first normal base)		 6330004
original gDNA sequence snippet TGATCCTCAACTACTGCCAGTGCCTGCTGAAGAAGGAGGAG
altered gDNA sequence snippet TGATCCTCAACTACTGCCAGCGCCTGCTGAAGAAGGAGGAG
original cDNA sequence snippet TGATCCTCAACTACTGCCAGTGCCTGCTGAAGAAGGAGGAG
altered cDNA sequence snippet TGATCCTCAACTACTGCCAGCGCCTGCTGAAGAAGGAGGAG
wildtype AA sequence MDAALLLNVE GVKKTILHGG TGELPNFITG SRVIFHFRTM KCDEERTVID DSRQVGQPMH
IIIGNMFKLE VWEILLTSMR VHEVAEFWCD TIHTGVYPIL SRSLRQMAQG KDPTEWHVHT
CGLANMFAYH TLGYEDLDEL QKEPQPLVFV IELLQVDAPS DYQRETWNLS NHEKMKAVPV
LHGEGNRLFK LGRYEEASSK YQEAIICLRN LQTKEKPWEV QWLKLEKMIN TLILNYCQCL
LKKEEYYEVL EHTSDILRHH PGARGCRGGQ *
mutated AA sequence MDAALLLNVE GVKKTILHGG TGELPNFITG SRVIFHFRTM KCDEERTVID DSRQVGQPMH
IIIGNMFKLE VWEILLTSMR VHEVAEFWCD TIHTGVYPIL SRSLRQMAQG KDPTEWHVHT
CGLANMFAYH TLGYEDLDEL QKEPQPLVFV IELLQVDAPS DYQRETWNLS NHEKMKAVPV
LHGEGNRLFK LGRYEEASSK YQEAIICLRN LQTKEKPWEV QWLKLEKMIN TLILNYCQRL
LKKEEYYEVL EHTSDILRHH PGARGCRGGQ *
speed 1.16 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