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 ENST00000345306
Genbank transcript ID NM_133344
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1637T>G
cDNA.1904T>G
g.30821T>G
AA changes L546R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 546
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      546LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    546LPALCRQTQLLPYLALL
Ptroglodytes  all identical  ENSPTRG00000016950  557ALCLQTQLLPYLALL
Mmulatta  all identical  ENSMMUG00000014881  557ALCLQTQLLPYLALL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021635  555ALCLQTQLLPYLALL
Ggallus  all identical  ENSGALG00000015571  568LFSSFCLSPECLQTELLPYLAKL
Trubripes  all identical  ENSTRUG00000002152  532FGSFCLTPVSLQTELLPYLPKL
Drerio  all identical  ENSDARG00000018918  547LFLSFCLTPVSLLTEMVPYLAKL
Dmelanogaster  no alignment  FBgn0025808  n/a
Celegans  no alignment  F32A11.2  n/a
Xtropicalis  all identical  ENSXETG00000018168  556SFCSSPMCLQTQVLPYLAML
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 2013 / 2013
position (AA) of stopcodon in wt / mu AA sequence 671 / 671
position of stopcodon in wt / mu cDNA 2280 / 2280
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 268 / 268
chromosome 5
strand 1
last intron/exon boundary 2019
theoretical NMD boundary in CDS 1701
length of CDS 2013
coding sequence (CDS) position 1637
cDNA position
(for ins/del: last normal base / first normal base)		 1904
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 MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCLQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
mutated AA sequence MNQVTDWVDP SFDDFLECSG VSTITATSLG VNNSSHRRKN GPSTLESSRF PARKRGNLSS
LEQIYGLENS KEYLSENEPW VDKYKPETQH ELAVHKKKIE EVETWLKAQV LERQPKQGGS
ILLITGPPGC GKTTTLKILS KEHGIQVQEW INPVLPDFQK DDFKGMFNTE SSFHMFPYQS
QIAVFKEFLL RATKYNKLQM LGDDLRTDKK IILVEDLPNQ FYRDSHTLHE VLRKYVRIGR
CPLIFIISDS LSGDNNQRLL FPKEIQEECS ISNISFNPVA PTIMMKFLNR IVTIEANKNG
GKITVPDKTS LELLCQGCSG DIRSAINSLQ FSSSKGENNL RPRKKGMSLK SDAVLSKSKR
RKKPDRVFEN QEVQAIGGKD VSLFLFRALG KILYCKRASL TELDSPRLPS HLSEYERDTL
LVEPEEVVEM SHMPGDLFNL YLHQNYIDFF MEIDDIVRAS EFLSFADILS GDWNTRSLLR
EYSTSIATRG VMHSNKARGY AHCQGGGSSF RPLHKPQWFL INKKYRENCL AAKALFPDFC
LPALCRQTQL LPYLALLTIP MRNQAQISFI QDIGRLPLKR HFGRLKMEAL TDREHGMIDP
DSGDEAQLNG GHSAEESLGE PTQATVPETW SLPLSQNSAS ELPASQPQPF SAQGDMEENI
IIEDYESDGT *
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