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: ENST00000263088
Querying Taster for transcript #2: ENST00000572940
MT speed 0 s - this script 3.225509 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PLD2	polymorphism_automatic	4.62609950346859e-11	simple_aae				T577I	single base exchange	rs1052748		show file
PLD2	polymorphism_automatic	4.62609950346859e-11	simple_aae				T577I	single base exchange	rs1052748		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999953739 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM030489)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:4720469C>TN/A show variant in all transcripts IGV

HGNC symbol

PLD2

Ensembl transcript ID

ENST00000263088

Genbank transcript ID

NM_002663

UniProt peptide

O14939

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1730C>T
cDNA.1861C>T
g.10079C>T

AA changes

T577I Score: 89 explain score(s)

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

577

frameshift

known variant

Reference ID: rs1052748

database	homozygous (T/T)	heterozygous	allele carriers
1000G	201	849	1050
ExAC	10505	11757	22262

known disease mutation at this position, please check HGMD for details (HGMD ID CM030489)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.288	0
	-1.899	0
(flanking)	-0.072	0.023

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

577

mutated

not conserved

577

Ptroglodytes

all identical

ENSPTRG00000008610

577

Mmulatta

all identical

ENSMMUG00000005666

573

Fcatus

not conserved

ENSFCAG00000008040

431

Mmusculus

not conserved

ENSMUSG00000020828

577

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000016291

583

Drerio

not conserved

ENSDARG00000034262

570

Dmelanogaster

not conserved

FBgn0033075

990

Celegans

not conserved

C04G6.3

1060

Xtropicalis

all identical

ENSXETG00000021019

582

protein features

start (aa)	end (aa)	feature	details
441	788	REGION	Catalytic.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2802 / 2802

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

934 / 934

position of stopcodon in wt / mu cDNA

2933 / 2933

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

132 / 132

chromosome

strand

last intron/exon boundary

2709

theoretical NMD boundary in CDS

2527

length of CDS

2802

coding sequence (CDS) position

1730

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

1861

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

10079

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

4720469

original gDNA sequence snippet

GGCCAAGTACAAGACTCCCACATACCCCTACCTGCTTCCCA

altered gDNA sequence snippet

GGCCAAGTACAAGACTCCCATATACCCCTACCTGCTTCCCA

original cDNA sequence snippet

GGCCAAGTACAAGACTCCCACATACCCCTACCTGCTTCCCA

altered cDNA sequence snippet

GGCCAAGTACAAGACTCCCATATACCCCTACCTGCTTCCCA

wildtype AA sequence

MTATPESLFP TGDELDSSQL QMESDEVDTL KEGEDPADRM HPFLAIYELQ SLKVHPLVFA
PGVPVTAQVV GTERYTSGSK VGTCTLYSVR LTHGDFSWTT KKKYRHFQEL HRDLLRHKVL
MSLLPLARFA VAYSPARDAG NREMPSLPRA GPEGSTRHAA SKQKYLENYL NRLLTMSFYR
NYHAMTEFLE VSQLSFIPDL GRKGLEGMIR KRSGGHRVPG LTCCGRDQVC YRWSKRWLVV
KDSFLLYMCL ETGAISFVQL FDPGFEVQVG KRSTEARHGV RIDTSHRSLI LKCSSYRQAR
WWAQEITELA QGPGRDFLQL HRHDSYAPPR PGTLARWFVN GAGYFAAVAD AILRAQEEIF
ITDWWLSPEV YLKRPAHSDD WRLDIMLKRK AEEGVRVSIL LFKEVELALG INSGYSKRAL
MLLHPNIKVM RHPDQVTLWA HHEKLLVVDQ VVAFLGGLDL AYGRWDDLHY RLTDLGDSSE
SAASQPPTPR PDSPATPDLS HNQFFWLGKD YSNLITKDWV QLDRPFEDFI DRETTPRMPW
RDVGVVVHGL PARDLARHFI QRWNFTKTTK AKYKTPTYPY LLPKSTSTAN QLPFTLPGGQ
CTTVQVLRSV DRWSAGTLEN SILNAYLHTI RESQHFLYIE NQFFISCSDG RTVLNKVGDE
IVDRILKAHK QGWCYRVYVL LPLLPGFEGD ISTGGGNSIQ AILHFTYRTL CRGEYSILHR
LKAAMGTAWR DYISICGLRT HGELGGHPVS ELIYIHSKVL IADDRTVIIG SANINDRSLL
GKRDSELAVL IEDTETEPSL MNGAEYQAGR FALSLRKHCF GVILGANTRP DLDLRDPICD
DFFQLWQDMA ESNANIYEQI FRCLPSNATR SLRTLREYVA VEPLATVSPP LARSELTQVQ
GHLVHFPLKF LEDESLLPPL GSKEGMIPLE VWT*

mutated AA sequence

MTATPESLFP TGDELDSSQL QMESDEVDTL KEGEDPADRM HPFLAIYELQ SLKVHPLVFA
PGVPVTAQVV GTERYTSGSK VGTCTLYSVR LTHGDFSWTT KKKYRHFQEL HRDLLRHKVL
MSLLPLARFA VAYSPARDAG NREMPSLPRA GPEGSTRHAA SKQKYLENYL NRLLTMSFYR
NYHAMTEFLE VSQLSFIPDL GRKGLEGMIR KRSGGHRVPG LTCCGRDQVC YRWSKRWLVV
KDSFLLYMCL ETGAISFVQL FDPGFEVQVG KRSTEARHGV RIDTSHRSLI LKCSSYRQAR
WWAQEITELA QGPGRDFLQL HRHDSYAPPR PGTLARWFVN GAGYFAAVAD AILRAQEEIF
ITDWWLSPEV YLKRPAHSDD WRLDIMLKRK AEEGVRVSIL LFKEVELALG INSGYSKRAL
MLLHPNIKVM RHPDQVTLWA HHEKLLVVDQ VVAFLGGLDL AYGRWDDLHY RLTDLGDSSE
SAASQPPTPR PDSPATPDLS HNQFFWLGKD YSNLITKDWV QLDRPFEDFI DRETTPRMPW
RDVGVVVHGL PARDLARHFI QRWNFTKTTK AKYKTPIYPY LLPKSTSTAN QLPFTLPGGQ
CTTVQVLRSV DRWSAGTLEN SILNAYLHTI RESQHFLYIE NQFFISCSDG RTVLNKVGDE
IVDRILKAHK QGWCYRVYVL LPLLPGFEGD ISTGGGNSIQ AILHFTYRTL CRGEYSILHR
LKAAMGTAWR DYISICGLRT HGELGGHPVS ELIYIHSKVL IADDRTVIIG SANINDRSLL
GKRDSELAVL IEDTETEPSL MNGAEYQAGR FALSLRKHCF GVILGANTRP DLDLRDPICD
DFFQLWQDMA ESNANIYEQI FRCLPSNATR SLRTLREYVA VEPLATVSPP LARSELTQVQ
GHLVHFPLKF LEDESLLPPL GSKEGMIPLE VWT*

speed

0.72 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: 0.999999999953739 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
homozygous in TGP or ExAC
known disease mutation at this position (HGMD CM030489)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr17:4720469C>TN/A show variant in all transcripts IGV

HGNC symbol

PLD2

Ensembl transcript ID

ENST00000572940

Genbank transcript ID

NM_001243108

UniProt peptide

O14939

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1730C>T
cDNA.1788C>T
g.10079C>T

AA changes

T577I Score: 89 explain score(s)

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

577

frameshift

known variant

Reference ID: rs1052748

database	homozygous (T/T)	heterozygous	allele carriers
1000G	201	849	1050
ExAC	10505	11757	22262

known disease mutation at this position, please check HGMD for details (HGMD ID CM030489)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.288	0
	-1.899	0
(flanking)	-0.072	0.023

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

577

mutated

not conserved

577

Ptroglodytes

all identical

ENSPTRG00000008610

577

Mmulatta

all identical

ENSMMUG00000005666

573

Fcatus

not conserved

ENSFCAG00000008040

431

Mmusculus

not conserved

ENSMUSG00000020828

577

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000016291

583

Drerio

not conserved

ENSDARG00000034262

570

Dmelanogaster

not conserved

FBgn0033075

990

Celegans

not conserved

C04G6.3

1060

Xtropicalis

all identical

ENSXETG00000021019

582

protein features

start (aa)	end (aa)	feature	details
441	788	REGION	Catalytic.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2769 / 2769

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

923 / 923

position of stopcodon in wt / mu cDNA

2827 / 2827

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

59 / 59

chromosome

strand

last intron/exon boundary

2603

theoretical NMD boundary in CDS

2494

length of CDS

2769

coding sequence (CDS) position

1730

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

1788

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

10079

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

4720469

original gDNA sequence snippet

GGCCAAGTACAAGACTCCCACATACCCCTACCTGCTTCCCA

altered gDNA sequence snippet

GGCCAAGTACAAGACTCCCATATACCCCTACCTGCTTCCCA

original cDNA sequence snippet

GGCCAAGTACAAGACTCCCACATACCCCTACCTGCTTCCCA

altered cDNA sequence snippet

GGCCAAGTACAAGACTCCCATATACCCCTACCTGCTTCCCA

wildtype AA sequence

MTATPESLFP TGDELDSSQL QMESDEVDTL KEGEDPADRM HPFLAIYELQ SLKVHPLVFA
PGVPVTAQVV GTERYTSGSK VGTCTLYSVR LTHGDFSWTT KKKYRHFQEL HRDLLRHKVL
MSLLPLARFA VAYSPARDAG NREMPSLPRA GPEGSTRHAA SKQKYLENYL NRLLTMSFYR
NYHAMTEFLE VSQLSFIPDL GRKGLEGMIR KRSGGHRVPG LTCCGRDQVC YRWSKRWLVV
KDSFLLYMCL ETGAISFVQL FDPGFEVQVG KRSTEARHGV RIDTSHRSLI LKCSSYRQAR
WWAQEITELA QGPGRDFLQL HRHDSYAPPR PGTLARWFVN GAGYFAAVAD AILRAQEEIF
ITDWWLSPEV YLKRPAHSDD WRLDIMLKRK AEEGVRVSIL LFKEVELALG INSGYSKRAL
MLLHPNIKVM RHPDQVTLWA HHEKLLVVDQ VVAFLGGLDL AYGRWDDLHY RLTDLGDSSE
SAASQPPTPR PDSPATPDLS HNQFFWLGKD YSNLITKDWV QLDRPFEDFI DRETTPRMPW
RDVGVVVHGL PARDLARHFI QRWNFTKTTK AKYKTPTYPY LLPKSTSTAN QLPFTLPGGQ
CTTVQVLRSV DRWSAGTLEN SILNAYLHTI RESQHFLYIE NQFFISCSDG RTVLNKVGDE
IVDRILKAHK QGWCYRVYVL LPLLPGFEGD ISTGGGNSIQ AILHFTYRTL CRGEYSILHR
LKAAMGTAWR DYISICGLRT HGELGGHPVS ELIYIHSKVL IADDRTVIIG SANINDRSLL
GKRDSELAVL IEDTETEPSL MNGAEYQAGS VILGANTRPD LDLRDPICDD FFQLWQDMAE
SNANIYEQIF RCLPSNATRS LRTLREYVAV EPLATVSPPL ARSELTQVQG HLVHFPLKFL
EDESLLPPLG SKEGMIPLEV WT*

mutated AA sequence

MTATPESLFP TGDELDSSQL QMESDEVDTL KEGEDPADRM HPFLAIYELQ SLKVHPLVFA
PGVPVTAQVV GTERYTSGSK VGTCTLYSVR LTHGDFSWTT KKKYRHFQEL HRDLLRHKVL
MSLLPLARFA VAYSPARDAG NREMPSLPRA GPEGSTRHAA SKQKYLENYL NRLLTMSFYR
NYHAMTEFLE VSQLSFIPDL GRKGLEGMIR KRSGGHRVPG LTCCGRDQVC YRWSKRWLVV
KDSFLLYMCL ETGAISFVQL FDPGFEVQVG KRSTEARHGV RIDTSHRSLI LKCSSYRQAR
WWAQEITELA QGPGRDFLQL HRHDSYAPPR PGTLARWFVN GAGYFAAVAD AILRAQEEIF
ITDWWLSPEV YLKRPAHSDD WRLDIMLKRK AEEGVRVSIL LFKEVELALG INSGYSKRAL
MLLHPNIKVM RHPDQVTLWA HHEKLLVVDQ VVAFLGGLDL AYGRWDDLHY RLTDLGDSSE
SAASQPPTPR PDSPATPDLS HNQFFWLGKD YSNLITKDWV QLDRPFEDFI DRETTPRMPW
RDVGVVVHGL PARDLARHFI QRWNFTKTTK AKYKTPIYPY LLPKSTSTAN QLPFTLPGGQ
CTTVQVLRSV DRWSAGTLEN SILNAYLHTI RESQHFLYIE NQFFISCSDG RTVLNKVGDE
IVDRILKAHK QGWCYRVYVL LPLLPGFEGD ISTGGGNSIQ AILHFTYRTL CRGEYSILHR
LKAAMGTAWR DYISICGLRT HGELGGHPVS ELIYIHSKVL IADDRTVIIG SANINDRSLL
GKRDSELAVL IEDTETEPSL MNGAEYQAGS VILGANTRPD LDLRDPICDD FFQLWQDMAE
SNANIYEQIF RCLPSNATRS LRTLREYVAV EPLATVSPPL ARSELTQVQG HLVHFPLKFL
EDESLLPPLG SKEGMIPLEV WT*

speed

0.57 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems