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: ENST00000382396
Querying Taster for transcript #2: ENST00000397272
MT speed 0 s - this script 3.641941 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PLA2G4F	polymorphism_automatic	1.02098118959226e-07	simple_aae		affected		L252V	single base exchange	rs73403546		show file
PLA2G4F	polymorphism_automatic	1.02098118959226e-07	simple_aae		affected		L252V	single base exchange	rs73403546		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999897901881 (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)

chr15:42442823G>CN/A show variant in all transcripts IGV

HGNC symbol

PLA2G4F

Ensembl transcript ID

ENST00000382396

Genbank transcript ID

NM_213600

UniProt peptide

Q68DD2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.754C>G
cDNA.841C>G
g.6017C>G

AA changes

L252V Score: 32 explain score(s)

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

252

frameshift

known variant

Reference ID: rs73403546

database	homozygous (C/C)	heterozygous	allele carriers
1000G	177	722	899
ExAC	1403	10269	11672

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.613	0.427
	-0.005	0.433
(flanking)	1.463	0.534

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 gained	6011	0.89	mu: AGCTGATGGAGGTGC	CTGA\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

252

mutated

all conserved

252

Ptroglodytes

all identical

ENSPTRG00000006970

252

Mmulatta

not conserved

ENSMMUG00000015449

252

Fcatus

no alignment

ENSFCAG00000009311

n/a

Mmusculus

not conserved

ENSMUSG00000046971

249

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
262	262	CONFLICT	A -> T (in Ref. 1; BAD18801).	might get lost (downstream of altered splice site)
306	849	DOMAIN	PLA2c.	might get lost (downstream of altered splice site)
363	363	CONFLICT	G -> E (in Ref. 3; CAH18288).	might get lost (downstream of altered splice site)
395	395	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
680	680	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2550 / 2550

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

850 / 850

position of stopcodon in wt / mu cDNA

2637 / 2637

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

88 / 88

chromosome

strand

-1

last intron/exon boundary

2417

theoretical NMD boundary in CDS

2279

length of CDS

2550

coding sequence (CDS) position

754

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

841

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

6017

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

42442823

original gDNA sequence snippet

TACACGTGGAGCTGATGGAGCTGCTGGCAGCTGTGCAGGTG

altered gDNA sequence snippet

TACACGTGGAGCTGATGGAGGTGCTGGCAGCTGTGCAGGTG

original cDNA sequence snippet

TACACGTGGAGCTGATGGAGCTGCTGGCAGCTGTGCAGAGT

altered cDNA sequence snippet

TACACGTGGAGCTGATGGAGGTGCTGGCAGCTGTGCAGAGT

wildtype AA sequence

MLWALWPRWL ADKMLPLLGA VLLQKREKRG PLWRHWRRET YPYYDLQVKV LRATNIRGTD
LLSKADCYVQ LWLPTASPSP AQTRIVANCS DPEWNETFHY QIHGAVKNVL ELTLYDKDIL
GSDQLSLLLF DLRSLKCGQP HKHTFPLNHQ DSQELQVEFV LEKSQVPASE VITNGVLVAH
PCLRIQGTLR GDGTAPREEY GSRQLQLAVP GAYEKPQLLP LQPPTEPGLP PTFTFHVNPV
LSSRLHVELM ELLAAVQSGP SAELEAQTSK LGEGGILLSS LPLGQEEQCS VALGEGQEVA
LSMKVEMSSG DLDLRLGFDL SDGEQEFLDR RKQVVSKALQ QVLGLSEALD SGQVPVVAVL
GSGGGTRAMS SLYGSLAGLQ ELGLLDTVTY LSGVSGSTWC ISTLYRDPAW SQVALQGPIE
RAQVHVCSSK MGALSTERLQ YYTQELGVRE RSGHSVSLID LWGLLVEYLL YQEENPAKLS
DQQEAVRQGQ NPYPIYTSVN VRTNLSGEDF AEWCEFTPYE VGFPKYGAYV PTELFGSELF
MGRLLQLQPE PRICYLQGMW GSAFATSLDE IFLKTAGSGL SFLEWYRGSV NITDDCQKPQ
LHNPSRLRTR LLTPQGPFSQ AVLDIFTSRF TSAQSFNFTR GLCLHKDYVA GREFVAWKDT
HPDAFPNQLT PMRDCLYLVD GGFAINSPFP LALLPQRAVD LILSFDYSLE APFEVLKMTE
KYCLDRGIPF PSIEVGPEDM EEARECYLFA KAEDPRSPIV LHFPLVNRTF RTHLAPGVER
QTAEEKAFGD FVINRPDTPY GMMNFTYEPQ DFYRLVALSR YNVLNNVETL KCALQLALDR
HQARERAGA*

mutated AA sequence

MLWALWPRWL ADKMLPLLGA VLLQKREKRG PLWRHWRRET YPYYDLQVKV LRATNIRGTD
LLSKADCYVQ LWLPTASPSP AQTRIVANCS DPEWNETFHY QIHGAVKNVL ELTLYDKDIL
GSDQLSLLLF DLRSLKCGQP HKHTFPLNHQ DSQELQVEFV LEKSQVPASE VITNGVLVAH
PCLRIQGTLR GDGTAPREEY GSRQLQLAVP GAYEKPQLLP LQPPTEPGLP PTFTFHVNPV
LSSRLHVELM EVLAAVQSGP SAELEAQTSK LGEGGILLSS LPLGQEEQCS VALGEGQEVA
LSMKVEMSSG DLDLRLGFDL SDGEQEFLDR RKQVVSKALQ QVLGLSEALD SGQVPVVAVL
GSGGGTRAMS SLYGSLAGLQ ELGLLDTVTY LSGVSGSTWC ISTLYRDPAW SQVALQGPIE
RAQVHVCSSK MGALSTERLQ YYTQELGVRE RSGHSVSLID LWGLLVEYLL YQEENPAKLS
DQQEAVRQGQ NPYPIYTSVN VRTNLSGEDF AEWCEFTPYE VGFPKYGAYV PTELFGSELF
MGRLLQLQPE PRICYLQGMW GSAFATSLDE IFLKTAGSGL SFLEWYRGSV NITDDCQKPQ
LHNPSRLRTR LLTPQGPFSQ AVLDIFTSRF TSAQSFNFTR GLCLHKDYVA GREFVAWKDT
HPDAFPNQLT PMRDCLYLVD GGFAINSPFP LALLPQRAVD LILSFDYSLE APFEVLKMTE
KYCLDRGIPF PSIEVGPEDM EEARECYLFA KAEDPRSPIV LHFPLVNRTF RTHLAPGVER
QTAEEKAFGD FVINRPDTPY GMMNFTYEPQ DFYRLVALSR YNVLNNVETL KCALQLALDR
HQARERAGA*

speed

0.68 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: 0.999999897901881 (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)

chr15:42442823G>CN/A show variant in all transcripts IGV

HGNC symbol

PLA2G4F

Ensembl transcript ID

ENST00000397272

Genbank transcript ID

N/A

UniProt peptide

Q68DD2

alteration type

single base exchange

alteration region

CDS

DNA changes

c.754C>G
cDNA.846C>G
g.6017C>G

AA changes

L252V Score: 32 explain score(s)

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

252

frameshift

known variant

Reference ID: rs73403546

database	homozygous (C/C)	heterozygous	allele carriers
1000G	177	722	899
ExAC	1403	10269	11672

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.613	0.427
	-0.005	0.433
(flanking)	1.463	0.534

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 gained	6011	0.89	mu: AGCTGATGGAGGTGC	CTGA\|tgga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

252

mutated

all conserved

252

Ptroglodytes

all identical

ENSPTRG00000006970

252

Mmulatta

not conserved

ENSMMUG00000015449

252

Fcatus

no alignment

ENSFCAG00000009311

n/a

Mmusculus

not conserved

ENSMUSG00000046971

249

Ggallus

no homologue

Trubripes

no homologue

Drerio

no homologue

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
262	262	CONFLICT	A -> T (in Ref. 1; BAD18801).	might get lost (downstream of altered splice site)
306	849	DOMAIN	PLA2c.	might get lost (downstream of altered splice site)
363	363	CONFLICT	G -> E (in Ref. 3; CAH18288).	might get lost (downstream of altered splice site)
395	395	ACT_SITE	Nucleophile (By similarity).	might get lost (downstream of altered splice site)
680	680	ACT_SITE	Proton acceptor (By similarity).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2556 / 2556

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

852 / 852

position of stopcodon in wt / mu cDNA

2648 / 2648

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

93 / 93

chromosome

strand

-1

last intron/exon boundary

2428

theoretical NMD boundary in CDS

2285

length of CDS

2556

coding sequence (CDS) position

754

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

846

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

6017

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

42442823

original gDNA sequence snippet

TACACGTGGAGCTGATGGAGCTGCTGGCAGCTGTGCAGGTG

altered gDNA sequence snippet

TACACGTGGAGCTGATGGAGGTGCTGGCAGCTGTGCAGGTG

original cDNA sequence snippet

TACACGTGGAGCTGATGGAGCTGCTGGCAGCTGTGCAGAGT

altered cDNA sequence snippet

TACACGTGGAGCTGATGGAGGTGCTGGCAGCTGTGCAGAGT

wildtype AA sequence

MLWALWPRWL ADKMLPLLGA VLLQKREKRG PLWRHWRRET YPYYDLQVKV LRATNIRGTD
LLSKADCYVQ LWLPTASPSP AQTRIVANCS DPEWNETFHY QIHGAVKNVL ELTLYDKDIL
GSDQLSLLLF DLRSLKCGQP HKHTFPLNHQ DSQELQVEFV LEKSQVPASE VITNGVLVAH
PCLRIQGTLR GDGTAPREEY GSRQLQLAVP GAYEKPQLLP LQPPTEPGLP PTFTFHVNPV
LSSRLHVELM ELLAAVQSGP SAELEAQTSK LGEGGILLSS LPLGQEEQCS VALGEGQEVA
LSMKVEMSSG DLDLRLGFDL SDGEQEFLDR RKQVVSKALQ QVLGLSEALD SGQTQVPVVA
VLGSGGGTRA MSSLYGSLAG LQELGLLDTV TYLSGVSGST WCISTLYRDP AWSQVALQGP
IERAQVHVCS SKMGALSTER LQYYTQELGV RERSGHSVSL IDLWGLLVEY LLYQEENPAK
LSDQQEAVRQ GQNPYPIYTS VNVRTNLSGE DFAEWCEFTP YEVGFPKYGA YVPTELFGSE
LFMGRLLQLQ PEPRICYLQG MWGSAFATSL DEIFLKTAGS GLSFLEWYRG SVNITDDCQK
PQLHNPSRLR TRLLTPQGPF SQAVLDIFTS RFTSAQSFNF TRGLCLHKDY VAGREFVAWK
DTHPDAFPNQ LTPMRDCLYL VDGGFAINSP FPLALLPQRA VDLILSFDYS LEAPFEVLKM
TEKYCLDRGI PFPSIEVGPE DMEEARECYL FAKAEDPRSP IVLHFPLVNR TFRTHLAPGV
ERQTAEEKAF GDFVINRPDT PYGMMNFTYE PQDFYRLVAL SRYNVLNNVE TLKCALQLAL
DRHQARERAG A*

mutated AA sequence

MLWALWPRWL ADKMLPLLGA VLLQKREKRG PLWRHWRRET YPYYDLQVKV LRATNIRGTD
LLSKADCYVQ LWLPTASPSP AQTRIVANCS DPEWNETFHY QIHGAVKNVL ELTLYDKDIL
GSDQLSLLLF DLRSLKCGQP HKHTFPLNHQ DSQELQVEFV LEKSQVPASE VITNGVLVAH
PCLRIQGTLR GDGTAPREEY GSRQLQLAVP GAYEKPQLLP LQPPTEPGLP PTFTFHVNPV
LSSRLHVELM EVLAAVQSGP SAELEAQTSK LGEGGILLSS LPLGQEEQCS VALGEGQEVA
LSMKVEMSSG DLDLRLGFDL SDGEQEFLDR RKQVVSKALQ QVLGLSEALD SGQTQVPVVA
VLGSGGGTRA MSSLYGSLAG LQELGLLDTV TYLSGVSGST WCISTLYRDP AWSQVALQGP
IERAQVHVCS SKMGALSTER LQYYTQELGV RERSGHSVSL IDLWGLLVEY LLYQEENPAK
LSDQQEAVRQ GQNPYPIYTS VNVRTNLSGE DFAEWCEFTP YEVGFPKYGA YVPTELFGSE
LFMGRLLQLQ PEPRICYLQG MWGSAFATSL DEIFLKTAGS GLSFLEWYRG SVNITDDCQK
PQLHNPSRLR TRLLTPQGPF SQAVLDIFTS RFTSAQSFNF TRGLCLHKDY VAGREFVAWK
DTHPDAFPNQ LTPMRDCLYL VDGGFAINSP FPLALLPQRA VDLILSFDYS LEAPFEVLKM
TEKYCLDRGI PFPSIEVGPE DMEEARECYL FAKAEDPRSP IVLHFPLVNR TFRTHLAPGV
ERQTAEEKAF GDFVINRPDT PYGMMNFTYE PQDFYRLVAL SRYNVLNNVE TLKCALQLAL
DRHQARERAG A*

speed

0.96 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems