mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999953 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
protein features (might be) affected
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

ENST00000370003

Genbank transcript ID

N/A

UniProt peptide

Q9NZ71

alteration type

single base exchange

alteration region

CDS

DNA changes

c.861A>C
cDNA.1106A>C
g.36948A>C

AA changes

Q287H Score: 24 explain score(s)

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

287

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

287

mutated

not conserved

287

Ptroglodytes

not conserved

ENSPTRG00000013746

1043

Mmulatta

no alignment

ENSMMUG00000000167

n/a

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000038685

1028

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

start (aa)	end (aa)	feature	details
7	296	DOMAIN	Helicase ATP-binding.	lost
845	845	CONFLICT	A -> V (in Ref. 5; BAG63785).	might get lost (downstream of altered splice site)
871	877	MOTIF	Nuclear localization signal (Potential).	might get lost (downstream of altered splice site)
929	929	CONFLICT	A -> T (in Ref. 5; BAG63785).	might get lost (downstream of altered splice site)
986	986	CONFLICT	R -> Q (in Ref. 5; BAG61337).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1638 / 1638

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

546 / 546

position of stopcodon in wt / mu cDNA

1883 / 1883

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

246 / 246

chromosome

strand

last intron/exon boundary

1803

theoretical NMD boundary in CDS

1507

length of CDS

1638

coding sequence (CDS) position

861

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

1106

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

MPAPAPRATA PSVRGEDAVS EAKSPGPFFS TRKAKSLDLH VPSLKQRSSG SPAAGDPESS
LCVEYEQEPV PARQRPRGLL AALEHSEQRA GSPGEEQAHS CSTLSLLSEK RPAEEPRGGR
KKIRLVSHPE EPVAGAQTDR AKLFMVAVKQ ELSQANFATF TQALQDYKGS DDFAALAACL
GPLFAEDPKK HNLLQGFYQF VRPHHKQQFE EVCIQLTGRG CGYRPEHSIP RRQRAQPVLD
PTGRTAPDPK LTVSTAAAQQ LDPQEHLNQG RPHLSPRPPP TGDPGSQPQW GSGVPRAGKQ
GQHAVSAYLA DARRALGSAG CSQLLAALTA YKQDDDLDKV LAVLAALTTA KPEDFPLLHR
FSMFVRPHHK QRFSQTCTDL TGRPYPGMEP PGPQEERLAV PPVLTHRAPQ PGPSRSEKTG
KTQSKISSFL RQRPAGTVGA GGEDAGPSQS SGPPHGPAAS EWGEPHGRDI AGQQATGAPG
GPLSAGCVCQ GCGAEDVVPF QCPACDFQRC QACWQRHLQA SRMCPACHTA SRKQSVMQVF
WPEPQ*

mutated AA sequence

MPAPAPRATA PSVRGEDAVS EAKSPGPFFS TRKAKSLDLH VPSLKQRSSG SPAAGDPESS
LCVEYEQEPV PARQRPRGLL AALEHSEQRA GSPGEEQAHS CSTLSLLSEK RPAEEPRGGR
KKIRLVSHPE EPVAGAQTDR AKLFMVAVKQ ELSQANFATF TQALQDYKGS DDFAALAACL
GPLFAEDPKK HNLLQGFYQF VRPHHKQQFE EVCIQLTGRG CGYRPEHSIP RRQRAQPVLD
PTGRTAPDPK LTVSTAAAQQ LDPQEHLNQG RPHLSPRPPP TGDPGSHPQW GSGVPRAGKQ
GQHAVSAYLA DARRALGSAG CSQLLAALTA YKQDDDLDKV LAVLAALTTA KPEDFPLLHR
FSMFVRPHHK QRFSQTCTDL TGRPYPGMEP PGPQEERLAV PPVLTHRAPQ PGPSRSEKTG
KTQSKISSFL RQRPAGTVGA GGEDAGPSQS SGPPHGPAAS EWGEPHGRDI AGQQATGAPG
GPLSAGCVCQ GCGAEDVVPF QCPACDFQRC QACWQRHLQA SRMCPACHTA SRKQSVMQVF
WPEPQ*

speed

1.47 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