mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.166626650653459 (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)

chr10:115393929G>AN/A show variant in all transcripts IGV

HGNC symbol

NRAP

Ensembl transcript ID

ENST00000359988

Genbank transcript ID

NM_001261463

UniProt peptide

Q86VF7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1469C>T
cDNA.1633C>T
g.29877C>T

AA changes

S490L Score: 145 explain score(s)

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

490

frameshift

known variant

Reference ID: rs3189030

database	homozygous (A/A)	heterozygous	allele carriers
1000G	255	946	1201
ExAC	6161	20445	26606

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.207	0.536
	1.461	0.948
(flanking)	1.727	0.993

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	29873	wt: 0.51 / mu: 0.78	wt: AGTACAGCTCGGTGA mu: AGTACAGCTTGGTGA	TACA\|gctc

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

490

mutated

not conserved

490

Ptroglodytes

all identical

ENSPTRG00000002951

490

Mmulatta

all identical

ENSMMUG00000001208

490

Fcatus

all identical

ENSFCAG00000011830

490

Mmusculus

all identical

ENSMUSG00000049134

487

Ggallus

no homologue

Trubripes

no homologue

Drerio

not conserved

ENSDARG00000009341

528

Dmelanogaster

all conserved

FBgn0063485

Celegans

not conserved

F42H10.3

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
487	521	REPEAT	Nebulin 11.	lost
522	556	REPEAT	Nebulin 12.	might get lost (downstream of altered splice site)
545	545	CONFLICT	V -> A (in Ref. 5; BAB71328).	might get lost (downstream of altered splice site)
558	592	REPEAT	Nebulin 13.	might get lost (downstream of altered splice site)
602	626	REPEAT	Nebulin 14.	might get lost (downstream of altered splice site)
627	661	REPEAT	Nebulin 15.	might get lost (downstream of altered splice site)
658	658	CONFLICT	E -> G (in Ref. 3; CAD89910).	might get lost (downstream of altered splice site)
662	692	REPEAT	Nebulin 16.	might get lost (downstream of altered splice site)
702	724	REPEAT	Nebulin 17.	might get lost (downstream of altered splice site)
726	760	REPEAT	Nebulin 18.	might get lost (downstream of altered splice site)
761	795	REPEAT	Nebulin 19.	might get lost (downstream of altered splice site)
797	831	REPEAT	Nebulin 20.	might get lost (downstream of altered splice site)
844	869	REPEAT	Nebulin 21.	might get lost (downstream of altered splice site)
862	862	CONFLICT	K -> E (in Ref. 3; CAD89910/CAE45846).	might get lost (downstream of altered splice site)
870	896	REPEAT	Nebulin 22.	might get lost (downstream of altered splice site)
901	935	REPEAT	Nebulin 23.	might get lost (downstream of altered splice site)
945	963	REPEAT	Nebulin 24.	might get lost (downstream of altered splice site)
969	1003	REPEAT	Nebulin 25.	might get lost (downstream of altered splice site)
1004	1038	REPEAT	Nebulin 26.	might get lost (downstream of altered splice site)
1040	1074	REPEAT	Nebulin 27.	might get lost (downstream of altered splice site)
1078	1112	REPEAT	Nebulin 28.	might get lost (downstream of altered splice site)
1113	1139	REPEAT	Nebulin 29.	might get lost (downstream of altered splice site)
1144	1178	REPEAT	Nebulin 30.	might get lost (downstream of altered splice site)
1183	1206	REPEAT	Nebulin 31.	might get lost (downstream of altered splice site)
1210	1210	CONFLICT	S -> P (in Ref. 3; CAE45846).	might get lost (downstream of altered splice site)
1212	1246	REPEAT	Nebulin 32.	might get lost (downstream of altered splice site)
1236	1236	CONFLICT	L -> F (in Ref. 3; CAD89910).	might get lost (downstream of altered splice site)
1247	1281	REPEAT	Nebulin 33.	might get lost (downstream of altered splice site)
1260	1260	CONFLICT	A -> V (in Ref. 3; CAE45846).	might get lost (downstream of altered splice site)
1283	1317	REPEAT	Nebulin 34.	might get lost (downstream of altered splice site)
1321	1355	REPEAT	Nebulin 35.	might get lost (downstream of altered splice site)
1348	1348	CONFLICT	R -> K (in Ref. 3; CAE45846).	might get lost (downstream of altered splice site)
1356	1390	REPEAT	Nebulin 36.	might get lost (downstream of altered splice site)
1357	1357	CONFLICT	F -> L (in Ref. 3; CAD89899).	might get lost (downstream of altered splice site)
1391	1421	REPEAT	Nebulin 37.	might get lost (downstream of altered splice site)
1414	1414	CONFLICT	S -> L (in Ref. 3; CAE45846).	might get lost (downstream of altered splice site)
1429	1449	REPEAT	Nebulin 38.	might get lost (downstream of altered splice site)
1455	1481	REPEAT	Nebulin 39.	might get lost (downstream of altered splice site)
1490	1524	REPEAT	Nebulin 40.	might get lost (downstream of altered splice site)
1526	1560	REPEAT	Nebulin 41.	might get lost (downstream of altered splice site)
1563	1563	CONFLICT	I -> V (in Ref. 3; CAD89910).	might get lost (downstream of altered splice site)
1564	1598	REPEAT	Nebulin 42.	might get lost (downstream of altered splice site)
1599	1626	REPEAT	Nebulin 43.	might get lost (downstream of altered splice site)
1607	1607	CONFLICT	P -> H (in Ref. 3; CAD89910).	might get lost (downstream of altered splice site)
1640	1664	REPEAT	Nebulin 44.	might get lost (downstream of altered splice site)
1672	1672	CONFLICT	S -> P (in Ref. 3; CAD38623).	might get lost (downstream of altered splice site)
1696	1696	CONFLICT	Y -> YQ (in Ref. 3; CAD89910/CAD89998 and 4).	might get lost (downstream of altered splice site)
1697	1697	CONFLICT	R -> Q (in Ref. 3; CAD89899).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

5193 / 5193

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

1731 / 1731

position of stopcodon in wt / mu cDNA

5357 / 5357

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

165 / 165

chromosome

strand

-1

last intron/exon boundary

5253

theoretical NMD boundary in CDS

5038

length of CDS

5193

coding sequence (CDS) position

1469

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

1633

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

29877

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

115393929

original gDNA sequence snippet

CGACAAGTTGAAGTACAGCTCGGTGACTGACACCCCACAGA

altered gDNA sequence snippet

CGACAAGTTGAAGTACAGCTTGGTGACTGACACCCCACAGA

original cDNA sequence snippet

CGACAAGTTGAAGTACAGCTCGGTGACTGACACCCCACAGA

altered cDNA sequence snippet

CGACAAGTTGAAGTACAGCTTGGTGACTGACACCCCACAGA

wildtype AA sequence

MNVQPCSRCG YGVYPAEKIS CIDQIWHKAC FHCEVCKMML SVNNFVSHQK KPYCHAHNPK
NNTFTSVYHT PLNLNVRTFP EAISGIHDQE DGEQCKSVFH WDMKSKDKEG APNRQPLANE
RAYWTGYGEG NAWCPGALPD PEIVRMVEAR KSLGEEYTED YEQPRGKGSF PAMITPAYQR
AKKANQLASQ VEYKRGHDER ISRFSTVVDT PELLRSKAGA QLQSDVRYTE DYEQQRGKGS
FPAMITPAYQ IAKRANELAS DVRYHQQYQK EMRGMAGPAI GAEGILTREC ADQYGQGYPE
EYEEHRGKGS FPAMITPAYQ NAKKAHELAS DIKYRQDFNK MKGAAHYHSL PAQDNLVLKQ
AQSVNKLVSE VEYKKDLESS RGHSINYCET PQFRNVSKIS KFTSDNKYKE NYQNHMRGRY
EGVGMDRRTL HAMKVGSLAS NVAYKADYKH DIVDYNYPAT LTPSYQTAMK LVPLKDANYR
QSIDKLKYSS VTDTPQIVQA KINAQQLSHV NYRADYEKNK LNYTLPQDVP QLVKAKTNAK
LFSEVKYKEG WEKTKGKGFE MKLDAMSLLA AKASGELASN IKYKEEYEKT KGKAMGTADS
RLLHSLQIAK MSSEVEYKKG FEESKTRFHL PMDMVNIRHA KKAQTLASDL DYRKKLHEYT
VLPEDMKTQW AKKAYGLQSE LQYKADLAWM KGVGWLTEGS LNLEQAKKAG QLVSEKNYRQ
RVDELKFTSV TDSSQMEHAK KSQELQSGVA YKAGNEQSVH QYTISKDEPL FLQARANAAN
LSEKLYKSSW ENQKAKGFEL RLDSLTFLAA KAKRDLASEV KYKEDYERSR GKLIGAKDVQ
GDSQMSHSLQ MSKLQSELEY KKGFEDTKSQ CHVSLDMVHL VHARKAQHLA TDVGYKTAEH
HFTALPTDMK VEWAKKAYGL QSDNQYRADV KWMKGMGWVA TGSLNVEQAK KAGELISEKK
YRQHPDALKF TSIKDTPEMV QARISYTQAV DRLYREQGEN IKHHYTPTAD LPEVLLAKLN
AMNISETRYK ESWSKLRDGG YKLRLDALPF QAAKASGEII SDYKYKEAFE KMKGQMLGSR
SLEDDISLAH SVYATSLQSD VNYKKGFEHS KAQFHLPLDM AALVHAKKAQ TLASNQDYKH
PLPQYTSLAE DLRLSCAKKA HKLQSENLYR SDLNFMRGVA CVIPGTLEIE GRKKASELIS
ESKYRQHPHS FKYTAVTDTP NLLHAKFSNQ ITNERLYKAA GEDARHEYTM TLGLPEFIRA
KTNAANLSDA RYKESWRNLR AQGYKLTIEA LPFQAARASG DIASDFLYRH DFVKERGKLI
GPQSVRDDPR IQHCRRMGQL QSELQYRRGA TSSQAQFHLP MDMVHLVHAK NAQALASDHD
YRTQYHKFTA LPEDLKMAWA KKAHALQSEL RYKSDLIGMK GIGWLALRSP QMESAKKAGE
LISETKYRKK PDSIKFTTVV DSPDLVHAKN SYMHCNERMY RSGDAESLHR YTLIPDHPDF
TRARLNALHL SDKVYRNSWE QTRAGSYDFR LDAIPFQTAR ASREIASDFR YKEAFLRDRG
LQIGYRSVDD DPRMKHFLNV GRLQSDNEYK KDFAKSRSQF HSSTDQPGLL QAKRSQQLAS
DVHYRQPLPQ PTCDPEQLGL RHAQKAHQLQ SDVKYKSDLN LTRGVGWTPP GSYKVEMARR
AAELANARGL GLQGAYRGAE AVEAGDHQSG EVNPDATEIL HVKKKKALLL *

mutated AA sequence

MNVQPCSRCG YGVYPAEKIS CIDQIWHKAC FHCEVCKMML SVNNFVSHQK KPYCHAHNPK
NNTFTSVYHT PLNLNVRTFP EAISGIHDQE DGEQCKSVFH WDMKSKDKEG APNRQPLANE
RAYWTGYGEG NAWCPGALPD PEIVRMVEAR KSLGEEYTED YEQPRGKGSF PAMITPAYQR
AKKANQLASQ VEYKRGHDER ISRFSTVVDT PELLRSKAGA QLQSDVRYTE DYEQQRGKGS
FPAMITPAYQ IAKRANELAS DVRYHQQYQK EMRGMAGPAI GAEGILTREC ADQYGQGYPE
EYEEHRGKGS FPAMITPAYQ NAKKAHELAS DIKYRQDFNK MKGAAHYHSL PAQDNLVLKQ
AQSVNKLVSE VEYKKDLESS RGHSINYCET PQFRNVSKIS KFTSDNKYKE NYQNHMRGRY
EGVGMDRRTL HAMKVGSLAS NVAYKADYKH DIVDYNYPAT LTPSYQTAMK LVPLKDANYR
QSIDKLKYSL VTDTPQIVQA KINAQQLSHV NYRADYEKNK LNYTLPQDVP QLVKAKTNAK
LFSEVKYKEG WEKTKGKGFE MKLDAMSLLA AKASGELASN IKYKEEYEKT KGKAMGTADS
RLLHSLQIAK MSSEVEYKKG FEESKTRFHL PMDMVNIRHA KKAQTLASDL DYRKKLHEYT
VLPEDMKTQW AKKAYGLQSE LQYKADLAWM KGVGWLTEGS LNLEQAKKAG QLVSEKNYRQ
RVDELKFTSV TDSSQMEHAK KSQELQSGVA YKAGNEQSVH QYTISKDEPL FLQARANAAN
LSEKLYKSSW ENQKAKGFEL RLDSLTFLAA KAKRDLASEV KYKEDYERSR GKLIGAKDVQ
GDSQMSHSLQ MSKLQSELEY KKGFEDTKSQ CHVSLDMVHL VHARKAQHLA TDVGYKTAEH
HFTALPTDMK VEWAKKAYGL QSDNQYRADV KWMKGMGWVA TGSLNVEQAK KAGELISEKK
YRQHPDALKF TSIKDTPEMV QARISYTQAV DRLYREQGEN IKHHYTPTAD LPEVLLAKLN
AMNISETRYK ESWSKLRDGG YKLRLDALPF QAAKASGEII SDYKYKEAFE KMKGQMLGSR
SLEDDISLAH SVYATSLQSD VNYKKGFEHS KAQFHLPLDM AALVHAKKAQ TLASNQDYKH
PLPQYTSLAE DLRLSCAKKA HKLQSENLYR SDLNFMRGVA CVIPGTLEIE GRKKASELIS
ESKYRQHPHS FKYTAVTDTP NLLHAKFSNQ ITNERLYKAA GEDARHEYTM TLGLPEFIRA
KTNAANLSDA RYKESWRNLR AQGYKLTIEA LPFQAARASG DIASDFLYRH DFVKERGKLI
GPQSVRDDPR IQHCRRMGQL QSELQYRRGA TSSQAQFHLP MDMVHLVHAK NAQALASDHD
YRTQYHKFTA LPEDLKMAWA KKAHALQSEL RYKSDLIGMK GIGWLALRSP QMESAKKAGE
LISETKYRKK PDSIKFTTVV DSPDLVHAKN SYMHCNERMY RSGDAESLHR YTLIPDHPDF
TRARLNALHL SDKVYRNSWE QTRAGSYDFR LDAIPFQTAR ASREIASDFR YKEAFLRDRG
LQIGYRSVDD DPRMKHFLNV GRLQSDNEYK KDFAKSRSQF HSSTDQPGLL QAKRSQQLAS
DVHYRQPLPQ PTCDPEQLGL RHAQKAHQLQ SDVKYKSDLN LTRGVGWTPP GSYKVEMARR
AAELANARGL GLQGAYRGAE AVEAGDHQSG EVNPDATEIL HVKKKKALLL *

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