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

ENST00000318100

Genbank transcript ID

N/A

UniProt peptide

Q9NZ71

alteration type

single base exchange

alteration region

CDS

DNA changes

c.3126A>C
cDNA.3953A>C
g.36948A>C

AA changes

Q1042H Score: 24 explain score(s)

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

1042

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

1042

mutated

not conserved

1042

Ptroglodytes

not conserved

ENSPTRG00000013746

1043

Mmulatta

no alignment

ENSMMUG00000000167

n/a

Fcatus

no homologue

Mmusculus

all conserved

ENSMUSG00000038685

1025

GCAVE

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

4203 / 4203

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

1401 / 1401

position of stopcodon in wt / mu cDNA

5030 / 5030

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

828 / 828

chromosome

strand

last intron/exon boundary

4727

theoretical NMD boundary in CDS

3849

length of CDS

4203

coding sequence (CDS) position

3126

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

3953

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 YRPKVCVLGS REQLCIHPEV KKQESNHLQI HLCRKKVASR SCHFYNNVEE
KSLEQELASP ILDIEDLVKS GSKHRVCPYY LSRNLKQQAD IIFMPYNYLL DAKSRRAHNI
DLKGTVVIFD EAHNVEKMCE ESASFDLTPH DLASGLDVID QVLEEQTKAA QQGEPHPEFS
ADSPSPGLNM ELEDIAKLKM ILLRLEGAID AVELPGDDSG VTKPGSYIFE LFAEAQITFQ
TKGCILDSLD QIIQHLAGRA GVFTNTAGLQ KLADIIQIVF SVDPSEGSPG SPAGLGALQS
YKVHIHPDAG HRRTAQRSDA WSTTAARKRG KVLSYWCFSP GHSMHELVRQ GVRSLILTSG
TLAPVSSFAL EMQIPFPVCL ENPHIIDKHQ IWVGVVPRGP DGAQLSSAFD RRFSEECLSS
LGKALGNIAR VVPYGLLIFF PSYPVMEKSL EFWRARDLAR KMEALKPLFV EPRSKGSFSE
TISAYYARVA APGSTGATFL AVCRGKASEG LDFSDTNGRG VIVTGLPYPP RMDPRVVLKM
QFLDEMKGQG GAGGQFLSGQ EWYRQQASRA VNQAIGRVIR HRQDYGAVFL CDHRFAFADA
RAQLPSWVRP HVRVYDNFGH VIRDVAQFFR VAERTMPAPA PRATAPSVRG EDAVSEAKSP
GPFFSTRKAK SLDLHVPSLK QRSSGSPAAG DPESSLCVEY EQEPVPARQR PRGLLAALEH
SEQRAGSPGE EQAHSCSTLS LLSEKRPAEE PRGGRKKIRL VSHPEEPVAG AQTDRAKLFM
VAVKQELSQA NFATFTQALQ DYKGSDDFAA LAACLGPLFA EDPKKHNLLQ GFYQFVRPHH
KQQFEEVCIQ LTGRGCGYRP EHSIPRRQRA QPVLDPTGRT APDPKLTVST AAAQQLDPQE
HLNQGRPHLS PRPPPTGDPG SQPQWGSGVP RAGKQGQHAV SAYLADARRA LGSAGCSQLL
AALTAYKQDD DLDKVLAVLA ALTTAKPEDF PLLHRFSMFV RPHHKQRFSQ TCTDLTGRPY
PGMEPPGPQE ERLAVPPVLT HRAPQPGPSR SEKTGKTQSK ISSFLRQRPA GTVGAGGEDA
GPSQSSGPPH GPAASEWGEP HGRDIAGQQA TGAPGGPLSA GCVCQGCGAE DVVPFQCPAC
DFQRCQACWQ RHLQASRMCP ACHTASRKQS VMQVFWPEPH KDHEGAGGAR PVAAVPGVGA
ACPAAGAGCT RSGRNTHLPL AGRRDRGAAG VRPVPPRHLC AAAVPPRQPH DVWPVSTAPL
HAVLELPRAL PLLQRPLRGA *

mutated AA sequence

MPKIVLNGVT VDFPFQPYKC QQEYMTKVLE CLQQKVNGIL ESPTGTGKTL CLLCTTLAWR
EHLRDGISAR KIAERAQGEL FPDRALSSWG NAAAAAGDPI ACYTDIPKII YASRTHSQLT
QVINELRNTS YRPKVCVLGS REQLCIHPEV KKQESNHLQI HLCRKKVASR SCHFYNNVEE
KSLEQELASP ILDIEDLVKS GSKHRVCPYY LSRNLKQQAD IIFMPYNYLL DAKSRRAHNI
DLKGTVVIFD EAHNVEKMCE ESASFDLTPH DLASGLDVID QVLEEQTKAA QQGEPHPEFS
ADSPSPGLNM ELEDIAKLKM ILLRLEGAID AVELPGDDSG VTKPGSYIFE LFAEAQITFQ
TKGCILDSLD QIIQHLAGRA GVFTNTAGLQ KLADIIQIVF SVDPSEGSPG SPAGLGALQS
YKVHIHPDAG HRRTAQRSDA WSTTAARKRG KVLSYWCFSP GHSMHELVRQ GVRSLILTSG
TLAPVSSFAL EMQIPFPVCL ENPHIIDKHQ IWVGVVPRGP DGAQLSSAFD RRFSEECLSS
LGKALGNIAR VVPYGLLIFF PSYPVMEKSL EFWRARDLAR KMEALKPLFV EPRSKGSFSE
TISAYYARVA APGSTGATFL AVCRGKASEG LDFSDTNGRG VIVTGLPYPP RMDPRVVLKM
QFLDEMKGQG GAGGQFLSGQ EWYRQQASRA VNQAIGRVIR HRQDYGAVFL CDHRFAFADA
RAQLPSWVRP HVRVYDNFGH VIRDVAQFFR VAERTMPAPA PRATAPSVRG EDAVSEAKSP
GPFFSTRKAK SLDLHVPSLK QRSSGSPAAG DPESSLCVEY EQEPVPARQR PRGLLAALEH
SEQRAGSPGE EQAHSCSTLS LLSEKRPAEE PRGGRKKIRL VSHPEEPVAG AQTDRAKLFM
VAVKQELSQA NFATFTQALQ DYKGSDDFAA LAACLGPLFA EDPKKHNLLQ GFYQFVRPHH
KQQFEEVCIQ LTGRGCGYRP EHSIPRRQRA QPVLDPTGRT APDPKLTVST AAAQQLDPQE
HLNQGRPHLS PRPPPTGDPG SHPQWGSGVP RAGKQGQHAV SAYLADARRA LGSAGCSQLL
AALTAYKQDD DLDKVLAVLA ALTTAKPEDF PLLHRFSMFV RPHHKQRFSQ TCTDLTGRPY
PGMEPPGPQE ERLAVPPVLT HRAPQPGPSR SEKTGKTQSK ISSFLRQRPA GTVGAGGEDA
GPSQSSGPPH GPAASEWGEP HGRDIAGQQA TGAPGGPLSA GCVCQGCGAE DVVPFQCPAC
DFQRCQACWQ RHLQASRMCP ACHTASRKQS VMQVFWPEPH KDHEGAGGAR PVAAVPGVGA
ACPAAGAGCT RSGRNTHLPL AGRRDRGAAG VRPVPPRHLC AAAVPPRQPH DVWPVSTAPL
HAVLELPRAL PLLQRPLRGA *

speed

0.91 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