MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000312358
MT speed 0 s - this script 3.465501 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SPEG	polymorphism_automatic	0.013684042767359	simple_aae				H3079R	single base exchange	rs12464085		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.986315957232641 (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

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr2:220355529A>GN/A show variant in all transcripts IGV

HGNC symbol

SPEG

Ensembl transcript ID

ENST00000312358

Genbank transcript ID

NM_005876

UniProt peptide

Q15772

alteration type

single base exchange

alteration region

CDS

DNA changes

c.9236A>G
cDNA.9368A>G
g.55962A>G

AA changes

H3079R Score: 29 explain score(s)

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

3079

frameshift

known variant

Reference ID: rs12464085

database	homozygous (G/G)	heterozygous	allele carriers
1000G	452	1104	1556
ExAC	8260	16247	24507

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.758	0.998
	0.319	0.861
(flanking)	-0.028	0.843

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
Acc marginally increased	55968	wt: 0.5809 / mu: 0.6081 (marginal change - not scored)	wt: CTACCTCCACGGCCACCACGTGCTCCACCTAGACATCAAGC mu: CTACCTCCACGGCCGCCACGTGCTCCACCTAGACATCAAGC	acgt\|GCTC
Donor marginally increased	55961	wt: 0.9194 / mu: 0.9959 (marginal change - not scored)	wt: ACGGCCACCACGTGC mu: ACGGCCGCCACGTGC	GGCC\|acca

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

3079

mutated

not conserved

3079

Ptroglodytes

not conserved

ENSPTRG00000012957

2981

Mmulatta

no alignment

ENSMMUG00000017936

n/a

Fcatus

no alignment

ENSFCAG00000006660

n/a

Mmusculus

all identical

ENSMUSG00000026207

3074

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000003675

3076

Drerio

not conserved

ENSDARG00000009567

171

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
2966	3218	DOMAIN	Protein kinase 2.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

9804 / 9804

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

3268 / 3268

position of stopcodon in wt / mu cDNA

9936 / 9936

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

133 / 133

chromosome

strand

last intron/exon boundary

9744

theoretical NMD boundary in CDS

9561

length of CDS

9804

coding sequence (CDS) position

9236

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

9368

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

55962

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

220355529

original gDNA sequence snippet

CCTGGACTACCTCCACGGCCACCACGTGCTCCACCTAGACA

altered gDNA sequence snippet

CCTGGACTACCTCCACGGCCGCCACGTGCTCCACCTAGACA

original cDNA sequence snippet

CCTGGACTACCTCCACGGCCACCACGTGCTCCACCTAGACA

altered cDNA sequence snippet

CCTGGACTACCTCCACGGCCGCCACGTGCTCCACCTAGACA

wildtype AA sequence

MQKARGTRGE DAGTRAPPSP GVPPKRAKVG AGGGAPVAVA GAPVFLRPLK NAAVCAGSDV
RLRVVVSGTP QPSLRWFRDG QLLPAPAPEP SCLWLRRCGA QDAGVYSCMA QNERGRASCE
AVLTVLEVGD SETAEDDISD VQGTQRLELR DDGAFSTPTG GSDTLVGTSL DTPPTSVTGT
SEEQVSWWGS GQTVLEQEAG SGGGTRRLPG SPRQAQATGA GPRHLGVEPL VRASRANLVG
ASWGSEDSLS VASDLYGSAF SLYRGRALSI HVSVPQSGLR REEPDLQPQL ASEAPRRPAQ
PPPSKSALLP PPSPRVGKRS PPGPPAQPAA TPTSPHRRTQ EPVLPEDTTT EEKRGKKSKS
SGPSLAGTAE SRPQTPLSEA SGRLSALGRS PRLVRAGSRI LDKLQFFEER RRSLERSDSP
PAPLRPWVPL RKARSLEQPK SERGAPWGTP GASQEELRAP GSVAERRRLF QQKAASLDER
TRQRSPASDL ELRFAQELGR IRRSTSREEL VRSHESLRAT LQRAPSPREP GEPPLFSRPS
TPKTSRAVSP AAAQPPSPSS AEKPGDEPGR PRSRGPAGRT EPGEGPQQEV RRRDQFPLTR
SRAIQECRSP VPPPAADPPE ARTKAPPGRK REPPAQAVRF LPWATPGLEG AAVPQTLEKN
RAGPEAEKRL RRGPEEDGPW GPWDRRGARS QGKGRRARPT SPELESSDDS YVSAGEEPLE
APVFEIPLQN VVVAPGADVL LKCIITANPP PQVSWHKDGS ALRSEGRLLL RAEGERHTLL
LREARAADAG SYMATATNEL GQATCAASLT VRPGGSTSPF SSPITSDEEY LSPPEEFPEP
GETWPRTPTM KPSPSQNRRS SDTGSKAPPT FKVSLMDQSV REGQDVIMSI RVQGEPKPVV
SWLRNRQPVR PDQRRFAEEA EGGLCRLRIL AAERGDAGFY TCKAVNEYGA RQCEARLEVR
AHPESRSLAV LAPLQDVDVG AGEMALFECL VAGPTDVEVD WLCRGRLLQP ALLKCKMHFD
GRKCKLLLTS VHEDDSGVYT CKLSTAKDEL TCSARLTVRP SLAPLFTRLL EDVEVLEGRA
ARFDCKISGT PPPVVTWTHF GCPMEESENL RLRQDGGLHS LHIAHVGSED EGLYAVSAVN
THGQAHCSAQ LYVEEPRTAA SGPSSKLEKM PSIPEEPEQG ELERLSIPDF LRPLQDLEVG
LAKEAMLECQ VTGLPYPTIS WFHNGHRIQS SDDRRMTQYR DVHRLVFPAV GPQHAGVYKS
VIANKLGKAA CYAHLYVTDV VPGPPDGAPQ VVAVTGRMVT LTWNPPRSLD MAIDPDSLTY
TVQHQVLGSD QWTALVTGLR EPGWAATGLR KGVQHIFRVL STTVKSSSKP SPPSEPVQLL
EHGPTLEEAP AMLDKPDIVY VVEGQPASVT VTFNHVEAQV VWRSCRGALL EARAGVYELS
QPDDDQYCLR ICRVSRRDMG ALTCTARNRH GTQTCSVTLE LAEAPRFESI MEDVEVGAGE
TARFAVVVEG KPLPDIMWYK DEVLLTESSH VSFVYEENEC SLVVLSTGAQ DGGVYTCTAQ
NLAGEVSCKA ELAVHSAQTA MEVEGVGEDE DHRGRRLSDF YDIHQEIGRG AFSYLRRIVE
RSSGLEFAAK FIPSQAKPKA SARREARLLA RLQHDCVLYF HEAFERRRGL VIVTELCTEE
LLERIARKPT VCESEIRAYM RQVLEGIHYL HQSHVLHLDV KPENLLVWDG AAGEQQVRIC
DFGNAQELTP GEPQYCQYGT PEFVAPEIVN QSPVSGVTDI WPVGVVAFLC LTGISPFVGE
NDRTTLMNIR NYNVAFEETT FLSLSREARG FLIKVLVQDR LRPTAEETLE HPWFKTQAKG
AEVSTDHLKL FLSRRRWQRS QISYKCHLVL RPIPELLRAP PERVWVTMPR RPPPSGGLSS
SSDSEEEELE ELPSVPRPLQ PEFSGSRVSL TDIPTEDEAL GTPETGAATP MDWQEQGRAP
SQDQEAPSPE ALPSPGQEPA AGASPRRGEL RRGSSAESAL PRAGPRELGR GLHKAASVEL
PQRRSPSPGA TRLARGGLGE GEYAQRLQAL RQRLLRGGPE DGKVSGLRGP LLESLGGRAR
DPRMARAASS EAAPHHQPPL ENRGLQKSSS FSQGEAEPRG RHRRAGAPLE IPVARLGARR
LQESPSLSAL SEAQPSSPAR PSAPKPSTPK SAEPSATTPS DAPQPPAPQP AQDKAPEPRP
EPVRASKPAP PPQALQTLAL PLTPYAQIIQ SLQLSGHAQG PSQGPAAPPS EPKPHAAVFA
RVASPPPGAP EKRVPSAGGP PVLAEKARVP TVPPRPGSSL SSSIENLESE AVFEAKFKRS
RESPLSLGLR LLSRSRSEER GPFRGAEEED GIYRPSPAGT PLELVRRPER SRSVQDLRAV
GEPGLVRRLS LSLSQRLRRT PPAQRHPAWE ARGGDGESSE GGSSARGSPV LAMRRRLSFT
LERLSSRLQR SGSSEDSGGA SGRSTPLFGR LRRATSEGES LRRLGLPHNQ LAAQAGATTP
SAESLGSEAS ATSGSSAPGE SRSRLRWGFS RPRKDKGLSP PNLSASVQEE LGHQYVRSES
DFPPVFHIKL KDQVLLEGEA ATLLCLPAAC PAPHISWMKD KKSLRSEPSV IIVSCKDGRQ
LLSIPRAGKR HAGLYECSAT NVLGSITSSC TVAVARVPGK LAPPEVPQTY QDTALVLWKP
GDSRAPCTYT LERRVDGESV WHPVSSGIPD CYYNVTHLPV GVTVRFRVAC ANRAGQGPFS
NSSEKVFVRG TQDSSAVPSA AHQEAPVTSR PARARPPDSP TSLAPPLAPA APTPPSVTVS
PSSPPTPPSQ ALSSLKAVGP PPQTPPRRHR GLQAARPAEP TLPSTHVTPS EPKPFVLDTG
TPIPASTPQG VKPVSSSTPV YVVTSFVSAP PAPEPPAPEP PPEPTKVTVQ SLSPAKEVVS
SPGSSPRSSP RPEGTTLRQG PPQKPYTFLE EKARGRFGVV RACRENATGR TFVAKIVPYA
AEGKRRVLQE YEVLRTLHHE RIMSLHEAYI TPRYLVLIAE SCGNRELLCG LSDRFRYSED
DVATYMVQLL QGLDYLHGHH VLHLDIKPDN LLLAPDNALK IVDFGSAQPY NPQALRPLGH
RTGTLEFMAP EMVKGEPIGS ATDIWGAGVL TYIMLSGRSP FYEPDPQETE ARIVGGRFDA
FQLYPNTSQS ATLFLRKVLS VHPWSRPSLQ DCLAHPWLQD AYLMKLRRQT LTFTTNRLKE
FLGEQRRRRA EAATRHKVLL RSYPGGP*

mutated AA sequence

MQKARGTRGE DAGTRAPPSP GVPPKRAKVG AGGGAPVAVA GAPVFLRPLK NAAVCAGSDV
RLRVVVSGTP QPSLRWFRDG QLLPAPAPEP SCLWLRRCGA QDAGVYSCMA QNERGRASCE
AVLTVLEVGD SETAEDDISD VQGTQRLELR DDGAFSTPTG GSDTLVGTSL DTPPTSVTGT
SEEQVSWWGS GQTVLEQEAG SGGGTRRLPG SPRQAQATGA GPRHLGVEPL VRASRANLVG
ASWGSEDSLS VASDLYGSAF SLYRGRALSI HVSVPQSGLR REEPDLQPQL ASEAPRRPAQ
PPPSKSALLP PPSPRVGKRS PPGPPAQPAA TPTSPHRRTQ EPVLPEDTTT EEKRGKKSKS
SGPSLAGTAE SRPQTPLSEA SGRLSALGRS PRLVRAGSRI LDKLQFFEER RRSLERSDSP
PAPLRPWVPL RKARSLEQPK SERGAPWGTP GASQEELRAP GSVAERRRLF QQKAASLDER
TRQRSPASDL ELRFAQELGR IRRSTSREEL VRSHESLRAT LQRAPSPREP GEPPLFSRPS
TPKTSRAVSP AAAQPPSPSS AEKPGDEPGR PRSRGPAGRT EPGEGPQQEV RRRDQFPLTR
SRAIQECRSP VPPPAADPPE ARTKAPPGRK REPPAQAVRF LPWATPGLEG AAVPQTLEKN
RAGPEAEKRL RRGPEEDGPW GPWDRRGARS QGKGRRARPT SPELESSDDS YVSAGEEPLE
APVFEIPLQN VVVAPGADVL LKCIITANPP PQVSWHKDGS ALRSEGRLLL RAEGERHTLL
LREARAADAG SYMATATNEL GQATCAASLT VRPGGSTSPF SSPITSDEEY LSPPEEFPEP
GETWPRTPTM KPSPSQNRRS SDTGSKAPPT FKVSLMDQSV REGQDVIMSI RVQGEPKPVV
SWLRNRQPVR PDQRRFAEEA EGGLCRLRIL AAERGDAGFY TCKAVNEYGA RQCEARLEVR
AHPESRSLAV LAPLQDVDVG AGEMALFECL VAGPTDVEVD WLCRGRLLQP ALLKCKMHFD
GRKCKLLLTS VHEDDSGVYT CKLSTAKDEL TCSARLTVRP SLAPLFTRLL EDVEVLEGRA
ARFDCKISGT PPPVVTWTHF GCPMEESENL RLRQDGGLHS LHIAHVGSED EGLYAVSAVN
THGQAHCSAQ LYVEEPRTAA SGPSSKLEKM PSIPEEPEQG ELERLSIPDF LRPLQDLEVG
LAKEAMLECQ VTGLPYPTIS WFHNGHRIQS SDDRRMTQYR DVHRLVFPAV GPQHAGVYKS
VIANKLGKAA CYAHLYVTDV VPGPPDGAPQ VVAVTGRMVT LTWNPPRSLD MAIDPDSLTY
TVQHQVLGSD QWTALVTGLR EPGWAATGLR KGVQHIFRVL STTVKSSSKP SPPSEPVQLL
EHGPTLEEAP AMLDKPDIVY VVEGQPASVT VTFNHVEAQV VWRSCRGALL EARAGVYELS
QPDDDQYCLR ICRVSRRDMG ALTCTARNRH GTQTCSVTLE LAEAPRFESI MEDVEVGAGE
TARFAVVVEG KPLPDIMWYK DEVLLTESSH VSFVYEENEC SLVVLSTGAQ DGGVYTCTAQ
NLAGEVSCKA ELAVHSAQTA MEVEGVGEDE DHRGRRLSDF YDIHQEIGRG AFSYLRRIVE
RSSGLEFAAK FIPSQAKPKA SARREARLLA RLQHDCVLYF HEAFERRRGL VIVTELCTEE
LLERIARKPT VCESEIRAYM RQVLEGIHYL HQSHVLHLDV KPENLLVWDG AAGEQQVRIC
DFGNAQELTP GEPQYCQYGT PEFVAPEIVN QSPVSGVTDI WPVGVVAFLC LTGISPFVGE
NDRTTLMNIR NYNVAFEETT FLSLSREARG FLIKVLVQDR LRPTAEETLE HPWFKTQAKG
AEVSTDHLKL FLSRRRWQRS QISYKCHLVL RPIPELLRAP PERVWVTMPR RPPPSGGLSS
SSDSEEEELE ELPSVPRPLQ PEFSGSRVSL TDIPTEDEAL GTPETGAATP MDWQEQGRAP
SQDQEAPSPE ALPSPGQEPA AGASPRRGEL RRGSSAESAL PRAGPRELGR GLHKAASVEL
PQRRSPSPGA TRLARGGLGE GEYAQRLQAL RQRLLRGGPE DGKVSGLRGP LLESLGGRAR
DPRMARAASS EAAPHHQPPL ENRGLQKSSS FSQGEAEPRG RHRRAGAPLE IPVARLGARR
LQESPSLSAL SEAQPSSPAR PSAPKPSTPK SAEPSATTPS DAPQPPAPQP AQDKAPEPRP
EPVRASKPAP PPQALQTLAL PLTPYAQIIQ SLQLSGHAQG PSQGPAAPPS EPKPHAAVFA
RVASPPPGAP EKRVPSAGGP PVLAEKARVP TVPPRPGSSL SSSIENLESE AVFEAKFKRS
RESPLSLGLR LLSRSRSEER GPFRGAEEED GIYRPSPAGT PLELVRRPER SRSVQDLRAV
GEPGLVRRLS LSLSQRLRRT PPAQRHPAWE ARGGDGESSE GGSSARGSPV LAMRRRLSFT
LERLSSRLQR SGSSEDSGGA SGRSTPLFGR LRRATSEGES LRRLGLPHNQ LAAQAGATTP
SAESLGSEAS ATSGSSAPGE SRSRLRWGFS RPRKDKGLSP PNLSASVQEE LGHQYVRSES
DFPPVFHIKL KDQVLLEGEA ATLLCLPAAC PAPHISWMKD KKSLRSEPSV IIVSCKDGRQ
LLSIPRAGKR HAGLYECSAT NVLGSITSSC TVAVARVPGK LAPPEVPQTY QDTALVLWKP
GDSRAPCTYT LERRVDGESV WHPVSSGIPD CYYNVTHLPV GVTVRFRVAC ANRAGQGPFS
NSSEKVFVRG TQDSSAVPSA AHQEAPVTSR PARARPPDSP TSLAPPLAPA APTPPSVTVS
PSSPPTPPSQ ALSSLKAVGP PPQTPPRRHR GLQAARPAEP TLPSTHVTPS EPKPFVLDTG
TPIPASTPQG VKPVSSSTPV YVVTSFVSAP PAPEPPAPEP PPEPTKVTVQ SLSPAKEVVS
SPGSSPRSSP RPEGTTLRQG PPQKPYTFLE EKARGRFGVV RACRENATGR TFVAKIVPYA
AEGKRRVLQE YEVLRTLHHE RIMSLHEAYI TPRYLVLIAE SCGNRELLCG LSDRFRYSED
DVATYMVQLL QGLDYLHGRH VLHLDIKPDN LLLAPDNALK IVDFGSAQPY NPQALRPLGH
RTGTLEFMAP EMVKGEPIGS ATDIWGAGVL TYIMLSGRSP FYEPDPQETE ARIVGGRFDA
FQLYPNTSQS ATLFLRKVLS VHPWSRPSLQ DCLAHPWLQD AYLMKLRRQT LTFTTNRLKE
FLGEQRRRRA EAATRHKVLL RSYPGGP*

speed

1.39 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
back to results table

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems