Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999995696 (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 ENST00000576776
Genbank transcript ID N/A
UniProt peptide Q9NZN9
alteration type single base exchange
alteration region CDS
DNA changes c.643T>C
cDNA.691T>C
g.8516T>C
AA changes C215R Score: 180 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 215
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 alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost8515.5sequence motif lost- wt: gcca|GTGC
 mu: gcca.GCGC
Acc increased8508wt: 0.21 / mu: 0.33wt: CAATACTCTGATCCTCAACTACTGCCAGTGCCTGCTGAAGA
mu: CAATACTCTGATCCTCAACTACTGCCAGCGCCTGCTGAAGA		 acta|CTGC
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      215AIICLRNLQTKCLLKKEEYYEVLE
mutated  not conserved    215AIICLRNLQTKRLLKKEEYYEVL
Ptroglodytes  all identical  ENSPTRG00000008640  215AIICLRNLQTKEKPWEVQWLKLEKMINTLILNYCQCL
Mmulatta  all identical  ENSMMUG00000017759  215AIICLRNLQTKEKPWEVQWLKLEKMINTLTLNYCQCL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000040554  215AIVCLRNLQTKEKPWEVEWLKLEKMINTLILNYCQCL
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000016169  215AIICLKNVQTKEKAWDVPWLKLEKMANTLTLNYCQCLLRME
Drerio  all identical  ENSDARG00000075067  215AIICIKNVQSKEKAWEAPWLKLEKMANTLTLNYCQCL
Dmelanogaster  all identical  FBgn0030345  208AVGIVEQLMLKEKPHDEEWQELAAIKTPLLLNYAQCRLIAG
Celegans  all identical  C56C10.10  250ANMSQCYLNIGDLHEAE
Xtropicalis  all identical  ENSXETG00000006821  215GVICLKNLQTKEKPWEVPWMKLEKMINTLVLNYCQCL
protein features
start (aa)end (aa)featuredetails 
230263REPEATTPR 2.might get lost (downstream of altered splice site)
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 1083 / 1083
position (AA) of stopcodon in wt / mu AA sequence 361 / 361
position of stopcodon in wt / mu cDNA 1131 / 1131
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 49 / 49
chromosome 17
strand -1
last intron/exon boundary 761
theoretical NMD boundary in CDS 662
length of CDS 1083
coding sequence (CDS) position 643
cDNA position
(for ins/del: last normal base / first normal base)		 691
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 TAAGGAACCTGCAGACCAAGTGCCTGCTGAAGAAGGAGGAG
altered cDNA sequence snippet TAAGGAACCTGCAGACCAAGCGCCTGCTGAAGAAGGAGGAG
wildtype AA sequence MDAALLLNVE GVKKTILHGG TGELPNFITG SRVIFHFRTM KCDEERTVID DSRQVGQPMH
IIIGNMFKLE VWEILLTSMR VHEVAEFWCD TIHTGVYPIL SRSLRQMAQG KDPTEWHVHT
CGLANMFAYH TLGYEDLDEL QKEPQPLVFV IELLQVDAPS DYQRETWNLS NHEKMKAVPV
LHGEGNRLFK LGRYEEASSK YQEAIICLRN LQTKCLLKKE EYYEVLEHTS DILRHHPGIV
KAYYVRARAH AEVWNEAEAK ADLQKVLELE PSMQKAVRRE LRLLENRMAE KQEEERLRCR
NMLSQGATQP PAEPPTEPPA QSSTEPPAEP PTAPSAELSA GPPAEPATEP PPSPGHSLQH
*
mutated AA sequence MDAALLLNVE GVKKTILHGG TGELPNFITG SRVIFHFRTM KCDEERTVID DSRQVGQPMH
IIIGNMFKLE VWEILLTSMR VHEVAEFWCD TIHTGVYPIL SRSLRQMAQG KDPTEWHVHT
CGLANMFAYH TLGYEDLDEL QKEPQPLVFV IELLQVDAPS DYQRETWNLS NHEKMKAVPV
LHGEGNRLFK LGRYEEASSK YQEAIICLRN LQTKRLLKKE EYYEVLEHTS DILRHHPGIV
KAYYVRARAH AEVWNEAEAK ADLQKVLELE PSMQKAVRRE LRLLENRMAE KQEEERLRCR
NMLSQGATQP PAEPPTEPPA QSSTEPPAEP PTAPSAELSA GPPAEPATEP PPSPGHSLQH
*
speed 1.27 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