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: ENST00000562955
MT speed 0 s - this script 2.870316 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
SZT2	polymorphism_automatic	0.00481246512388001	simple_aae				P446S	single base exchange	rs2782643		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.99518753487612 (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)

chr1:43886494C>TN/A show variant in all transcripts IGV

HGNC symbol

SZT2

Ensembl transcript ID

ENST00000562955

Genbank transcript ID

NM_015284

UniProt peptide

Q5T011

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1336C>T
cDNA.1336C>T
g.30942C>T

AA changes

P446S Score: 74 explain score(s)

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

446

frameshift

known variant

Reference ID: rs2782643

database	homozygous (T/T)	heterozygous	allele carriers
1000G	152	688	840
ExAC	6698	19371	26069

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-1.289	0.52
	1.583	0.961
(flanking)	4.098	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

446

mutated

not conserved

446

Ptroglodytes

no alignment

ENSPTRG00000039671

n/a

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

no homologue

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000076578

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
446	446	CONFLICT	P -> S (in Ref. 5; BAC85157).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

10128 / 10128

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

3376 / 3376

position of stopcodon in wt / mu cDNA

10128 / 10128

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

1 / 1

chromosome

strand

last intron/exon boundary

9985

theoretical NMD boundary in CDS

9934

length of CDS

10128

coding sequence (CDS) position

1336

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

1336

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

30942

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

43886494

original gDNA sequence snippet

TTGAGTATGTGGCTATGGCACCCTGGCCCCTGGAGCCTGAG

altered gDNA sequence snippet

TTGAGTATGTGGCTATGGCATCCTGGCCCCTGGAGCCTGAG

original cDNA sequence snippet

TTGAGTATGTGGCTATGGCACCCTGGCCCCTGGAGCCTGAG

altered cDNA sequence snippet

TTGAGTATGTGGCTATGGCATCCTGGCCCCTGGAGCCTGAG

wildtype AA sequence

MASERPEPEV EEAGQVFLLM KKDYRISRNV RLAWFLSHLH QTVQATPQEM LLQSEQELEV
LSVLPPGWQP DEPVVPRPFL LVPSTRVTFL AWQYRFVIEL DLSPSTGIVD DSTGEILFDE
VFHALSRCLG GLLRPFRVPG SCIDFQPEIY VTIQAYSSII GLQSHQVLVQ GCLLDPSQRE
VFLQQIYEQL CLFEDKVATM LQQQYDPQSQ AEDQSPDSGD LLGRKVGVSM VTADLGLVSM
IRQGILALQL LPSNSSAGII VITDGVTSVP DVAVCETLLN QLRSGTVACS FVQVGGVYSY
DCSFGHVPNV ELMKFIAMAT FGSYLSTCPE PEPGNLGLTV YHRAFLLYSF LRSGEALNPE
YYCGSQHRLF NEHLVSASSN PALALRRKKH TEKEVPADLV STVSVRLREG YSVREVTLAK
GGSQLEVKLV LLWKHNMRIE YVAMAPWPLE PEGPRVTRVE VTMEGGYDIL HDVSCALRQP
IRSLYRTHVI RRFWNTLQSI NQTDQMLAHL QSFSSVPEHF TLPDSTKSGV PLFYIPPGST
TPVLSLQPSG SDSSHAQFAA YWKPVLSMDA NSWQRWLHMH RLVLILEHDT PIPKHLHTPG
SNGRYSTIQC RISHSSLTSL LRDWSSFVLV EGYSYVKLLS SAPDQPPNSF YMVRIISKAP
CMVLRLGFPI GTPAPARHKI VSGLREEILR LRFPHRVQSK EPTPKVKRKG LGGAGGGSSP
SKSPPVLGPQ QALSDRPCLV VLHKPLDKLL IRYEKLPLDY RAPFLLTLEP PGPLPLVSGR
SASSSLASLS RYLYHQRWLW SVPSGLAPAL PLSAIAQLLS ILTEVRLSEG FHFACSGEGI
INMVLELPIQ NEPPGQAAAE EKHTCVVQYI LFPPHSTSTK DSFSTDDDND VEVEALEGDS
ELNLVTEVWV EPQYGRVGPG PGIWKHLQDL TYSEIPQALH PRDAACIGSM LSFEYLIQLC
QSKEWGPLPP EPRVSDGLDQ GGDTCVHEIP FHFDLMGLLP QCQQLQMFFL LLARGAEGPL
LGVHGIPKEQ AVGSTQATGD SAFTSLSVGL PETLKPLISA QPPQWRCYAR LVNPQHVFLT
FLPATFSDVQ RLAACGLEGP PQEETKPKFG DWSGAPSLKD LGGTGIKATK SHVPVLSVTL
ASDNAQNQGE LSPPFRRDLQ AYAGRQASQT ESADGPRTRC PVYIYSCSLE ALREQMVGMQ
PPQAPRDLIF RTQFLDHPSP SSAWMEPRYK EAANHCALLQ EHAQRCYVRG LFRSLQQAQS
VTSQDLLTAV DACEELLQEI DITPFLLALC GHTWGLPHAP PSPGPLSPGP FSSSMEEGAE
PRERAILASE SSIETEDLSE PEFQSTRVPG IPDPGPEISL TDVCQLRGEA HGALHSVIQE
KFLEISRLHF RTVPSNPHYF FYCPPSSRRE DEGPRDTVDR KISDLEFSEA ELMGEEGDTS
ACCVVTESDP ELEVEYRESR ESDLGPAGLD SASLSDVDTV NPDEDSFSIL GGDSPTGPES
FLHDLPPLFL HLTCSVRLRG QHSSVPVCSL PTCLGQVLSS LEGPPVGGRV PLRDLSVTLD
VFMLTLPLEV ELPTASDPQH HRSTSESSAS FPRSPGQPSS LRSDDGLGPP LPPPEEERHP
GLSNLATPHR LAIETTMNEI RWLLEDEMVG ALRRGGIPQS PALHRAAAHI HSSPGRSTCL
RQTLPLSFVF GPERSLTQFK EEFRRLHLPG HVLLEDPDSG FFFVAAGQQP GGSHGEPSSA
AWAWHSHEDR AEGIEGETLT ASPQAPGSPE DSEGVPLISL PRVPQGGSQP GPSRGLSLMS
SQGSVDSDHL GYDGGSSGSD SEGPNDTLGE KAPFTLRTPP GPAPPQPSLS GLPGPCLPDF
WLIVRVLQDR VEVYAHARSL IREDGGPGTE CRHLQQLLVR RVGEICREVN QRLLLQDLHD
SHVCNSLLVA ESEEDLWRSE TPFHSRQRAP LPSDDYAADE SCAPRGYLAA TMQFVPGHFS
CDVVWGTVIR VHSRLKMGPS MGVSRAIQAL RSVLNAFSVV NRKNMFVYQE RATKAVYYLR
LLETSCSDRP WKGDALPPSL ALSRSQEPIY SEEASGPRSP LDMVSSRSSD AARPVGQVDR
HIQLLVHGVG QAGPEITDEL VRVLCRRLDE ATLDVITVML VRNCKLTPAD VEFIQPPGSL
PSEVLHLALP TSCRPWLPAL AWYLRQNLLI FLHSPKYTDS NSRNHFQHPL PPQGGLPDLD
IYLYNKPGGQ GTGGKGVACI TLAFVDEGGA PLSLALWPPS SPGPPDPLRE EEFEQLTQVI
RCPVVVDSSS AQNGAPRLRL DVWEKGNISI VQLEEKLRGA ARQALADAII ELQLLPASLC
TEDTPTGSLR NGSLETKSSA GRASTFPPAP VPGEPVTPPS KAGRRSFWDM LSKTECGDLG
SPKTTDDIVL DRPEDTRGRR RHKTESVRTP GGAERAPGSD SGAQRQKRRT TQLEEGEVGT
LHPVFARVAQ RWMEFMVQIG CASVSRSSAH MVSRFLLPSI LSEFTALVTS MAGDTSVRIF
EQHLGSEPEI FGPCSPGQLG PSPRPAAERH LLLLGRNFLQ WRRPTQQAAK AMQRFEPGGD
GSSGRNAPRQ RLLLLEVVDK KLQLLTYNWA PDLGAALGRA LVRLVQWQNA RAHLIFCLLS
QKLGLFHHYG QLDFPVRDEK EPNPFLLPTM EVETLIRSAS PPLSREQGRL SGSSRGGGPL
PLDTFPFDEA LRDITAARPS SVLGPVPRPP DPVTYHGQQF LEIKMAERRE LERQMKMENL
FVTWQQRSTP ATMPISAGEL ETLKQSSRLV HYCATAMLFD PAAWLHGPPE TSGPPDGQRR
HRPESGSGSR EAPTSCESLD VSPPGAREEP WLKELSLAFL QQYVQYLQSI GFVLVPLRPP
SPARSTSRPR AMAILGTEGR GSFSCPKTKT DGSPKSTSSP VTTYHLQRAL PGGIILMELA
FQGCYFCVKQ FALECSRIPM GQAVNSQLSM LFTEECDKVR DLMHVHSFSY DFHLRLVHQH
VLGAHLVLRH GYHLTTFLRH FLAHHPDGPH FGRNHIYQGT LELPTPLIAA HQLYNYVADH
ASSYHMKPLR MARPGGPEHN EYALVSAWHS SGSYLDSEGL RHQDDFDVSL LVCHCAAPFE
EQGEAERHVL RLQFFVVLTS QRELFPRLTA DMRRFRKPPR LPPEPEAPGS SAGSPGEASG
LILAPGPAPL FPPLAAEVGM ARARLAQLVR LAGGHCRRDT LWKRLFLLEP PGPDRLRLGG
RLALAELEEL LEAVHAKSIG DIDPQLDCFL SMTVSWYQSL IKVLLSRFPQ SCRHFQSPDL
GTQYLVVLNQ KFTDCFVLVF LDSHLGKTSL TVVFREPFPV QPQDSESPPA QLVSTYHHLE
SVINTACFTL WTRLL*

mutated AA sequence

MASERPEPEV EEAGQVFLLM KKDYRISRNV RLAWFLSHLH QTVQATPQEM LLQSEQELEV
LSVLPPGWQP DEPVVPRPFL LVPSTRVTFL AWQYRFVIEL DLSPSTGIVD DSTGEILFDE
VFHALSRCLG GLLRPFRVPG SCIDFQPEIY VTIQAYSSII GLQSHQVLVQ GCLLDPSQRE
VFLQQIYEQL CLFEDKVATM LQQQYDPQSQ AEDQSPDSGD LLGRKVGVSM VTADLGLVSM
IRQGILALQL LPSNSSAGII VITDGVTSVP DVAVCETLLN QLRSGTVACS FVQVGGVYSY
DCSFGHVPNV ELMKFIAMAT FGSYLSTCPE PEPGNLGLTV YHRAFLLYSF LRSGEALNPE
YYCGSQHRLF NEHLVSASSN PALALRRKKH TEKEVPADLV STVSVRLREG YSVREVTLAK
GGSQLEVKLV LLWKHNMRIE YVAMASWPLE PEGPRVTRVE VTMEGGYDIL HDVSCALRQP
IRSLYRTHVI RRFWNTLQSI NQTDQMLAHL QSFSSVPEHF TLPDSTKSGV PLFYIPPGST
TPVLSLQPSG SDSSHAQFAA YWKPVLSMDA NSWQRWLHMH RLVLILEHDT PIPKHLHTPG
SNGRYSTIQC RISHSSLTSL LRDWSSFVLV EGYSYVKLLS SAPDQPPNSF YMVRIISKAP
CMVLRLGFPI GTPAPARHKI VSGLREEILR LRFPHRVQSK EPTPKVKRKG LGGAGGGSSP
SKSPPVLGPQ QALSDRPCLV VLHKPLDKLL IRYEKLPLDY RAPFLLTLEP PGPLPLVSGR
SASSSLASLS RYLYHQRWLW SVPSGLAPAL PLSAIAQLLS ILTEVRLSEG FHFACSGEGI
INMVLELPIQ NEPPGQAAAE EKHTCVVQYI LFPPHSTSTK DSFSTDDDND VEVEALEGDS
ELNLVTEVWV EPQYGRVGPG PGIWKHLQDL TYSEIPQALH PRDAACIGSM LSFEYLIQLC
QSKEWGPLPP EPRVSDGLDQ GGDTCVHEIP FHFDLMGLLP QCQQLQMFFL LLARGAEGPL
LGVHGIPKEQ AVGSTQATGD SAFTSLSVGL PETLKPLISA QPPQWRCYAR LVNPQHVFLT
FLPATFSDVQ RLAACGLEGP PQEETKPKFG DWSGAPSLKD LGGTGIKATK SHVPVLSVTL
ASDNAQNQGE LSPPFRRDLQ AYAGRQASQT ESADGPRTRC PVYIYSCSLE ALREQMVGMQ
PPQAPRDLIF RTQFLDHPSP SSAWMEPRYK EAANHCALLQ EHAQRCYVRG LFRSLQQAQS
VTSQDLLTAV DACEELLQEI DITPFLLALC GHTWGLPHAP PSPGPLSPGP FSSSMEEGAE
PRERAILASE SSIETEDLSE PEFQSTRVPG IPDPGPEISL TDVCQLRGEA HGALHSVIQE
KFLEISRLHF RTVPSNPHYF FYCPPSSRRE DEGPRDTVDR KISDLEFSEA ELMGEEGDTS
ACCVVTESDP ELEVEYRESR ESDLGPAGLD SASLSDVDTV NPDEDSFSIL GGDSPTGPES
FLHDLPPLFL HLTCSVRLRG QHSSVPVCSL PTCLGQVLSS LEGPPVGGRV PLRDLSVTLD
VFMLTLPLEV ELPTASDPQH HRSTSESSAS FPRSPGQPSS LRSDDGLGPP LPPPEEERHP
GLSNLATPHR LAIETTMNEI RWLLEDEMVG ALRRGGIPQS PALHRAAAHI HSSPGRSTCL
RQTLPLSFVF GPERSLTQFK EEFRRLHLPG HVLLEDPDSG FFFVAAGQQP GGSHGEPSSA
AWAWHSHEDR AEGIEGETLT ASPQAPGSPE DSEGVPLISL PRVPQGGSQP GPSRGLSLMS
SQGSVDSDHL GYDGGSSGSD SEGPNDTLGE KAPFTLRTPP GPAPPQPSLS GLPGPCLPDF
WLIVRVLQDR VEVYAHARSL IREDGGPGTE CRHLQQLLVR RVGEICREVN QRLLLQDLHD
SHVCNSLLVA ESEEDLWRSE TPFHSRQRAP LPSDDYAADE SCAPRGYLAA TMQFVPGHFS
CDVVWGTVIR VHSRLKMGPS MGVSRAIQAL RSVLNAFSVV NRKNMFVYQE RATKAVYYLR
LLETSCSDRP WKGDALPPSL ALSRSQEPIY SEEASGPRSP LDMVSSRSSD AARPVGQVDR
HIQLLVHGVG QAGPEITDEL VRVLCRRLDE ATLDVITVML VRNCKLTPAD VEFIQPPGSL
PSEVLHLALP TSCRPWLPAL AWYLRQNLLI FLHSPKYTDS NSRNHFQHPL PPQGGLPDLD
IYLYNKPGGQ GTGGKGVACI TLAFVDEGGA PLSLALWPPS SPGPPDPLRE EEFEQLTQVI
RCPVVVDSSS AQNGAPRLRL DVWEKGNISI VQLEEKLRGA ARQALADAII ELQLLPASLC
TEDTPTGSLR NGSLETKSSA GRASTFPPAP VPGEPVTPPS KAGRRSFWDM LSKTECGDLG
SPKTTDDIVL DRPEDTRGRR RHKTESVRTP GGAERAPGSD SGAQRQKRRT TQLEEGEVGT
LHPVFARVAQ RWMEFMVQIG CASVSRSSAH MVSRFLLPSI LSEFTALVTS MAGDTSVRIF
EQHLGSEPEI FGPCSPGQLG PSPRPAAERH LLLLGRNFLQ WRRPTQQAAK AMQRFEPGGD
GSSGRNAPRQ RLLLLEVVDK KLQLLTYNWA PDLGAALGRA LVRLVQWQNA RAHLIFCLLS
QKLGLFHHYG QLDFPVRDEK EPNPFLLPTM EVETLIRSAS PPLSREQGRL SGSSRGGGPL
PLDTFPFDEA LRDITAARPS SVLGPVPRPP DPVTYHGQQF LEIKMAERRE LERQMKMENL
FVTWQQRSTP ATMPISAGEL ETLKQSSRLV HYCATAMLFD PAAWLHGPPE TSGPPDGQRR
HRPESGSGSR EAPTSCESLD VSPPGAREEP WLKELSLAFL QQYVQYLQSI GFVLVPLRPP
SPARSTSRPR AMAILGTEGR GSFSCPKTKT DGSPKSTSSP VTTYHLQRAL PGGIILMELA
FQGCYFCVKQ FALECSRIPM GQAVNSQLSM LFTEECDKVR DLMHVHSFSY DFHLRLVHQH
VLGAHLVLRH GYHLTTFLRH FLAHHPDGPH FGRNHIYQGT LELPTPLIAA HQLYNYVADH
ASSYHMKPLR MARPGGPEHN EYALVSAWHS SGSYLDSEGL RHQDDFDVSL LVCHCAAPFE
EQGEAERHVL RLQFFVVLTS QRELFPRLTA DMRRFRKPPR LPPEPEAPGS SAGSPGEASG
LILAPGPAPL FPPLAAEVGM ARARLAQLVR LAGGHCRRDT LWKRLFLLEP PGPDRLRLGG
RLALAELEEL LEAVHAKSIG DIDPQLDCFL SMTVSWYQSL IKVLLSRFPQ SCRHFQSPDL
GTQYLVVLNQ KFTDCFVLVF LDSHLGKTSL TVVFREPFPV QPQDSESPPA QLVSTYHHLE
SVINTACFTL WTRLL*

speed

0.86 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