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: ENST00000359568
MT speed 0 s - this script 2.890239 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PCNT	polymorphism_automatic	4.9960036108132e-15	simple_aae		affected		W2239R	single base exchange	rs35346764		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999995 (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)

chr21:47836547T>CN/A show variant in all transcripts IGV

HGNC symbol

PCNT

Ensembl transcript ID

ENST00000359568

Genbank transcript ID

NM_006031

UniProt peptide

O95613

alteration type

single base exchange

alteration region

CDS

DNA changes

c.6715T>C
cDNA.6822T>C
g.92512T>C

AA changes

W2239R Score: 101 explain score(s)

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

2239

frameshift

known variant

Reference ID: rs35346764

database	homozygous (C/C)	heterozygous	allele carriers
1000G	173	562	735
ExAC	1182	9011	10193

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.35	0
	0.033	0
(flanking)	-2.475	0

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	92507	wt: 0.23 / mu: 0.37	wt: CCTGGAGCCCTGGCC mu: CCTGGAGCCCCGGCC	TGGA\|gccc
Donor increased	92513	wt: 0.44 / mu: 0.63	wt: GCCCTGGCCCAGCCT mu: GCCCCGGCCCAGCCT	CCTG\|gccc

distance from splice site

207

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

2239

mutated

not conserved

2239

Ptroglodytes

not conserved

ENSPTRG00000014023

2073

Mmulatta

not conserved

ENSMMUG00000012914

2220

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000001151

1875

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no alignment

C18C4.5

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
2327	2327	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
2536	3086	COILED	Potential.	might get lost (downstream of altered splice site)
2900	2900	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
2963	2963	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
2983	3246	REGION	Interaction with NEK2.	might get lost (downstream of altered splice site)
3136	3136	CONFLICT	Y -> S (in Ref. 1; AAD10838).	might get lost (downstream of altered splice site)
3195	3208	REGION	Calmodulin-binding.	might get lost (downstream of altered splice site)
3196	3197	MUTAGEN	FR->AA: Decrease in calmodulin binding.	might get lost (downstream of altered splice site)
3203	3203	MUTAGEN	V->A: Decrease in calmodulin binding.	might get lost (downstream of altered splice site)
3208	3209	MUTAGEN	RL->AA: Decrease in calmodulin binding.	might get lost (downstream of altered splice site)
3274	3274	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
3300	3300	CONFLICT	E -> G (in Ref. 1; AAD10838).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

10011 / 10011

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

3337 / 3337

position of stopcodon in wt / mu cDNA

10118 / 10118

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

108 / 108

chromosome

strand

last intron/exon boundary

10075

theoretical NMD boundary in CDS

9917

length of CDS

10011

coding sequence (CDS) position

6715

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

6822

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

92512

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

47836547

original gDNA sequence snippet

AGGACTGGACCCTGGAGCCCTGGCCCAGCCTCCCCGTGACA

altered gDNA sequence snippet

AGGACTGGACCCTGGAGCCCCGGCCCAGCCTCCCCGTGACA

original cDNA sequence snippet

AGGACTGGACCCTGGAGCCCTGGCCCAGCCTCCCCGTGACA

altered cDNA sequence snippet

AGGACTGGACCCTGGAGCCCCGGCCCAGCCTCCCCGTGACA

wildtype AA sequence

MEVEQEQRRR KVEAGRTKLA HFRQRKTKGD SSHSEKKTAK RKGSAVDASV QEESPVTKED
SALCGGGDIC KSTSCDDTPD GAGGAFAAQP EDCDGEKRED LEQLQQKQVN DHPPEQCGMF
TVSDHPPEQH GMFTVGDHPP EQRGMFTVSD HPPEQHGMFT VSDHPPEQRG MFTISDHQPE
QRGMFTVSDH TPEQRGIFTI SDHPAEQRGM FTKECEQECE LAITDLESGR EDEAGLHQSQ
AVHGLELEAL RLSLSNMHTA QLELTQANLQ KEKETALTEL REMLNSRRAQ ELALLQSRQQ
HELELLREQH AREKEEVVLR CGQEAAELKE KLQSEMEKNA QIVKTLKEDW ESEKDLCLEN
LRKELSAKHQ SEMEDLQNQF QKELAEQRAE LEKIFQDKNQ AERALRNLES HHQAAIEKLR
EDLQSEHGRC LEDLEFKFKE SEKEKQLELE NLQASYEDLK AQSQEEIRRL WSQLDSARTS
RQELSELHEQ LLARTSRVED LEQLKQREKT QHESELEQLR IYFEKKLRDA EKTYQEDLTL
LQQRLQGARE DALLDSVEVG LSCVGLEEKP EKGRKDHVDE LEPERHKESL PRFQAELEES
HRHQLEALES PLCIQHEGHV SDRCCVETSA LGHEWRLEPS EGHSQELPWV HLQGVQDGDL
EADTERAARV LGLETEHKVQ LSLLQTELKE EIELLKIENR NLYGKLQHET RLKDDLEKVK
HNLIEDHQKE LNNAKQKTEL MKQEFQRKET DWKVMKEELQ REAEEKLTLM LLELREKAES
EKQTIINKFE LREAEMRQLQ DQQAAQILDL ERSLTEQQGR LQQLEQDLTS DDALHCSQCG
REPPTAQDGE LAALHVKEDC ALQLMLARSR FLEERKEITE KFSAEQDAFL QEAQEQHARE
LQLLQERHQQ QLLSVTAELE ARHQAALGEL TASLESKQGA LLAARVAELQ TKHAADLGAL
ETRHLSSLDS LESCYLSEFQ TIREEHRQAL ELLRADFEEQ LWKKDSLHQT ILTQELEKLK
RKHEGELQSV RDHLRTEVST ELAGTVAHEL QGVHQGEFGS EKKTALHEKE ETLRLQSAQA
QPFHQEEKES LSLQLQKKNH QVQQLKDQVL SLSHEIEECR SELEVLQQRR ERENREGANL
LSMLKADVNL SHSERGALQD ALRRLLGLFG ETLRAAVTLR SRIGERVGLC LDDAGAGLAL
STAPALEETW SDVALPELDR TLSECAEMSS VAEISSHMRE SFLMSPESVR ECEQPIRRVF
QSLSLAVDGL MEMALDSSRQ LEEARQIHSR FEKEFSFKNE ETAQVVRKHQ ELLECLKEES
AAKAELALEL HKTQGTLEGF KVETADLKEV LAGKEDSEHR LVLELESLRR QLQQAAQEQA
ALREECTRLW SRGEATATDA EAREAALRKE VEDLTKEQSE TRKQAEKDRS ALLSQMKILE
SELEEQLSQH RGCAKQAEAV TALEQQVASL DKHLRNQRQF MDEQAAEREH EREEFQQEIQ
RLEGQLRQAA KPQPWGPRDS QQAPLDGEVE LLQQKLREKL DEFNELAIQK ESADRQVLMQ
EEEIKRLEEM NINIRKKVAQ LQEEVEKQKN IVKGLEQDKE VLKKQQMSSL LLASTLQSTL
DAGRCPEPPS GSPPEGPEIQ LEVTQRALLR RESEVLDLKE QLEKMKGDLE SKNEEILHLN
LKLDMQNSQT AVSLRELEEE NTSLKVIYTR SSEIEELKAT IENLQENQKR LQKEKAEEIE
QLHEVIEKLQ HELSLMGPVV HEVSDSQAGS LQSELLCSQA GGPRGQALQG ELEAALEAKE
ALSRLLADQE RRHSQALEAL QQRLQGAEEA AELQLAELER NVALREAEVE DMASRIQEFE
AALKAKEATI AERNLEIDAL NQRKAAHSAE LEAVLLALAR IRRALEQQPL AAGAAPPELQ
WLRAQCARLS RQLQVLHQRF LRCQVELDRR QARRATAHTR VPGAHPQPRM DGGAKAQVTG
DVEASHDAAL EPVVPDPQGD LQPVLVTLKD APLCKQEGVM SVLTVCQRQL QSELLLVKNE
MRLSLEDGGK GKEKVLEDCQ LPKVDLVAQV KQLQEKLNRL LYSMTFQNVD AADTKSLWPM
ASAHLLESSW SDDSCDGEEP DISPHIDTCD ANTATGGVTD VIKNQAIDAC DANTTPGGVT
DVIKNWDSLI PDEMPDSPIQ EKSECQDMSL SSPTSVLGGS RHQSHTAEAG PRKSPVGMLD
LSSWSSPEVL RKDWTLEPWP SLPVTPHSGA LSLCSADTSL GDRADTSLPQ TQGPGLLCSP
GVSAAALALQ WAESPPADDH HVQRTAVEKD VEDFITTSFD SQETLSSPPP GLEGKADRSE
KSDGSGFGAR LSPGSGGPEA QTAGPVTPAS ISGRFQPLPE AMKEKEVRPK HVKALLQMVR
DESHQILALS EGLAPPSGEP HPPRKEDEIQ DISLHGGKTQ EVPTACPDWR GDLLQVVQEA
FEKEQEMQGV ELQPRLSGSD LGGHSSLLER LEKIIREQGD LQEKSLEHLR LPDRSSLLSE
IQALRAQLRM THLQNQEKLQ HLRTALTSAE ARGSQQEHQL RRQVELLAYK VEQEKCIAGD
LQKTLSEEQE KANSVQKLLA AEQTVVRDLK SDLCESRQKS EQLSRSLCEV QQEVLQLRSM
LSSKENELKA ALQELESEQG KGRALQSQLE EEQLRHLQRE SQSAKALEEL RASLETQRAQ
SSRLCVALKH EQTAKDNLQK ELRIEHSRCE ALLAQERSQL SELQKDLAAE KSRTLELSEA
LRHERLLTEQ LSQRTQEACV HQDTQAHHAL LQKLKEEKSR VVDLQAMLEK VQQQALHSQQ
QLEAEAQKHC EALRREKEVS ATLKSTVEAL HTQKRELRCS LEREREKPAW LQAELEQSHP
RLKEQEGRKA ARRSAEARQS PAAAEQWRKW QRDKEKLREL ELQRQRDLHK IKQLQQTVRD
LESKDEVPGS RLHLGSARRA AGSDADHLRE QQRELEAMRQ RLLSAARLLT SFTSQAVDRT
VNDWTSSNEK AVMSLLHTLE ELKSDLSRPT SSQKKMAAEL QFQFVDVLLK DNVSLTKALS
TVTQEKLELS RAVSKLEKLL KHHLQKGCSP SRSERSAWKP DETAPQSSLR RPDPGRLPPA
ASEEAHTSNV KMEKLYLHYL RAESFRKALI YQKKYLLLLI GGFQDSEQET LSMIAHLGVF
PSKAERKITS RPFTRFRTAV RVVIAILRLR FLVKKWQEVD RKGALAQGKA PRPGPRARQP
QSPPRTRESP PTRDVPSGHT RDPARGRRLA AAASPHSGGR ATPSPNSRLE RSLTASQDPE
HSLTEYIHHL EVIQQRLGGV LPDSTSKKSC HPMIKQ*

mutated AA sequence

MEVEQEQRRR KVEAGRTKLA HFRQRKTKGD SSHSEKKTAK RKGSAVDASV QEESPVTKED
SALCGGGDIC KSTSCDDTPD GAGGAFAAQP EDCDGEKRED LEQLQQKQVN DHPPEQCGMF
TVSDHPPEQH GMFTVGDHPP EQRGMFTVSD HPPEQHGMFT VSDHPPEQRG MFTISDHQPE
QRGMFTVSDH TPEQRGIFTI SDHPAEQRGM FTKECEQECE LAITDLESGR EDEAGLHQSQ
AVHGLELEAL RLSLSNMHTA QLELTQANLQ KEKETALTEL REMLNSRRAQ ELALLQSRQQ
HELELLREQH AREKEEVVLR CGQEAAELKE KLQSEMEKNA QIVKTLKEDW ESEKDLCLEN
LRKELSAKHQ SEMEDLQNQF QKELAEQRAE LEKIFQDKNQ AERALRNLES HHQAAIEKLR
EDLQSEHGRC LEDLEFKFKE SEKEKQLELE NLQASYEDLK AQSQEEIRRL WSQLDSARTS
RQELSELHEQ LLARTSRVED LEQLKQREKT QHESELEQLR IYFEKKLRDA EKTYQEDLTL
LQQRLQGARE DALLDSVEVG LSCVGLEEKP EKGRKDHVDE LEPERHKESL PRFQAELEES
HRHQLEALES PLCIQHEGHV SDRCCVETSA LGHEWRLEPS EGHSQELPWV HLQGVQDGDL
EADTERAARV LGLETEHKVQ LSLLQTELKE EIELLKIENR NLYGKLQHET RLKDDLEKVK
HNLIEDHQKE LNNAKQKTEL MKQEFQRKET DWKVMKEELQ REAEEKLTLM LLELREKAES
EKQTIINKFE LREAEMRQLQ DQQAAQILDL ERSLTEQQGR LQQLEQDLTS DDALHCSQCG
REPPTAQDGE LAALHVKEDC ALQLMLARSR FLEERKEITE KFSAEQDAFL QEAQEQHARE
LQLLQERHQQ QLLSVTAELE ARHQAALGEL TASLESKQGA LLAARVAELQ TKHAADLGAL
ETRHLSSLDS LESCYLSEFQ TIREEHRQAL ELLRADFEEQ LWKKDSLHQT ILTQELEKLK
RKHEGELQSV RDHLRTEVST ELAGTVAHEL QGVHQGEFGS EKKTALHEKE ETLRLQSAQA
QPFHQEEKES LSLQLQKKNH QVQQLKDQVL SLSHEIEECR SELEVLQQRR ERENREGANL
LSMLKADVNL SHSERGALQD ALRRLLGLFG ETLRAAVTLR SRIGERVGLC LDDAGAGLAL
STAPALEETW SDVALPELDR TLSECAEMSS VAEISSHMRE SFLMSPESVR ECEQPIRRVF
QSLSLAVDGL MEMALDSSRQ LEEARQIHSR FEKEFSFKNE ETAQVVRKHQ ELLECLKEES
AAKAELALEL HKTQGTLEGF KVETADLKEV LAGKEDSEHR LVLELESLRR QLQQAAQEQA
ALREECTRLW SRGEATATDA EAREAALRKE VEDLTKEQSE TRKQAEKDRS ALLSQMKILE
SELEEQLSQH RGCAKQAEAV TALEQQVASL DKHLRNQRQF MDEQAAEREH EREEFQQEIQ
RLEGQLRQAA KPQPWGPRDS QQAPLDGEVE LLQQKLREKL DEFNELAIQK ESADRQVLMQ
EEEIKRLEEM NINIRKKVAQ LQEEVEKQKN IVKGLEQDKE VLKKQQMSSL LLASTLQSTL
DAGRCPEPPS GSPPEGPEIQ LEVTQRALLR RESEVLDLKE QLEKMKGDLE SKNEEILHLN
LKLDMQNSQT AVSLRELEEE NTSLKVIYTR SSEIEELKAT IENLQENQKR LQKEKAEEIE
QLHEVIEKLQ HELSLMGPVV HEVSDSQAGS LQSELLCSQA GGPRGQALQG ELEAALEAKE
ALSRLLADQE RRHSQALEAL QQRLQGAEEA AELQLAELER NVALREAEVE DMASRIQEFE
AALKAKEATI AERNLEIDAL NQRKAAHSAE LEAVLLALAR IRRALEQQPL AAGAAPPELQ
WLRAQCARLS RQLQVLHQRF LRCQVELDRR QARRATAHTR VPGAHPQPRM DGGAKAQVTG
DVEASHDAAL EPVVPDPQGD LQPVLVTLKD APLCKQEGVM SVLTVCQRQL QSELLLVKNE
MRLSLEDGGK GKEKVLEDCQ LPKVDLVAQV KQLQEKLNRL LYSMTFQNVD AADTKSLWPM
ASAHLLESSW SDDSCDGEEP DISPHIDTCD ANTATGGVTD VIKNQAIDAC DANTTPGGVT
DVIKNWDSLI PDEMPDSPIQ EKSECQDMSL SSPTSVLGGS RHQSHTAEAG PRKSPVGMLD
LSSWSSPEVL RKDWTLEPRP SLPVTPHSGA LSLCSADTSL GDRADTSLPQ TQGPGLLCSP
GVSAAALALQ WAESPPADDH HVQRTAVEKD VEDFITTSFD SQETLSSPPP GLEGKADRSE
KSDGSGFGAR LSPGSGGPEA QTAGPVTPAS ISGRFQPLPE AMKEKEVRPK HVKALLQMVR
DESHQILALS EGLAPPSGEP HPPRKEDEIQ DISLHGGKTQ EVPTACPDWR GDLLQVVQEA
FEKEQEMQGV ELQPRLSGSD LGGHSSLLER LEKIIREQGD LQEKSLEHLR LPDRSSLLSE
IQALRAQLRM THLQNQEKLQ HLRTALTSAE ARGSQQEHQL RRQVELLAYK VEQEKCIAGD
LQKTLSEEQE KANSVQKLLA AEQTVVRDLK SDLCESRQKS EQLSRSLCEV QQEVLQLRSM
LSSKENELKA ALQELESEQG KGRALQSQLE EEQLRHLQRE SQSAKALEEL RASLETQRAQ
SSRLCVALKH EQTAKDNLQK ELRIEHSRCE ALLAQERSQL SELQKDLAAE KSRTLELSEA
LRHERLLTEQ LSQRTQEACV HQDTQAHHAL LQKLKEEKSR VVDLQAMLEK VQQQALHSQQ
QLEAEAQKHC EALRREKEVS ATLKSTVEAL HTQKRELRCS LEREREKPAW LQAELEQSHP
RLKEQEGRKA ARRSAEARQS PAAAEQWRKW QRDKEKLREL ELQRQRDLHK IKQLQQTVRD
LESKDEVPGS RLHLGSARRA AGSDADHLRE QQRELEAMRQ RLLSAARLLT SFTSQAVDRT
VNDWTSSNEK AVMSLLHTLE ELKSDLSRPT SSQKKMAAEL QFQFVDVLLK DNVSLTKALS
TVTQEKLELS RAVSKLEKLL KHHLQKGCSP SRSERSAWKP DETAPQSSLR RPDPGRLPPA
ASEEAHTSNV KMEKLYLHYL RAESFRKALI YQKKYLLLLI GGFQDSEQET LSMIAHLGVF
PSKAERKITS RPFTRFRTAV RVVIAILRLR FLVKKWQEVD RKGALAQGKA PRPGPRARQP
QSPPRTRESP PTRDVPSGHT RDPARGRRLA AAASPHSGGR ATPSPNSRLE RSLTASQDPE
HSLTEYIHHL EVIQQRLGGV LPDSTSKKSC HPMIKQ*

speed

0.83 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
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MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

Problems