Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 7.35150531844384e-08 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM1610774)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:68695940T>GN/A show variant in all transcripts   IGV
HGNC symbol RAD17
Ensembl transcript ID ENST00000509734
Genbank transcript ID NM_133339
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1670T>G
cDNA.2348T>G
g.30821T>G
AA changes L557R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 557
frameshift no
known variant Reference ID: rs1045051
databasehomozygous (G/G)heterozygousallele carriers
1000G2108561066
ExAC58002116726967

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610774)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.921
4.5711
(flanking)0.2390.998
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 increased30815wt: 0.2064 / mu: 0.2296 (marginal change - not scored)wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT
mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT		 cttt|ATGC
Acc marginally increased30811wt: 0.5326 / mu: 0.5471 (marginal change - not scored)wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG
mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG		 ccag|CTTT
Donor increased30821wt: 0.29 / mu: 0.57wt: ATGCCTCCAAACTCA
mu: ATGCCGCCAAACTCA		 GCCT|ccaa
Donor gained308200.90mu: TATGCCGCCAAACTC TGCC|gcca
distance from splice site 57
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      557LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    557LFPDFCLPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557LFPDFCLPALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557LFPDFCLPALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555LFVDFCLPALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532LFGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556LFSSFCSSPMCLQTQVLPYLAML
protein features
start (aa)end (aa)featuredetails 
432681REGIONInteraction with MCM7.lost
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
646646MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-656.might get lost (downstream of altered splice site)
646646MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-656.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
656656MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
656656MUTAGENS->A: Reduces by 50% phosphorylation by ATR, and abolishes interaction with RAD1. Abolishes phosphorylation by ATR and checkpoint activation without affecting interaction with RFC3, RFC4, ATM or ATR; when associated with A-646.might get lost (downstream of altered splice site)
656656MUTAGENS->D: Abolishes interaction with RAD1; when associated with D-646.might get lost (downstream of altered splice site)
672672CONFLICTI -> M (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2046 / 2046
position (AA) of stopcodon in wt / mu AA sequence 682 / 682
position of stopcodon in wt / mu cDNA 2724 / 2724
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 679 / 679
chromosome 5
strand 1
last intron/exon boundary 2463
theoretical NMD boundary in CDS 1734
length of CDS 2046
coding sequence (CDS) position 1670
cDNA position
(for ins/del: last normal base / first normal base)		 2348
gDNA position
(for ins/del: last normal base / first normal base)		 30821
chromosomal position
(for ins/del: last normal base / first normal base)		 68695940
original gDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered gDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
original cDNA sequence snippet CTGCCTACCAGCTTTATGCCTCCAAACTCAGCTATTGCCAT
altered cDNA sequence snippet CTGCCTACCAGCTTTATGCCGCCAAACTCAGCTATTGCCAT
wildtype AA sequence MSKTFLRPKV SSTKVTDWVD PSFDDFLECS GVSTITATSL GVNNSSHRRK NGPSTLESSR
FPARKRGNLS SLEQIYGLEN SKEYLSENEP WVDKYKPETQ HELAVHKKKI EEVETWLKAQ
VLERQPKQGG SILLITGPPG CGKTTTLKIL SKEHGIQVQE WINPVLPDFQ KDDFKGMFNT
ESSFHMFPYQ SQIAVFKEFL LRATKYNKLQ MLGDDLRTDK KIILVEDLPN QFYRDSHTLH
EVLRKYVRIG RCPLIFIISD SLSGDNNQRL LFPKEIQEEC SISNISFNPV APTIMMKFLN
RIVTIEANKN GGKITVPDKT SLELLCQGCS GDIRSAINSL QFSSSKGENN LRPRKKGMSL
KSDAVLSKSK RRKKPDRVFE NQEVQAIGGK DVSLFLFRAL GKILYCKRAS LTELDSPRLP
SHLSEYERDT LLVEPEEVVE MSHMPGDLFN LYLHQNYIDF FMEIDDIVRA SEFLSFADIL
SGDWNTRSLL REYSTSIATR GVMHSNKARG YAHCQGGGSS FRPLHKPQWF LINKKYRENC
LAAKALFPDF CLPALCLQTQ LLPYLALLTI PMRNQAQISF IQDIGRLPLK RHFGRLKMEA
LTDREHGMID PDSGDEAQLN GGHSAEESLG EPTQATVPET WSLPLSQNSA SELPASQPQP
FSAQGDMEEN IIIEDYESDG T*
mutated AA sequence MSKTFLRPKV SSTKVTDWVD PSFDDFLECS GVSTITATSL GVNNSSHRRK NGPSTLESSR
FPARKRGNLS SLEQIYGLEN SKEYLSENEP WVDKYKPETQ HELAVHKKKI EEVETWLKAQ
VLERQPKQGG SILLITGPPG CGKTTTLKIL SKEHGIQVQE WINPVLPDFQ KDDFKGMFNT
ESSFHMFPYQ SQIAVFKEFL LRATKYNKLQ MLGDDLRTDK KIILVEDLPN QFYRDSHTLH
EVLRKYVRIG RCPLIFIISD SLSGDNNQRL LFPKEIQEEC SISNISFNPV APTIMMKFLN
RIVTIEANKN GGKITVPDKT SLELLCQGCS GDIRSAINSL QFSSSKGENN LRPRKKGMSL
KSDAVLSKSK RRKKPDRVFE NQEVQAIGGK DVSLFLFRAL GKILYCKRAS LTELDSPRLP
SHLSEYERDT LLVEPEEVVE MSHMPGDLFN LYLHQNYIDF FMEIDDIVRA SEFLSFADIL
SGDWNTRSLL REYSTSIATR GVMHSNKARG YAHCQGGGSS FRPLHKPQWF LINKKYRENC
LAAKALFPDF CLPALCRQTQ LLPYLALLTI PMRNQAQISF IQDIGRLPLK RHFGRLKMEA
LTDREHGMID PDSGDEAQLN GGHSAEESLG EPTQATVPET WSLPLSQNSA SELPASQPQP
FSAQGDMEEN IIIEDYESDG T*
speed 0.68 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