Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 9.57227350036922e-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 ENST00000521422
Genbank transcript ID N/A
UniProt peptide O75943
alteration type single base exchange
alteration region CDS
DNA changes c.1142T>G
cDNA.1879T>G
g.30821T>G
AA changes L381R Score: 102 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 381
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      381LFPDFCLPALCLQTQLLPYLALLT
mutated  not conserved    381LFPDFCLPALCRQTQLLPYLALL
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.might get lost (downstream of altered splice site)
445445CONFLICTP -> S (in Ref. 5; AAC36334).might get lost (downstream of altered splice site)
462462CONFLICTM -> T (in Ref. 5; AAC36334).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)
646646MOD_RESPhosphoserine; by ATR and ATM.might get lost (downstream of altered splice site)
648648CONFLICTN -> D (in Ref. 5; AAC36334).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)
656656MOD_RESPhosphoserine; by ATR and ATM.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 1518 / 1518
position (AA) of stopcodon in wt / mu AA sequence 506 / 506
position of stopcodon in wt / mu cDNA 2255 / 2255
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 738 / 738
chromosome 5
strand 1
last intron/exon boundary 1994
theoretical NMD boundary in CDS 1206
length of CDS 1518
coding sequence (CDS) position 1142
cDNA position
(for ins/del: last normal base / first normal base)		 1879
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 MFNTESSFHM FPYQSQIAVF KEFLLRATKY NKLQMLGDDL RTDKKIILVE DLPNQFYRDS
HTLHEVLRKY VRIGRCPLIF IISDSLSGDN NQRLLFPKEI QEECSISNIS FNPVAPTIMM
KFLNRIVTIE ANKNGGKITV PDKTSLELLC QGCSGDIRSA INSLQFSSSK GENNLRPRKK
GMSLKSDAVL SKSKRRKKPD RVFENQEVQA IGGKDVSLFL FRALGKILYC KRASLTELDS
PRLPSHLSEY ERDTLLVEPE EVVEMSHMPG DLFNLYLHQN YIDFFMEIDD IVRASEFLSF
ADILSGDWNT RSLLREYSTS IATRGVMHSN KARGYAHCQG GGSSFRPLHK PQWFLINKKY
RENCLAAKAL FPDFCLPALC LQTQLLPYLA LLTIPMRNQA QISFIQDIGR LPLKRHFGRL
KMEALTDREH GMIDPDSGDE AQLNGGHSAE ESLGEPTQAT VPETWSLPLS QNSASELPAS
QPQPFSAQGD MEENIIIEDY ESDGT*
mutated AA sequence MFNTESSFHM FPYQSQIAVF KEFLLRATKY NKLQMLGDDL RTDKKIILVE DLPNQFYRDS
HTLHEVLRKY VRIGRCPLIF IISDSLSGDN NQRLLFPKEI QEECSISNIS FNPVAPTIMM
KFLNRIVTIE ANKNGGKITV PDKTSLELLC QGCSGDIRSA INSLQFSSSK GENNLRPRKK
GMSLKSDAVL SKSKRRKKPD RVFENQEVQA IGGKDVSLFL FRALGKILYC KRASLTELDS
PRLPSHLSEY ERDTLLVEPE EVVEMSHMPG DLFNLYLHQN YIDFFMEIDD IVRASEFLSF
ADILSGDWNT RSLLREYSTS IATRGVMHSN KARGYAHCQG GGSSFRPLHK PQWFLINKKY
RENCLAAKAL FPDFCLPALC RQTQLLPYLA LLTIPMRNQA QISFIQDIGR LPLKRHFGRL
KMEALTDREH GMIDPDSGDE AQLNGGHSAE ESLGEPTQAT VPETWSLPLS QNSASELPAS
QPQPFSAQGD MEENIIIEDY ESDGT*
speed 1.05 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