mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.509319301403224 (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)

chr9:134020092C>TN/A show variant in all transcripts IGV

HGNC symbol

NUP214

Ensembl transcript ID

ENST00000451030

Genbank transcript ID

N/A

UniProt peptide

P35658

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1720C>T
cDNA.1831C>T
g.19145C>T

AA changes

P574S Score: 74 explain score(s)

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

574

frameshift

known variant

Reference ID: rs103612

database	homozygous (T/T)	heterozygous	allele carriers
1000G	1021	1173	2194
ExAC	26812	-20857	5955

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.466	0.972
	0.575	0.676
(flanking)	0.855	0.463

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 marginally increased	19138	wt: 0.9924 / mu: 0.9960 (marginal change - not scored)	wt: ATAGCAATGAAGCCC mu: ATAGCAATGAAGTCC	AGCA\|atga
Acc gained	19155	0.31	mu: AGCAATGAAGTCCTCCTTCCCACCCTCAACCTCTGCTGTCA	tccc\|ACCC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

574

mutated

not conserved

574

Ptroglodytes

all identical

ENSPTRG00000021482

871

STEEATSSALPEKPGDSEV

LLEEQQS

KKEPVLAQPAVSNS

Mmulatta

all identical

ENSMMUG00000021724

574

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000001855

572

Ggallus

not conserved

ENSGALG00000003830

567

Trubripes

not conserved

ENSTRUG00000007589

569

Drerio

not conserved

ENSDARG00000016212

573

PPA

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000001475

582

protein features

start (aa)	end (aa)	feature	details
481	2076	REGION	11 X 5 AA approximate repeats.	lost
646	646	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
651	651	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
655	655	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
657	657	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
666	666	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
670	670	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
678	678	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
740	768	REGION	Leucine-zipper 1.	might get lost (downstream of altered splice site)
812	813	SITE	Breakpoint.	might get lost (downstream of altered splice site)
861	882	REGION	Leucine-zipper 2.	might get lost (downstream of altered splice site)
940	940	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
970	970	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
974	974	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
985	985	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
987	987	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
989	989	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1081	1081	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1091	1092	CONFLICT	AA -> QL (in Ref. 1; CAA45535).	might get lost (downstream of altered splice site)
1136	1136	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1156	1156	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1181	1181	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1203	1203	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1213	2090	COMPBIAS	Pro/Ser/Thr-rich.	might get lost (downstream of altered splice site)
1312	1312	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
1333	1333	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1356	1356	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
1409	2084	REGION	18 X 4 AA approximate repeats.	might get lost (downstream of altered splice site)
1427	2085	REGION	11 X 3 AA approximate repeats.	might get lost (downstream of altered splice site)
1872	1872	CONFLICT	S -> N (in Ref. 5; AAH45620).	might get lost (downstream of altered splice site)
1963	1963	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

6276 / 6276

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

2092 / 2092

position of stopcodon in wt / mu cDNA

6387 / 6387

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

112 / 112

chromosome

strand

last intron/exon boundary

6354

theoretical NMD boundary in CDS

6192

length of CDS

6276

coding sequence (CDS) position

1720

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

1831

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

19145

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

134020092

original gDNA sequence snippet

CTCCAAATATAGCAATGAAGCCCTCCTTCCCACCCTCAACC

altered gDNA sequence snippet

CTCCAAATATAGCAATGAAGTCCTCCTTCCCACCCTCAACC

original cDNA sequence snippet

CTCCAAATATAGCAATGAAGCCCTCCTTCCCACCCTCAACC

altered cDNA sequence snippet

CTCCAAATATAGCAATGAAGTCCTCCTTCCCACCCTCAACC

wildtype AA sequence

MGDEMDAMIP EREMKDFQFR ALKKVRIFDS PEELPKERSS LLAVSNKYGL VFAGGASGLQ
IFPTKNLLIQ NKPGDDPNKI VDKVQGLLVP MKFPIHHLAL SCDNLTLSAC MMSSEYGSII
AFFDVRTFSN EAKQQKRPFA YHKLLKDAGG MVIDMKWNPT VPSMVAVCLA DGSIAVLQVT
ETVKVCATLP STVAVTSVCW SPKGKQLAVG KQNGTVVQYL PTLQEKKVIP CPPFYESDHP
VRVLDVLWIG TYVFAIVYAA ADGTLETSPD VVMALLPKKE EKHPEIFVNF MEPCYGSCTE
RQHHYYLSYI EEWDLVLAAS AASTEVSILA RQSDQINWES WLLEDSSRAE LPVTDKSDDS
LPMGVVVDYT NQVEITISDE KTLPPAPVLM LLSTDGVLCP FYMINQNPGV KSLIKTPERL
SLEGERQPKS PGSTPTTPTS SQAPQKLDAS AAAAPASLPP SSPAAPIATF SLLPAGGAPT
VFSFGSSSLK SSATVTGEPP SYSSGSDSSK AAPGPGPSTF SFVPPSKASL APTPAASPVA
PSAASFSFGS SGFKPTLEST PVPSVSAPNI AMKPSFPPST SAVKVNLSEK FTAAATSTPV
SSSQSAPPMS PFSSASKPAA SGPLSHPTPL SAPPSSVPLK SSVLPSPSAG RSAQGSSSPV
PSMVQKSPRI TPPAAKPGSP QAKSLQPAVA EKQGHQWKDS DPVMAGIGEE IAHFQKELEE
LKARTSKACF QVGTSEEMKM LRTESDDLHT FLLEIKETTE SLHGDISSLK TTLLEGFAGV
EEAREQNERN RDSGYLHLLY KRPLDPKSEA QLQEIRRLHQ YVKFAVQDVN DVLDLEWDQH
LEQKKKQRHL LVPERETLFN TLANNREIIN QQRKRLNHLV DSLQQLRLYK QTSLWSLSSA
VPSQSSIHSF DSDLESLCNA LLKTTIESHT KSLPKVPAKL SPMKQAQLRN FLAKRKTPPV
RSTAPASLSR SAFLSQRYYE DLDEVSSTSS VSQSLESEDA RTSCKDDEAV VQAPRHAPVV
RTPSIQPSLL PHAAPFAKSH LVHGSSPGVM GTSVATSASK IIPQGADSTM LATKTVKHGA
PSPSHPISAP QAAAAAALRR QMASQAPAVN TLTESTLKNV PQVVNVQELK NNPATPSTAM
GSSVPYSTAK TPHPVLTPVA ANQAKQGSLI NSLKPSGPTP ASGQLSSGDK ASGTAKIETA
VTSTPSASGQ FSKPFSFSPS GTGFNFGIIT PTPSSNFTAA QGATPSTKES SQPDAFSSGG
GSKPSYEAIP ESSPPSGITS ASNTTPGEPA ASSSRPVAPS GTALSTTSSK LETPPSKLGE
LLFPSSLAGE TLGSFSGLRV GQADDSTKPT NKASSTSLTS TQPTKTSGVP SGFNFTAPPV
LGKHTEPPVT SSATTTSVAP PAATSTSSTA VFGSLPVTSA GSSGVISFGG TSLSAGKTSF
SFGSQQTNST VPPSAPPPTT AATPLPTSFP TLSFGSLLSS ATTPSLPMSA GRSTEEATSS
ALPEKPGDSE VSASAASLLE EQQSAQLPQA PPQTSDSVKK EPVLAQPAVS NSGTAASSTS
LVALSAEATP ATTGVPDART EAVPPASSFS VPGQTAVTAA AISSAGPVAV ETSSTPIASS
TTSIVAPGPS AEAAAFGTVT SGSSVFAQPP AASSSSAFNQ LTNNTATAPS ATPVFGQVAA
STAPSLFGQQ TGSTASTAAA TPQVSSSGFS SPAFGTTAPG VFGQTTFGQA SVFGQSASSA
ASVFSFSQPG FSSVPAFGQP ASSTPTSTSG SVFGAASSTS SSSSFSFGQS SPNTGGGLFG
QSNAPAFGQS PGFGQGGSVF GGTSAATTTA ATSGFSFCQA SGFGSSNTGS VFGQAASTGG
IVFGQQSSSS SGSVFGSGNT GRGGGFFSGL GGKPSQDAAN KNPFSSASGG FGSTATSNTS
NLFGNSGAKT FGGFASSSFG EQKPTGTFSS GGGSVASQGF GFSSPNKTGG FGAAPVFGSP
PTFGGSPGFG GVPAFGSAPA FTSPLGSTGG KVFGEGTAAA SAGGFGFGSS SNTTSFGTLA
SQNAPTFGSL SQQTSGFGTQ SSGFSGFGSG TGGFSFGSNN SSVQGFGGWR S*

mutated AA sequence

MGDEMDAMIP EREMKDFQFR ALKKVRIFDS PEELPKERSS LLAVSNKYGL VFAGGASGLQ
IFPTKNLLIQ NKPGDDPNKI VDKVQGLLVP MKFPIHHLAL SCDNLTLSAC MMSSEYGSII
AFFDVRTFSN EAKQQKRPFA YHKLLKDAGG MVIDMKWNPT VPSMVAVCLA DGSIAVLQVT
ETVKVCATLP STVAVTSVCW SPKGKQLAVG KQNGTVVQYL PTLQEKKVIP CPPFYESDHP
VRVLDVLWIG TYVFAIVYAA ADGTLETSPD VVMALLPKKE EKHPEIFVNF MEPCYGSCTE
RQHHYYLSYI EEWDLVLAAS AASTEVSILA RQSDQINWES WLLEDSSRAE LPVTDKSDDS
LPMGVVVDYT NQVEITISDE KTLPPAPVLM LLSTDGVLCP FYMINQNPGV KSLIKTPERL
SLEGERQPKS PGSTPTTPTS SQAPQKLDAS AAAAPASLPP SSPAAPIATF SLLPAGGAPT
VFSFGSSSLK SSATVTGEPP SYSSGSDSSK AAPGPGPSTF SFVPPSKASL APTPAASPVA
PSAASFSFGS SGFKPTLEST PVPSVSAPNI AMKSSFPPST SAVKVNLSEK FTAAATSTPV
SSSQSAPPMS PFSSASKPAA SGPLSHPTPL SAPPSSVPLK SSVLPSPSAG RSAQGSSSPV
PSMVQKSPRI TPPAAKPGSP QAKSLQPAVA EKQGHQWKDS DPVMAGIGEE IAHFQKELEE
LKARTSKACF QVGTSEEMKM LRTESDDLHT FLLEIKETTE SLHGDISSLK TTLLEGFAGV
EEAREQNERN RDSGYLHLLY KRPLDPKSEA QLQEIRRLHQ YVKFAVQDVN DVLDLEWDQH
LEQKKKQRHL LVPERETLFN TLANNREIIN QQRKRLNHLV DSLQQLRLYK QTSLWSLSSA
VPSQSSIHSF DSDLESLCNA LLKTTIESHT KSLPKVPAKL SPMKQAQLRN FLAKRKTPPV
RSTAPASLSR SAFLSQRYYE DLDEVSSTSS VSQSLESEDA RTSCKDDEAV VQAPRHAPVV
RTPSIQPSLL PHAAPFAKSH LVHGSSPGVM GTSVATSASK IIPQGADSTM LATKTVKHGA
PSPSHPISAP QAAAAAALRR QMASQAPAVN TLTESTLKNV PQVVNVQELK NNPATPSTAM
GSSVPYSTAK TPHPVLTPVA ANQAKQGSLI NSLKPSGPTP ASGQLSSGDK ASGTAKIETA
VTSTPSASGQ FSKPFSFSPS GTGFNFGIIT PTPSSNFTAA QGATPSTKES SQPDAFSSGG
GSKPSYEAIP ESSPPSGITS ASNTTPGEPA ASSSRPVAPS GTALSTTSSK LETPPSKLGE
LLFPSSLAGE TLGSFSGLRV GQADDSTKPT NKASSTSLTS TQPTKTSGVP SGFNFTAPPV
LGKHTEPPVT SSATTTSVAP PAATSTSSTA VFGSLPVTSA GSSGVISFGG TSLSAGKTSF
SFGSQQTNST VPPSAPPPTT AATPLPTSFP TLSFGSLLSS ATTPSLPMSA GRSTEEATSS
ALPEKPGDSE VSASAASLLE EQQSAQLPQA PPQTSDSVKK EPVLAQPAVS NSGTAASSTS
LVALSAEATP ATTGVPDART EAVPPASSFS VPGQTAVTAA AISSAGPVAV ETSSTPIASS
TTSIVAPGPS AEAAAFGTVT SGSSVFAQPP AASSSSAFNQ LTNNTATAPS ATPVFGQVAA
STAPSLFGQQ TGSTASTAAA TPQVSSSGFS SPAFGTTAPG VFGQTTFGQA SVFGQSASSA
ASVFSFSQPG FSSVPAFGQP ASSTPTSTSG SVFGAASSTS SSSSFSFGQS SPNTGGGLFG
QSNAPAFGQS PGFGQGGSVF GGTSAATTTA ATSGFSFCQA SGFGSSNTGS VFGQAASTGG
IVFGQQSSSS SGSVFGSGNT GRGGGFFSGL GGKPSQDAAN KNPFSSASGG FGSTATSNTS
NLFGNSGAKT FGGFASSSFG EQKPTGTFSS GGGSVASQGF GFSSPNKTGG FGAAPVFGSP
PTFGGSPGFG GVPAFGSAPA FTSPLGSTGG KVFGEGTAAA SAGGFGFGSS SNTTSFGTLA
SQNAPTFGSL SQQTSGFGTQ SSGFSGFGSG TGGFSFGSNN SSVQGFGGWR S*

speed

0.71 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