Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999728021834 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM025985)
  • known disease mutation: rs4429 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr9:32984797T>CN/A show variant in all transcripts   IGV
HGNC symbol APTX
Ensembl transcript ID ENST00000309615
Genbank transcript ID NM_175069
UniProt peptide Q7Z2E3
alteration type single base exchange
alteration region CDS
DNA changes c.644A>G
cDNA.668A>G
g.40370A>G
AA changes H215R Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 215
frameshift no
known variant Reference ID: rs121908133
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs4429 (pathogenic for Ataxia-oculomotor apraxia type 1) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)

known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
known disease mutation at this position, please check HGMD for details (HGMD ID CM025985)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.591
3.1561
(flanking)4.0661
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased40377wt: 0.33 / mu: 0.47wt: AAGGCCCGTTACCATTGGCTGGTCTTACCGTGGACCTCCAT
mu: AAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGACCTCCAT		 gctg|GTCT
distance from splice site 59
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      215VIKDKYPKARYHWLVLPWTSISSL
mutated  not conserved    215VIKDKYPKARYRWLVLPWTSISS
Ptroglodytes  all identical  ENSPTRG00000020850  201VIKDKYPKARYHWLVLPWTSISN
Mmulatta  all identical  ENSMMUG00000007724  229VIKDKYPKARYHWLVLPWTAISS
Fcatus  not conserved  ENSFCAG00000008728  215XXXXXXXXXXXXXXXXXXXXXXX
Mmusculus  all identical  ENSMUSG00000028411  201VIKDKYPKARHHWLVLPWASISS
Ggallus  all identical  ENSGALG00000001954  225VIKDKYPKARYHWLVLPWDSISS
Trubripes  all identical  ENSTRUG00000009794  211VIKDKYPKARYHWLVLPWQSISS
Drerio  all identical  ENSDARG00000027143  183VIKDKYPKARYHWLVLPWQSISS
Dmelanogaster  all identical  FBgn0038704  37VIADKFPKAQHHYLVLPLADIPS
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000024143  206VIKDKYPKARYHWLVLPWQSIAN
protein features
start (aa)end (aa)featuredetails 
182287DOMAINHIT.lost
272276MOTIFHistidine triad motif.might get lost (downstream of altered splice site)
274274ACT_SITETele-AMP-histidine intermediate (Probable).might get lost (downstream of altered splice site)
274274MUTAGENH->A: Abolishes enzyme activity.might get lost (downstream of altered splice site)
331353ZN_FINGC2H2-type.might get lost (downstream of altered splice site)
333333MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-336.might get lost (downstream of altered splice site)
336336MUTAGENC->A: Abolishes DNA-binding and enzyme activity; when associated with A-333.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 921 / 921
position (AA) of stopcodon in wt / mu AA sequence 307 / 307
position of stopcodon in wt / mu cDNA 945 / 945
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 25 / 25
chromosome 9
strand -1
last intron/exon boundary 941
theoretical NMD boundary in CDS 866
length of CDS 921
coding sequence (CDS) position 644
cDNA position
(for ins/del: last normal base / first normal base)		 668
gDNA position
(for ins/del: last normal base / first normal base)		 40370
chromosomal position
(for ins/del: last normal base / first normal base)		 32984797
original gDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered gDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
original cDNA sequence snippet ATACCCAAAGGCCCGTTACCATTGGCTGGTCTTACCGTGGA
altered cDNA sequence snippet ATACCCAAAGGCCCGTTACCGTTGGCTGGTCTTACCGTGGA
wildtype AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMVNELYPY IVEFEEEAKN
PGLETHRKRK RSGNSDSIER DAAQEAEAGT GLEPGSNSGQ CSVPLKKGKD APIKKESLGH
WSQGLKISMQ DPKMQVYKDE QVVVIKDKYP KARYHWLVLP WTSISSLKAV AREHLELLKH
MHTVGEKVIV DFAGSSKLRF RLGYHAIPSM SHVHLHVISQ DFDSPCLKNK KHWNSFNTEY
FLESQE*
mutated AA sequence MSNVNLSVSD FWRVMMRVCW LVRQDSRHQR IRLPHLEAVV IGRGPETKIT DKKCSRQQVQ
LKAECNKGYV KVKQVGVNPT SIDSVVIGKD QEVKLQPGQV LHMVNELYPY IVEFEEEAKN
PGLETHRKRK RSGNSDSIER DAAQEAEAGT GLEPGSNSGQ CSVPLKKGKD APIKKESLGH
WSQGLKISMQ DPKMQVYKDE QVVVIKDKYP KARYRWLVLP WTSISSLKAV AREHLELLKH
MHTVGEKVIV DFAGSSKLRF RLGYHAIPSM SHVHLHVISQ DFDSPCLKNK KHWNSFNTEY
FLESQE*
speed 1.22 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