mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.212641294252466 (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

ENST00000369360

Genbank transcript ID

N/A

UniProt peptide

Q86VF7

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1364C>T
cDNA.1528C>T
g.29877C>T

AA changes

S455L Score: 145 explain score(s)

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

455

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

455

mutated

not conserved

455

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.	might get lost (downstream of altered splice site)
488	488	CONFLICT	Y -> H (in Ref. 3; CAE45811).	might get lost (downstream of altered splice site)
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

5112 / 5112

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

1704 / 1704

position of stopcodon in wt / mu cDNA

5276 / 5276

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

5172

theoretical NMD boundary in CDS

4957

length of CDS

5112

coding sequence (CDS) position

1364

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

1528

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 NKYKENYQNH MRGRYEGVGM DRRTLHAMKV GSLASNVAYK ADYKHDIVDY
NYPATLTPSY QTAMKLVPLK DANYRQSIDK LKYSSVTDTP QIVQAKINAQ QLSHVNYRAD
YEKNKLNYTL PQDVPQLVKA KTNAKLFSEV KYKEGWEKTK GKGFEMKLDA MSLLAAKASG
ELASNVHLLL SLKIKYKEEY EKTKGKAMGT ADSRLLHSLQ IAKMSSEVEY KKGFEESKTR
FHLPMDMVNI RHAKKAQTLA SDLDYRKKLH EYTVLPEDMK TQWAKKAYGL QSELQYKADL
AWMKGVGWLT EGSLNLEQAK KAGQLVSEKN YRQRVDELKF TSVTDSSQME HAKKSQELQS
GVAYKAGNEQ SVHQYTISKD EPLFLQARAN AANLSEKLYK SSWENQKAKG FELRLDSLTF
LAAKAKRDLA SEVKYKEDYE RSRGKLIGAK DVQGDSQMSH SLQMSKLQSE LEYKKGFEDT
KSQCHVSLDM VHLVHARKAQ HLATDVGYKT AEHHFTALPT DMKVEWAKKA YGLQSDNQYR
ADVKWMKGMG WVATGSLNVE QAKKAGELIS EKKYRQHPDA LKFTSIKDTP EMVQARISYT
QAVDRLYREQ GENIKHHYTP TADLPEVLLA KLNAMNISET RYKESWSKLR DGGYKLRLDA
LPFQAAKASG EIISDYKYKE AFEKMKGQML GSRSLEDDIS LAHSVYATSL QSDVNYKKGF
EHSKAQFHLP LDMAALVHAK KAQTLASNQD YKHPLPQYTS LAEDLRLSCA KKAHKLQSEN
LYRSDLNFMR GVACVIPGTL EIEGRKKASE LISESKYRQH PHSFKYTAVT DTPNLLHAKF
SNQITNERLY KAAGEDARHE YTMTLGLPEF IRAKTNAANL SDARYKESWR NLRAQGYKLT
IEALPFQAAR ASGDIASDFL YRHDFVKERG KLIGPQSVRD DPRIQHCRRM GQLQSELQYR
RGATSSQAQF HLPMDMVHLV HAKNAQALAS DHDYRTQYHK FTALPEDLKM AWAKKAHALQ
SELRYKSDLI GMKGIGWLAL RSPQMESAKK AGELISETKY RKKPDSIKFT TVVDSPDLVH
AKNSYMHCNE RMYRSGDAES LHRYTLIPDH PDFTRARLNA LHLSDKVYRN SWEQTRAGSY
DFRLDAIPFQ TARASREIAS DFRYKEAFLR DRGLQIGYRS VDDDPRMKHF LNVGRLQSDN
EYKKDFAKSR SQFHSSTDQP GLLQAKRSQQ LASDVHYRQP LPQPTCDPEQ LGLRHAQKAH
QLQSDVKYKS DLNLTRGVGW TPPGSYKVEM ARRAAELANA RGLGLQGAYR GAEAVEAGDH
QSGEVNPDAT EILHVKKKKA LLL*

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 NKYKENYQNH MRGRYEGVGM DRRTLHAMKV GSLASNVAYK ADYKHDIVDY
NYPATLTPSY QTAMKLVPLK DANYRQSIDK LKYSLVTDTP QIVQAKINAQ QLSHVNYRAD
YEKNKLNYTL PQDVPQLVKA KTNAKLFSEV KYKEGWEKTK GKGFEMKLDA MSLLAAKASG
ELASNVHLLL SLKIKYKEEY EKTKGKAMGT ADSRLLHSLQ IAKMSSEVEY KKGFEESKTR
FHLPMDMVNI RHAKKAQTLA SDLDYRKKLH EYTVLPEDMK TQWAKKAYGL QSELQYKADL
AWMKGVGWLT EGSLNLEQAK KAGQLVSEKN YRQRVDELKF TSVTDSSQME HAKKSQELQS
GVAYKAGNEQ SVHQYTISKD EPLFLQARAN AANLSEKLYK SSWENQKAKG FELRLDSLTF
LAAKAKRDLA SEVKYKEDYE RSRGKLIGAK DVQGDSQMSH SLQMSKLQSE LEYKKGFEDT
KSQCHVSLDM VHLVHARKAQ HLATDVGYKT AEHHFTALPT DMKVEWAKKA YGLQSDNQYR
ADVKWMKGMG WVATGSLNVE QAKKAGELIS EKKYRQHPDA LKFTSIKDTP EMVQARISYT
QAVDRLYREQ GENIKHHYTP TADLPEVLLA KLNAMNISET RYKESWSKLR DGGYKLRLDA
LPFQAAKASG EIISDYKYKE AFEKMKGQML GSRSLEDDIS LAHSVYATSL QSDVNYKKGF
EHSKAQFHLP LDMAALVHAK KAQTLASNQD YKHPLPQYTS LAEDLRLSCA KKAHKLQSEN
LYRSDLNFMR GVACVIPGTL EIEGRKKASE LISESKYRQH PHSFKYTAVT DTPNLLHAKF
SNQITNERLY KAAGEDARHE YTMTLGLPEF IRAKTNAANL SDARYKESWR NLRAQGYKLT
IEALPFQAAR ASGDIASDFL YRHDFVKERG KLIGPQSVRD DPRIQHCRRM GQLQSELQYR
RGATSSQAQF HLPMDMVHLV HAKNAQALAS DHDYRTQYHK FTALPEDLKM AWAKKAHALQ
SELRYKSDLI GMKGIGWLAL RSPQMESAKK AGELISETKY RKKPDSIKFT TVVDSPDLVH
AKNSYMHCNE RMYRSGDAES LHRYTLIPDH PDFTRARLNA LHLSDKVYRN SWEQTRAGSY
DFRLDAIPFQ TARASREIAS DFRYKEAFLR DRGLQIGYRS VDDDPRMKHF LNVGRLQSDN
EYKKDFAKSR SQFHSSTDQP GLLQAKRSQQ LASDVHYRQP LPQPTCDPEQ LGLRHAQKAH
QLQSDVKYKS DLNLTRGVGW TPPGSYKVEM ARRAAELANA RGLGLQGAYR GAEAVEAGDH
QSGEVNPDAT EILHVKKKKA LLL*

speed

1.33 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