mutation t@sting

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

ENST00000282891

Genbank transcript ID

NM_133341

UniProt peptide

O75943

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1379T>G
cDNA.1691T>G
g.30821T>G

AA changes

L460R Score: 102 explain score(s)

position(s) of altered AA
if AA alteration in CDS

460

frameshift

known variant

Reference ID: rs1045051

database	homozygous (G/G)	heterozygous	allele carriers
1000G	210	856	1066
ExAC	5800	21167	26967

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

	PhyloP	PhastCons
(flanking)	3.92	1
	4.571	1
(flanking)	0.239	0.998

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Acc marginally increased	30815	wt: 0.2064 / mu: 0.2296 (marginal change - not scored)	wt: TGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAGCTAT mu: TGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAGCTAT	cttt\|ATGC
Acc marginally increased	30811	wt: 0.5326 / mu: 0.5471 (marginal change - not scored)	wt: TTCCTGACTTCTGCCTACCAGCTTTATGCCTCCAAACTCAG mu: TTCCTGACTTCTGCCTACCAGCTTTATGCCGCCAAACTCAG	ccag\|CTTT
Donor increased	30821	wt: 0.29 / mu: 0.57	wt: ATGCCTCCAAACTCA mu: ATGCCGCCAAACTCA	GCCT\|ccaa
Donor gained	30820	0.90	mu: TATGCCGCCAAACTC	TGCC\|gcca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

460

mutated

not conserved

460

Ptroglodytes

all identical

ENSPTRG00000016950

557

Mmulatta

all identical

ENSMMUG00000014881

557

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000021635

555

Ggallus

all identical

ENSGALG00000015571

569

Trubripes

all identical

ENSTRUG00000002152

538

Drerio

all identical

ENSDARG00000018918

548

Dmelanogaster

no alignment

FBgn0025808

n/a

Celegans

no alignment

F32A11.2

n/a

Xtropicalis

all identical

ENSXETG00000018168

557

protein features

start (aa)	end (aa)	feature	details
432	681	REGION	Interaction with MCM7.	lost
462	462	CONFLICT	M -> T (in Ref. 5; AAC36334).	might get lost (downstream of altered splice site)
646	646	MOD_RES	Phosphoserine; by ATR and ATM.	might get lost (downstream of altered splice site)
646	646	MUTAGEN	S->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)
646	646	MUTAGEN	S->D: Abolishes interaction with RAD1; when associated with D-656.	might get lost (downstream of altered splice site)
648	648	CONFLICT	N -> D (in Ref. 5; AAC36334).	might get lost (downstream of altered splice site)
656	656	MUTAGEN	S->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)
656	656	MOD_RES	Phosphoserine; by ATR and ATM.	might get lost (downstream of altered splice site)
656	656	MUTAGEN	S->D: Abolishes interaction with RAD1; when associated with D-646.	might get lost (downstream of altered splice site)
672	672	CONFLICT	I -> 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

1755 / 1755

position (AA) of stopcodon in wt / mu AA sequence

585 / 585

position of stopcodon in wt / mu cDNA

2067 / 2067

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

313 / 313

chromosome

strand

last intron/exon boundary

1806

theoretical NMD boundary in CDS

1443

length of CDS

1755

coding sequence (CDS) position

1379

cDNA position
(for ins/del: last normal base / first normal base)

1691

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

MNQHELAVHK KKIEEVETWL KAQVLERQPK QGGSILLITG PPGCGKTTTL KILSKEHGIQ
VQEWINPVLP DFQKDDFKGM FNTESSFHMF PYQSQIAVFK EFLLRATKYN KLQMLGDDLR
TDKKIILVED LPNQFYRDSH TLHEVLRKYV RIGRCPLIFI ISDSLSGDNN QRLLFPKEIQ
EECSISNISF NPVAPTIMMK FLNRIVTIEA NKNGGKITVP DKTSLELLCQ GCSGDIRSAI
NSLQFSSSKG ENNLRPRKKG MSLKSDAVLS KSKRRKKPDR VFENQEVQAI GGKDVSLFLF
RALGKILYCK RASLTELDSP RLPSHLSEYE RDTLLVEPEE VVEMSHMPGD LFNLYLHQNY
IDFFMEIDDI VRASEFLSFA DILSGDWNTR SLLREYSTSI ATRGVMHSNK ARGYAHCQGG
GSSFRPLHKP QWFLINKKYR ENCLAAKALF PDFCLPALCL QTQLLPYLAL LTIPMRNQAQ
ISFIQDIGRL PLKRHFGRLK MEALTDREHG MIDPDSGDEA QLNGGHSAEE SLGEPTQATV
PETWSLPLSQ NSASELPASQ PQPFSAQGDM EENIIIEDYE SDGT*

mutated AA sequence

MNQHELAVHK KKIEEVETWL KAQVLERQPK QGGSILLITG PPGCGKTTTL KILSKEHGIQ
VQEWINPVLP DFQKDDFKGM FNTESSFHMF PYQSQIAVFK EFLLRATKYN KLQMLGDDLR
TDKKIILVED LPNQFYRDSH TLHEVLRKYV RIGRCPLIFI ISDSLSGDNN QRLLFPKEIQ
EECSISNISF NPVAPTIMMK FLNRIVTIEA NKNGGKITVP DKTSLELLCQ GCSGDIRSAI
NSLQFSSSKG ENNLRPRKKG MSLKSDAVLS KSKRRKKPDR VFENQEVQAI GGKDVSLFLF
RALGKILYCK RASLTELDSP RLPSHLSEYE RDTLLVEPEE VVEMSHMPGD LFNLYLHQNY
IDFFMEIDDI VRASEFLSFA DILSGDWNTR SLLREYSTSI ATRGVMHSNK ARGYAHCQGG
GSSFRPLHKP QWFLINKKYR ENCLAAKALF PDFCLPALCR QTQLLPYLAL LTIPMRNQAQ
ISFIQDIGRL PLKRHFGRLK MEALTDREHG MIDPDSGDEA QLNGGHSAEE SLGEPTQATV
PETWSLPLSQ NSASELPASQ PQPFSAQGDM EENIIIEDYE SDGT*

speed

1.42 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