MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000327757
Querying Taster for transcript #2: ENST00000422425
MT speed 0 s - this script 3.769269 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PLB1	polymorphism_automatic	0.958692511030614	simple_aae				V212L	single base exchange	rs6753929		show file
PLB1	polymorphism_automatic	0.958692511030614	simple_aae				V223L	single base exchange	rs6753929		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0413074889693856 (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)

chr2:28761981G>CN/A show variant in all transcripts IGV

HGNC symbol

PLB1

Ensembl transcript ID

ENST00000327757

Genbank transcript ID

NM_153021

UniProt peptide

Q6P1J6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.634G>C
cDNA.678G>C
g.81970G>C

AA changes

V212L Score: 32 explain score(s)

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

212

frameshift

known variant

Reference ID: rs6753929

database	homozygous (C/C)	heterozygous	allele carriers
1000G	115	769	884
ExAC	4035	22406	26441

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
PU1, Transcription Factor, PU1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
SP1, Transcription Factor, SP1 Transcription Factor Binding
USF1, Transcription Factor, USF1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.455	0.997
	3.309	1
(flanking)	2.782	1

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	81961	wt: 0.4642 / mu: 0.5073 (marginal change - not scored)	wt: GTGTGTCCTCCTAGGTCCCCAGAGCATTTGTAAACCTGGTG mu: GTGTGTCCTCCTAGGTCCCCAGAGCATTTCTAAACCTGGTG	ccca\|GAGC
Acc marginally increased	81962	wt: 0.2939 / mu: 0.3321 (marginal change - not scored)	wt: TGTGTCCTCCTAGGTCCCCAGAGCATTTGTAAACCTGGTGG mu: TGTGTCCTCCTAGGTCCCCAGAGCATTTCTAAACCTGGTGG	ccag\|AGCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

212

mutated

all conserved

212

Ptroglodytes

all identical

ENSPTRG00000011786

213

Mmulatta

no alignment

ENSMMUG00000008352

n/a

Fcatus

all identical

ENSFCAG00000005165

213

Mmusculus

all identical

ENSMUSG00000029134

219

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000096445

154

Dmelanogaster

no alignment

FBgn0036939

n/a

Celegans

no alignment

F09C8.1

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
22	1417	TOPO_DOM	Extracellular (Potential).	lost
39	347	REPEAT	1.	lost
39	1402	REGION	4 X 308-326 AA approximate repeats.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4377 / 4377

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

1459 / 1459

position of stopcodon in wt / mu cDNA

4421 / 4421

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

45 / 45

chromosome

strand

last intron/exon boundary

4218

theoretical NMD boundary in CDS

4123

length of CDS

4377

coding sequence (CDS) position

634

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

678

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

81970

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

28761981

original gDNA sequence snippet

CCTAGGTCCCCAGAGCATTTGTAAACCTGGTGGACCTCTCT

altered gDNA sequence snippet

CCTAGGTCCCCAGAGCATTTCTAAACCTGGTGGACCTCTCT

original cDNA sequence snippet

AGGAGGTCCCCAGAGCATTTGTAAACCTGGTGGACCTCTCT

altered cDNA sequence snippet

AGGAGGTCCCCAGAGCATTTCTAAACCTGGTGGACCTCTCT

wildtype AA sequence

MGLRPGIFLL ELLLLLGQGT PQIHTSPRKS TLEGQLWPET LKNSPFPCNP NKLGVNMPSK
SVHSLKPSDI KFVAAIGNLE IPPDPGTGDL EKQDWTERPQ QVCMGVMTVL SDIIRYFSPS
VPMPVCHTGK RVIPHDGAED LWIQAQELVR NMKENLQLDF QFDWKLINVF FSNASQCYLC
PSAQQNGLAA GGVDELMGVL DYLQQEVPRA FVNLVDLSEV AEVSRQYHGT WLSPAPEPCN
CSEETTRLAK VVMQWSYQEA WNSLLASSRY SEQESFTVVF QPFFYETTPS LHSEDPRLQD
STTLAWHLWN RMMEPAGEKD EPLSVKHGRP MKCPSQESPY LFSYRNSNYL TRLQKPQDKL
EVREGAEIRC PDKDPSDTVP TSVHRLKPAD INVIGALGDS LTAGNGAGST PGNVLDVLTQ
YRGLSWSVGG DENIGTVTTL ANILREFNPS LKGFSVGTGK ETSPNAFLNQ AVAGGRAEDL
PVQARRLVDL MKNDTRIHFQ EDWKIITLFI GGNDLCDFCN DLVHYSPQNF TDNIGKALDI
LHAEVPRAFV NLVTVLEIVN LRELYQEKKV YCPRMILRSL CPCVLKFDDN STELATLIEF
NKKFQEKTHQ LIESGRYDTR EDFTVVVQPF FENVDMPKTS EGLPDNSFFA PDCFHFSSKS
HSRAASALWN NMLEPVGQKT TRHKFENKIN ITCPNQVQPF LRTYKNSMQG HGTWLPCRDR
APSALHPTSV HALRPADIQV VAALGDSLTA GNGIGSKPDD LPDVTTQYRG LSYSAGGDGS
LENVTTLPNI LREFNRNLTG YAVGTGDAND TNAFLNQAVP GAKAEDLMSQ VQTLMQKMKD
DHRVNFHEDW KVITVLIGGS DLCDYCTDSN LYSAANFVHH LRNALDVLHR EVPRVLVNLV
DFLNPTIMRQ VFLGNPDKCP VQQASVLCNC VLTLRENSQE LARLEAFSRA YRSSMRELVG
SGRYDTQEDF SVVLQPFFQN IQLPVLADGL PDTSFFAPDC IHPNQKFHSQ LARALWTNML
EPLGSKTETL DLRAEMPITC PTQNEPFLRT PRNSNYTYPI KPAIENWGSD FLCTEWKASN
SVPTSVHQLR PADIKVVAAL GDSLTTAVGA RPNNSSDLPT SWRGLSWSIG GDGNLETHTT
LPNILKKFNP YLLGFSTSTW EGTAGLNVAA EGARARDMPA QAWDLVERMK NSPDINLEKD
WKLVTLFIGV NDLCHYCENP EAHLATEYVQ HIQQALDILS EELPRAFVNV VEVMELASLY
QGQGGKCAML AAQNNCTCLR HSQSSLEKQE LKKVNWNLQH GISSFSYWHQ YTQREDFAVV
VQPFFQNTLT PLNERGDTDL TFFSEDCFHF SDRGHAEMAI ALWNNMLEPV GRKTTSNNFT
HSRAKLKCPS PESPYLYTLR NSRLLPDQAE EAPEVLYWAV PVAAGVGLVV GIIGTVVWRC
RRGGRREDPP MSLRTVAL*

mutated AA sequence

MGLRPGIFLL ELLLLLGQGT PQIHTSPRKS TLEGQLWPET LKNSPFPCNP NKLGVNMPSK
SVHSLKPSDI KFVAAIGNLE IPPDPGTGDL EKQDWTERPQ QVCMGVMTVL SDIIRYFSPS
VPMPVCHTGK RVIPHDGAED LWIQAQELVR NMKENLQLDF QFDWKLINVF FSNASQCYLC
PSAQQNGLAA GGVDELMGVL DYLQQEVPRA FLNLVDLSEV AEVSRQYHGT WLSPAPEPCN
CSEETTRLAK VVMQWSYQEA WNSLLASSRY SEQESFTVVF QPFFYETTPS LHSEDPRLQD
STTLAWHLWN RMMEPAGEKD EPLSVKHGRP MKCPSQESPY LFSYRNSNYL TRLQKPQDKL
EVREGAEIRC PDKDPSDTVP TSVHRLKPAD INVIGALGDS LTAGNGAGST PGNVLDVLTQ
YRGLSWSVGG DENIGTVTTL ANILREFNPS LKGFSVGTGK ETSPNAFLNQ AVAGGRAEDL
PVQARRLVDL MKNDTRIHFQ EDWKIITLFI GGNDLCDFCN DLVHYSPQNF TDNIGKALDI
LHAEVPRAFV NLVTVLEIVN LRELYQEKKV YCPRMILRSL CPCVLKFDDN STELATLIEF
NKKFQEKTHQ LIESGRYDTR EDFTVVVQPF FENVDMPKTS EGLPDNSFFA PDCFHFSSKS
HSRAASALWN NMLEPVGQKT TRHKFENKIN ITCPNQVQPF LRTYKNSMQG HGTWLPCRDR
APSALHPTSV HALRPADIQV VAALGDSLTA GNGIGSKPDD LPDVTTQYRG LSYSAGGDGS
LENVTTLPNI LREFNRNLTG YAVGTGDAND TNAFLNQAVP GAKAEDLMSQ VQTLMQKMKD
DHRVNFHEDW KVITVLIGGS DLCDYCTDSN LYSAANFVHH LRNALDVLHR EVPRVLVNLV
DFLNPTIMRQ VFLGNPDKCP VQQASVLCNC VLTLRENSQE LARLEAFSRA YRSSMRELVG
SGRYDTQEDF SVVLQPFFQN IQLPVLADGL PDTSFFAPDC IHPNQKFHSQ LARALWTNML
EPLGSKTETL DLRAEMPITC PTQNEPFLRT PRNSNYTYPI KPAIENWGSD FLCTEWKASN
SVPTSVHQLR PADIKVVAAL GDSLTTAVGA RPNNSSDLPT SWRGLSWSIG GDGNLETHTT
LPNILKKFNP YLLGFSTSTW EGTAGLNVAA EGARARDMPA QAWDLVERMK NSPDINLEKD
WKLVTLFIGV NDLCHYCENP EAHLATEYVQ HIQQALDILS EELPRAFVNV VEVMELASLY
QGQGGKCAML AAQNNCTCLR HSQSSLEKQE LKKVNWNLQH GISSFSYWHQ YTQREDFAVV
VQPFFQNTLT PLNERGDTDL TFFSEDCFHF SDRGHAEMAI ALWNNMLEPV GRKTTSNNFT
HSRAKLKCPS PESPYLYTLR NSRLLPDQAE EAPEVLYWAV PVAAGVGLVV GIIGTVVWRC
RRGGRREDPP MSLRTVAL*

speed

0.94 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

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.0413074889693856 (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)

chr2:28761981G>CN/A show variant in all transcripts IGV

HGNC symbol

PLB1

Ensembl transcript ID

ENST00000422425

Genbank transcript ID

NM_001170585

UniProt peptide

Q6P1J6

alteration type

single base exchange

alteration region

CDS

DNA changes

c.667G>C
cDNA.711G>C
g.81970G>C

AA changes

V223L Score: 32 explain score(s)

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

223

frameshift

known variant

Reference ID: rs6753929

database	homozygous (C/C)	heterozygous	allele carriers
1000G	115	769	884
ExAC	4035	22406	26441

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.455	0.997
	3.309	1
(flanking)	2.782	1

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	81961	wt: 0.4642 / mu: 0.5073 (marginal change - not scored)	wt: GTGTGTCCTCCTAGGTCCCCAGAGCATTTGTAAACCTGGTG mu: GTGTGTCCTCCTAGGTCCCCAGAGCATTTCTAAACCTGGTG	ccca\|GAGC
Acc marginally increased	81962	wt: 0.2939 / mu: 0.3321 (marginal change - not scored)	wt: TGTGTCCTCCTAGGTCCCCAGAGCATTTGTAAACCTGGTGG mu: TGTGTCCTCCTAGGTCCCCAGAGCATTTCTAAACCTGGTGG	ccag\|AGCA

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

223

mutated

all conserved

223

Ptroglodytes

all identical

ENSPTRG00000011786

224

Mmulatta

no alignment

ENSMMUG00000008352

n/a

Fcatus

all identical

ENSFCAG00000005165

213

Mmusculus

all identical

ENSMUSG00000029134

230

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000096445

153

Dmelanogaster

no alignment

FBgn0036939

n/a

Celegans

no alignment

F09C8.1

n/a

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
22	1417	TOPO_DOM	Extracellular (Potential).	lost
39	347	REPEAT	1.	lost
39	1402	REGION	4 X 308-326 AA approximate repeats.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

4344 / 4344

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

1448 / 1448

position of stopcodon in wt / mu cDNA

4388 / 4388

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

45 / 45

chromosome

strand

last intron/exon boundary

4185

theoretical NMD boundary in CDS

4090

length of CDS

4344

coding sequence (CDS) position

667

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

711

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

81970

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

28761981

original gDNA sequence snippet

CCTAGGTCCCCAGAGCATTTGTAAACCTGGTGGACCTCTCT

altered gDNA sequence snippet

CCTAGGTCCCCAGAGCATTTCTAAACCTGGTGGACCTCTCT

original cDNA sequence snippet

AGGAGGTCCCCAGAGCATTTGTAAACCTGGTGGACCTCTCT

altered cDNA sequence snippet

AGGAGGTCCCCAGAGCATTTCTAAACCTGGTGGACCTCTCT

wildtype AA sequence

MGLRPGIFLL ELLLLLGQGT PQIHTSPRKS TLEGQLWPET LKNSPFPCNP NKLGVNMPSK
SVHSLKPSDI KFVAAIGNLE IPPDPGTGDL EKQDWTERPQ QVCMGVMTVL SDIIRYFSPS
VPMPVCHTGK RVIPHDGAED LWIQAQELVR NMKENLQLDF QFDWKLINVF FSNASQCYLC
PSAQQAPSLS TVLLSQNGLA AGGVDELMGV LDYLQQEVPR AFVNLVDLSE VAEVSRQYHG
TWLSPAPEPC NCSEETTRLA KVVMQWSYQE AWNSLLASSR YSEQESFTVV FQPFFYETTP
SLHSEDPRLQ DSTTLAWHLW NRMMEPAGEK DEPLSVKHGR PMKCPSQESP YLFSYRNSNY
LTRLQKPQDK LEVREGAEIR CPDKDPSDTV PTSVHRLKPA DINVIGALGD SLTAGNGAGS
TPGNVLDVLT QYRGLSWSVG GDENIGTVTT LANILREFNP SLKGFSVGTG KETSPNAFLN
QAVAGGRAED LPVQARRLVD LMKNDTRIHF QEDWKIITLF IGGNDLCDFC NDLVPRAFVN
LVTVLEIVNL RELYQEKKVY CPRMILRSLC PCVLKFDDNS TELATLIEFN KKFQEKTHQL
IESGRYDTRE DFTVVVQPFF ENVDMPKTSE GLPDNSFFAP DCFHFSSKSH SRAASALWNN
MLEPVGQKTT RHKFENKINI TCPNQVQPFL RTYKNSMQGH GTWLPCRDRA PSALHPTSVH
ALRPADIQVV AALGDSLTAG NGIGSKPDDL PDVTTQYRGL SYSAGGDGSL ENVTTLPNIL
REFNRNLTGY AVGTGDANDT NAFLNQAVPG AKAEDLMSQV QTLMQKMKDD HRVNFHEDWK
VITVLIGGSD LCDYCTDSNL YSAANFVHHL RNALDVLHRE VPRVLVNLVD FLNPTIMRQV
FLGNPDKCPV QQASVLCNCV LTLRENSQEL ARLEAFSRAY RSSMRELVGS GRYDTQEDFS
VVLQPFFQNI QLPVLADGLP DTSFFAPDCI HPNQKFHSQL ARALWTNMLE PLGSKTETLD
LRAEMPITCP TQNEPFLRTP RNSNYTYPIK PAIENWGSDF LCTEWKASNS VPTSVHQLRP
ADIKVVAALG DSLTTAVGAR PNNSSDLPTS WRGLSWSIGG DGNLETHTTL PNILKKFNPY
LLGFSTSTWE GTAGLNVAAE GARARDMPAQ AWDLVERMKN SPDINLEKDW KLVTLFIGVN
DLCHYCENPE AHLATEYVQH IQQALDILSE ELPRAFVNVV EVMELASLYQ GQGGKCAMLA
AQNNCTCLRH SQSSLEKQEL KKVNWNLQHG ISSFSYWHQY TQREDFAVVV QPFFQNTLTP
LNERGDTDLT FFSEDCFHFS DRGHAEMAIA LWNNMLEPVG RKTTSNNFTH SRAKLKCPSP
ESPYLYTLRN SRLLPDQAEE APEVLYWAVP VAAGVGLVVG IIGTVVWRCR RGGRREDPPM
SLRTVAL*

mutated AA sequence

MGLRPGIFLL ELLLLLGQGT PQIHTSPRKS TLEGQLWPET LKNSPFPCNP NKLGVNMPSK
SVHSLKPSDI KFVAAIGNLE IPPDPGTGDL EKQDWTERPQ QVCMGVMTVL SDIIRYFSPS
VPMPVCHTGK RVIPHDGAED LWIQAQELVR NMKENLQLDF QFDWKLINVF FSNASQCYLC
PSAQQAPSLS TVLLSQNGLA AGGVDELMGV LDYLQQEVPR AFLNLVDLSE VAEVSRQYHG
TWLSPAPEPC NCSEETTRLA KVVMQWSYQE AWNSLLASSR YSEQESFTVV FQPFFYETTP
SLHSEDPRLQ DSTTLAWHLW NRMMEPAGEK DEPLSVKHGR PMKCPSQESP YLFSYRNSNY
LTRLQKPQDK LEVREGAEIR CPDKDPSDTV PTSVHRLKPA DINVIGALGD SLTAGNGAGS
TPGNVLDVLT QYRGLSWSVG GDENIGTVTT LANILREFNP SLKGFSVGTG KETSPNAFLN
QAVAGGRAED LPVQARRLVD LMKNDTRIHF QEDWKIITLF IGGNDLCDFC NDLVPRAFVN
LVTVLEIVNL RELYQEKKVY CPRMILRSLC PCVLKFDDNS TELATLIEFN KKFQEKTHQL
IESGRYDTRE DFTVVVQPFF ENVDMPKTSE GLPDNSFFAP DCFHFSSKSH SRAASALWNN
MLEPVGQKTT RHKFENKINI TCPNQVQPFL RTYKNSMQGH GTWLPCRDRA PSALHPTSVH
ALRPADIQVV AALGDSLTAG NGIGSKPDDL PDVTTQYRGL SYSAGGDGSL ENVTTLPNIL
REFNRNLTGY AVGTGDANDT NAFLNQAVPG AKAEDLMSQV QTLMQKMKDD HRVNFHEDWK
VITVLIGGSD LCDYCTDSNL YSAANFVHHL RNALDVLHRE VPRVLVNLVD FLNPTIMRQV
FLGNPDKCPV QQASVLCNCV LTLRENSQEL ARLEAFSRAY RSSMRELVGS GRYDTQEDFS
VVLQPFFQNI QLPVLADGLP DTSFFAPDCI HPNQKFHSQL ARALWTNMLE PLGSKTETLD
LRAEMPITCP TQNEPFLRTP RNSNYTYPIK PAIENWGSDF LCTEWKASNS VPTSVHQLRP
ADIKVVAALG DSLTTAVGAR PNNSSDLPTS WRGLSWSIGG DGNLETHTTL PNILKKFNPY
LLGFSTSTWE GTAGLNVAAE GARARDMPAQ AWDLVERMKN SPDINLEKDW KLVTLFIGVN
DLCHYCENPE AHLATEYVQH IQQALDILSE ELPRAFVNVV EVMELASLYQ GQGGKCAMLA
AQNNCTCLRH SQSSLEKQEL KKVNWNLQHG ISSFSYWHQY TQREDFAVVV QPFFQNTLTP
LNERGDTDLT FFSEDCFHFS DRGHAEMAIA LWNNMLEPVG RKTTSNNFTH SRAKLKCPSP
ESPYLYTLRN SRLLPDQAEE APEVLYWAVP VAAGVGLVVG IIGTVVWRCR RGGRREDPPM
SLRTVAL*

speed

0.84 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems