mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999972 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr20:62326110A>CN/A show variant in all transcripts IGV

HGNC symbol

RTEL1

Ensembl transcript ID

ENST00000508582

Genbank transcript ID

NM_032957

UniProt peptide

Q9NZ71

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3198A>C
cDNA.3544A>C
g.36948A>C

AA changes

Q1066H Score: 24 explain score(s)

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

1066

frameshift

known variant

Reference ID: rs3208008

database	homozygous (C/C)	heterozygous	allele carriers
1000G	1486	718	2204
ExAC	-	-	-

regulatory features

PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H2BK5me1, Histone, Histone 2B Lysine 5 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.042	0
	-1.975	0
(flanking)	0.815	0.001

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
Donor increased	36947	wt: 0.23 / mu: 0.30	wt: CAGCCAACCACAGTG mu: CAGCCACCCACAGTG	GCCA\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

1066

mutated

not conserved

1066

Ptroglodytes

not conserved

ENSPTRG00000013746

1043

Mmulatta

no alignment

ENSMMUG00000000167

n/a

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000038685

1027

GCA

Ggallus

no homologue

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000035074

1048

Dmelanogaster

no alignment

FBgn0029798

n/a

Celegans

no alignment

F25H2.13

n/a

Xtropicalis

no homologue

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3732 / 3732

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

1244 / 1244

position of stopcodon in wt / mu cDNA

4078 / 4078

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

347 / 347

chromosome

strand

last intron/exon boundary

4071

theoretical NMD boundary in CDS

3674

length of CDS

3732

coding sequence (CDS) position

3198

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

3544

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

36948

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

62326110

original gDNA sequence snippet

CCAGGAGACCCTGGCAGCCAACCACAGTGGGGGTCTGGAGT

altered gDNA sequence snippet

CCAGGAGACCCTGGCAGCCACCCACAGTGGGGGTCTGGAGT

original cDNA sequence snippet

ACAGGAGACCCTGGCAGCCAACCACAGTGGGGGTCTGGAGT

altered cDNA sequence snippet

ACAGGAGACCCTGGCAGCCACCCACAGTGGGGGTCTGGAGT

wildtype AA sequence

MPKIVLNGVT VDFPFQPYKC QQEYMTKVLE CLQQKVNGIL ESPTGTGKTL CLLCTTLAWR
EHLRDGISAR KIAERAQGEL FPDRALSSWG NAAAAAGDPI ACYTDIPKII YASRTHSQLT
QVINELRNTS YRSRCRATLW VLETAPPRPT VLSPTRPKVC VLGSREQLCI HPEVKKQESN
HLQIHLCRKK VASRSCHFYN NVEEKSLEQE LASPILDIED LVKSGSKHRV CPYYLSRNLK
QQADIIFMPY NYLLDAKSRR AHNIDLKGTV VIFDEAHNVE KMCEESASFD LTPHDLASGL
DVIDQVLEEQ TKAAQQGEPH PEFSADSPSP GLNMELEDIA KLKMILLRLE GAIDAVELPG
DDSGVTKPGS YIFELFAEAQ ITFQTKGCIL DSLDQIIQHL AGRAGVFTNT AGLQKLADII
QIVFSVDPSE GSPGSPAGLG ALQSYKVHIH PDAGHRRTAQ RSDAWSTTAA RKRGKVLSYW
CFSPGHSMHE LVRQGVRSLI LTSGTLAPVS SFALEMQIPF PVCLENPHII DKHQIWVGVV
PRGPDGAQLS SAFDRRFSEE CLSSLGKALG NIARVVPYGL LIFFPSYPVM EKSLEFWRAR
DLARKMEALK PLFVEPRSKG SFSETISAYY ARVAAPGSTG ATFLAVCRGK ASEGLDFSDT
NGRGVIVTGL PYPPRMDPRV VLKMQFLDEM KGQGGAGGQF LSGQEWYRQQ ASRAVNQAIG
RVIRHRQDYG AVFLCDHRFA FADARAQLPS WVRPHVRVYD NFGHVIRDVA QFFRVAERTM
PAPAPRATAP SVRGEDAVSE AKSPGPFFST RKAKSLDLHV PSLKQRSSGS PAAGDPESSL
CVEYEQEPVP ARQRPRGLLA ALEHSEQRAG SPGEEQAHSC STLSLLSEKR PAEEPRGGRK
KIRLVSHPEE PVAGAQTDRA KLFMVAVKQE LSQANFATFT QALQDYKGSD DFAALAACLG
PLFAEDPKKH NLLQGFYQFV RPHHKQQFEE VCIQLTGRGC GYRPEHSIPR RQRAQPVLDP
TGRTAPDPKL TVSTAAAQQL DPQEHLNQGR PHLSPRPPPT GDPGSQPQWG SGVPRAGKQG
QHAVSAYLAD ARRALGSAGC SQLLAALTAY KQDDDLDKVL AVLAALTTAK PEDFPLLHSN
SMFVRPHHKQ RFSQTCTDLT GRPYPGMEPP GPQEERLAVP PVLTHRAPQP GPSRSEKTGK
TQSKISSFLR QRPAGTVGAG GEDAGPSQSS GPPHGPAASE WGL*

mutated AA sequence

MPKIVLNGVT VDFPFQPYKC QQEYMTKVLE CLQQKVNGIL ESPTGTGKTL CLLCTTLAWR
EHLRDGISAR KIAERAQGEL FPDRALSSWG NAAAAAGDPI ACYTDIPKII YASRTHSQLT
QVINELRNTS YRSRCRATLW VLETAPPRPT VLSPTRPKVC VLGSREQLCI HPEVKKQESN
HLQIHLCRKK VASRSCHFYN NVEEKSLEQE LASPILDIED LVKSGSKHRV CPYYLSRNLK
QQADIIFMPY NYLLDAKSRR AHNIDLKGTV VIFDEAHNVE KMCEESASFD LTPHDLASGL
DVIDQVLEEQ TKAAQQGEPH PEFSADSPSP GLNMELEDIA KLKMILLRLE GAIDAVELPG
DDSGVTKPGS YIFELFAEAQ ITFQTKGCIL DSLDQIIQHL AGRAGVFTNT AGLQKLADII
QIVFSVDPSE GSPGSPAGLG ALQSYKVHIH PDAGHRRTAQ RSDAWSTTAA RKRGKVLSYW
CFSPGHSMHE LVRQGVRSLI LTSGTLAPVS SFALEMQIPF PVCLENPHII DKHQIWVGVV
PRGPDGAQLS SAFDRRFSEE CLSSLGKALG NIARVVPYGL LIFFPSYPVM EKSLEFWRAR
DLARKMEALK PLFVEPRSKG SFSETISAYY ARVAAPGSTG ATFLAVCRGK ASEGLDFSDT
NGRGVIVTGL PYPPRMDPRV VLKMQFLDEM KGQGGAGGQF LSGQEWYRQQ ASRAVNQAIG
RVIRHRQDYG AVFLCDHRFA FADARAQLPS WVRPHVRVYD NFGHVIRDVA QFFRVAERTM
PAPAPRATAP SVRGEDAVSE AKSPGPFFST RKAKSLDLHV PSLKQRSSGS PAAGDPESSL
CVEYEQEPVP ARQRPRGLLA ALEHSEQRAG SPGEEQAHSC STLSLLSEKR PAEEPRGGRK
KIRLVSHPEE PVAGAQTDRA KLFMVAVKQE LSQANFATFT QALQDYKGSD DFAALAACLG
PLFAEDPKKH NLLQGFYQFV RPHHKQQFEE VCIQLTGRGC GYRPEHSIPR RQRAQPVLDP
TGRTAPDPKL TVSTAAAQQL DPQEHLNQGR PHLSPRPPPT GDPGSHPQWG SGVPRAGKQG
QHAVSAYLAD ARRALGSAGC SQLLAALTAY KQDDDLDKVL AVLAALTTAK PEDFPLLHSN
SMFVRPHHKQ RFSQTCTDLT GRPYPGMEPP GPQEERLAVP PVLTHRAPQP GPSRSEKTGK
TQSKISSFLR QRPAGTVGAG GEDAGPSQSS GPPHGPAASE WGL*

speed

1.34 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