Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999999 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr22:32586854C>TN/A show variant in all transcripts   IGV
HGNC symbol RFPL2
Ensembl transcript ID ENST00000248983
Genbank transcript ID NM_001159545
UniProt peptide O75678
alteration type single base exchange
alteration region CDS
DNA changes c.772G>A
cDNA.1020G>A
g.13865G>A
AA changes V258I Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 258
frameshift no
known variant Reference ID: rs136467
databasehomozygous (T/T)heterozygousallele carriers
1000G6919811672
ExAC11441988521326
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.1250
-3.0510
(flanking)-0.4610.007
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 increased13860wt: 0.2945 / mu: 0.3144 (marginal change - not scored)wt: ATTGCGCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTG
mu: ATTGCGCCCATTTTTGGCTCCTTCAATTCCACCTAATGGTG		 ctcc|TTCA
Acc increased13869wt: 0.51 / mu: 0.61wt: ATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTG
mu: ATTTTTGGCTCCTTCAATTCCACCTAATGGTGATCAAGGTG		 ttcc|ACCT
Acc marginally increased13873wt: 0.5920 / mu: 0.6064 (marginal change - not scored)wt: TTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTCTT
mu: TTGGCTCCTTCAATTCCACCTAATGGTGATCAAGGTGTCTT		 acct|AATG
Acc increased13871wt: 0.23 / mu: 0.25wt: TTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGTGTC
mu: TTTTGGCTCCTTCAATTCCACCTAATGGTGATCAAGGTGTC		 ccac|CTAA
Acc increased13868wt: 0.68 / mu: 0.83wt: CATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAAGGT
mu: CATTTTTGGCTCCTTCAATTCCACCTAATGGTGATCAAGGT		 gttc|CACC
Acc marginally increased13865wt: 0.8409 / mu: 0.8632 (marginal change - not scored)wt: GCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAA
mu: GCCCATTTTTGGCTCCTTCAATTCCACCTAATGGTGATCAA		 tcag|TTCC
Donor increased13870wt: 0.22 / mu: 0.27wt: GTTCCACCTAATGGT
mu: ATTCCACCTAATGGT		 TCCA|ccta
Donor gained138600.71mu: GGCTCCTTCAATTCC CTCC|ttca
distance from splice site 433
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      258EEPLRPFLAPSVPPNGDQGVLSIC
mutated  all conserved    258EEPLRPFLAPSIPPNGDQGVLSI
Ptroglodytes  all conserved  ENSPTRG00000014283  348EEPLRPFLAPSIPPNGDQGVLSI
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
168362DOMAINB30.2/SPRY.lost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 867 / 867
position (AA) of stopcodon in wt / mu AA sequence 289 / 289
position of stopcodon in wt / mu cDNA 1115 / 1115
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 249 / 249
chromosome 22
strand -1
last intron/exon boundary 535
theoretical NMD boundary in CDS 236
length of CDS 867
coding sequence (CDS) position 772
cDNA position
(for ins/del: last normal base / first normal base)		 1020
gDNA position
(for ins/del: last normal base / first normal base)		 13865
chromosomal position
(for ins/del: last normal base / first normal base)		 32586854
original gDNA sequence snippet GCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAA
altered gDNA sequence snippet GCCCATTTTTGGCTCCTTCAATTCCACCTAATGGTGATCAA
original cDNA sequence snippet GCCCATTTTTGGCTCCTTCAGTTCCACCTAATGGTGATCAA
altered cDNA sequence snippet GCCCATTTTTGGCTCCTTCAATTCCACCTAATGGTGATCAA
wildtype AA sequence MAALFQEASS CPVCSDYLEK PMSLECGCAV CLKCINSLQK EPHGEDLLCC CSSMVSRKNK
IRRNRQLERL ASHIKELEPK LKKILQMNPR MRKFQVDMTL DANTANNFLL ISDDLRSVRS
GRIRQNRQDL AERFDVSVCI LGSPRFTCGR HCWEVDVGTS TEWDLGVCRE SVHRKGRIQL
TTELGFWTVS LRDGGRLSAT TVPLTFLFVD RKLQRVGIFL DMGMQNVSFF DAESGSHVYT
FRSVSAEEPL RPFLAPSVPP NGDQGVLSIC PLMNSGTTDA PVRPGEAK*
mutated AA sequence MAALFQEASS CPVCSDYLEK PMSLECGCAV CLKCINSLQK EPHGEDLLCC CSSMVSRKNK
IRRNRQLERL ASHIKELEPK LKKILQMNPR MRKFQVDMTL DANTANNFLL ISDDLRSVRS
GRIRQNRQDL AERFDVSVCI LGSPRFTCGR HCWEVDVGTS TEWDLGVCRE SVHRKGRIQL
TTELGFWTVS LRDGGRLSAT TVPLTFLFVD RKLQRVGIFL DMGMQNVSFF DAESGSHVYT
FRSVSAEEPL RPFLAPSIPP NGDQGVLSIC PLMNSGTTDA PVRPGEAK*
speed 0.36 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