MutationTaster - study a chromosomal position

NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000377252
Querying Taster for transcript #2: ENST00000377242
Querying Taster for transcript #3: ENST00000377238
MT speed 3.29 s - this script 4.422158 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PLXDC2	polymorphism_automatic	1.19119047958804e-10	simple_aae		affected		V396I	single base exchange	rs3817405		show file
PLXDC2	polymorphism_automatic	4.77632045026155e-10	simple_aae		affected		V259I	single base exchange	rs3817405		show file
PLXDC2	polymorphism_automatic	7.93153986933248e-10	simple_aae		affected		V347I	single base exchange	rs3817405		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999880881 (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)

chr10:20506418G>AN/A show variant in all transcripts IGV

HGNC symbol

PLXDC2

Ensembl transcript ID

ENST00000377252

Genbank transcript ID

NM_032812

UniProt peptide

Q6UX71

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1186G>A
cDNA.2027G>A
g.401251G>A

AA changes

V396I Score: 29 explain score(s)

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

396

frameshift

known variant

Reference ID: rs3817405

database	homozygous (A/A)	heterozygous	allele carriers
1000G	898	1040	1938
ExAC	24194	-15621	8573

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.391	0.218
	-2.485	0
(flanking)	-0.278	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	401243	wt: 0.44 / mu: 0.66	wt: AACCACCACAACCGT mu: AACCACCACAACCAT	CCAC\|caca
Donor marginally increased	401251	wt: 0.8847 / mu: 0.9345 (marginal change - not scored)	wt: CAACCGTAGGAGCGA mu: CAACCATAGGAGCGA	ACCG\|tagg
Donor increased	401253	wt: 0.54 / mu: 0.89	wt: ACCGTAGGAGCGACA mu: ACCATAGGAGCGACA	CGTA\|ggag
Donor increased	401256	wt: 0.72 / mu: 0.88	wt: GTAGGAGCGACAACC mu: ATAGGAGCGACAACC	AGGA\|gcga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

396

mutated

all conserved

396

Ptroglodytes

all identical

ENSPTRG00000002342

396

Mmulatta

all identical

ENSMMUG00000015370

396

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000026748

396

Ggallus

all conserved

ENSGALG00000007956

395

Trubripes

not conserved

ENSTRUG00000008838

348

Drerio

all identical

ENSDARG00000059950

390

Dmelanogaster

not conserved

FBgn0028331

497

Celegans

not conserved

C36E8.3

397

Xtropicalis

all conserved

ENSXETG00000016596

371

protein features

start (aa)	end (aa)	feature	details
31	454	TOPO_DOM	Extracellular (Potential).	lost
383	427	COMPBIAS	Thr-rich.	lost
455	475	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
476	529	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
506	506	MOD_RES	Phosphoserine (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

1590 / 1590

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

530 / 530

position of stopcodon in wt / mu cDNA

2431 / 2431

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

842 / 842

chromosome

strand

last intron/exon boundary

2315

theoretical NMD boundary in CDS

1423

length of CDS

1590

coding sequence (CDS) position

1186

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

2027

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

401251

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

20506418

original gDNA sequence snippet

CTTCTCGAACCACCACAACCGTAGGAGCGACAACCACCCAG

altered gDNA sequence snippet

CTTCTCGAACCACCACAACCATAGGAGCGACAACCACCCAG

original cDNA sequence snippet

CTTCTCGAACCACCACAACCGTAGGAGCGACAACCACCCAG

altered cDNA sequence snippet

CTTCTCGAACCACCACAACCATAGGAGCGACAACCACCCAG

wildtype AA sequence

MARFPKADLA AAGVMLLCHF FTDQFQFADG KPGDQILDWQ YGVTQAFPHT EEEVEVDSHA
YSHRWKRNLD FLKAVDTNRA SVGQDSPEPR SFTDLLLDDG QDNNTQIEED TDHNYYISRI
YGPSDSASRD LWVNIDQMEK DKVKIHGILS NTHRQAARVN LSFDFPFYGH FLREITVATG
GFIYTGEVVH RMLTATQYIA PLMANFDPSV SRNSTVRYFD NGTALVVQWD HVHLQDNYNL
GSFTFQATLL MDGRIIFGYK EIPVLVTQIS STNHPVKVGL SDAFVVVHRI QQIPNVRRRT
IYEYHRVELQ MSKITNISAV EMTPLPTCLQ FNRCGPCVSS QIGFNCSWCS KLQRCSSGFD
RHRQDWVDSG CPEESKEKMC ENTEPVETSS RTTTTVGATT TQFRVLTTTR RAVTSQFPTS
LPTEDDTKIA LHLKDNGAST DDSAAEKKGG TLHAGLIIGI LILVLIVATA ILVTVYMYHH
PTSAASIFFI ERRPSRWPAM KFRRGSGHPA YAEVEPVGEK EGFIVSEQC*

mutated AA sequence

MARFPKADLA AAGVMLLCHF FTDQFQFADG KPGDQILDWQ YGVTQAFPHT EEEVEVDSHA
YSHRWKRNLD FLKAVDTNRA SVGQDSPEPR SFTDLLLDDG QDNNTQIEED TDHNYYISRI
YGPSDSASRD LWVNIDQMEK DKVKIHGILS NTHRQAARVN LSFDFPFYGH FLREITVATG
GFIYTGEVVH RMLTATQYIA PLMANFDPSV SRNSTVRYFD NGTALVVQWD HVHLQDNYNL
GSFTFQATLL MDGRIIFGYK EIPVLVTQIS STNHPVKVGL SDAFVVVHRI QQIPNVRRRT
IYEYHRVELQ MSKITNISAV EMTPLPTCLQ FNRCGPCVSS QIGFNCSWCS KLQRCSSGFD
RHRQDWVDSG CPEESKEKMC ENTEPVETSS RTTTTIGATT TQFRVLTTTR RAVTSQFPTS
LPTEDDTKIA LHLKDNGAST DDSAAEKKGG TLHAGLIIGI LILVLIVATA ILVTVYMYHH
PTSAASIFFI ERRPSRWPAM KFRRGSGHPA YAEVEPVGEK EGFIVSEQC*

speed

1.16 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: 0.999999999522368 (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)

chr10:20506418G>AN/A show variant in all transcripts IGV

HGNC symbol

PLXDC2

Ensembl transcript ID

ENST00000377238

Genbank transcript ID

N/A

UniProt peptide

Q6UX71

alteration type

single base exchange

alteration region

CDS

DNA changes

c.775G>A
cDNA.2126G>A
g.401251G>A

AA changes

V259I Score: 29 explain score(s)

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

259

frameshift

known variant

Reference ID: rs3817405

database	homozygous (A/A)	heterozygous	allele carriers
1000G	898	1040	1938
ExAC	24194	-15621	8573

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.391	0.218
	-2.485	0
(flanking)	-0.278	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	401243	wt: 0.44 / mu: 0.66	wt: AACCACCACAACCGT mu: AACCACCACAACCAT	CCAC\|caca
Donor marginally increased	401251	wt: 0.8847 / mu: 0.9345 (marginal change - not scored)	wt: CAACCGTAGGAGCGA mu: CAACCATAGGAGCGA	ACCG\|tagg
Donor increased	401253	wt: 0.54 / mu: 0.89	wt: ACCGTAGGAGCGACA mu: ACCATAGGAGCGACA	CGTA\|ggag
Donor increased	401256	wt: 0.72 / mu: 0.88	wt: GTAGGAGCGACAACC mu: ATAGGAGCGACAACC	AGGA\|gcga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

259

mutated

all conserved

259

Ptroglodytes

all identical

ENSPTRG00000002342

396

Mmulatta

all identical

ENSMMUG00000015370

396

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000026748

398

Ggallus

all conserved

ENSGALG00000007956

395

Trubripes

not conserved

ENSTRUG00000008838

350

Drerio

all identical

ENSDARG00000059950

390

Dmelanogaster

not conserved

FBgn0028331

497

Celegans

not conserved

C36E8.3

397

Xtropicalis

all conserved

ENSXETG00000016596

371

protein features

start (aa)	end (aa)	feature	details
31	454	TOPO_DOM	Extracellular (Potential).	lost
327	372	DOMAIN	PSI.	might get lost (downstream of altered splice site)
383	427	COMPBIAS	Thr-rich.	might get lost (downstream of altered splice site)
455	475	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
476	529	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
506	506	MOD_RES	Phosphoserine (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

1179 / 1179

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

393 / 393

position of stopcodon in wt / mu cDNA

2530 / 2530

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

1352 / 1352

chromosome

strand

last intron/exon boundary

2414

theoretical NMD boundary in CDS

1012

length of CDS

1179

coding sequence (CDS) position

775

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

2126

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

401251

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

20506418

original gDNA sequence snippet

CTTCTCGAACCACCACAACCGTAGGAGCGACAACCACCCAG

altered gDNA sequence snippet

CTTCTCGAACCACCACAACCATAGGAGCGACAACCACCCAG

original cDNA sequence snippet

CTTCTCGAACCACCACAACCGTAGGAGCGACAACCACCCAG

altered cDNA sequence snippet

CTTCTCGAACCACCACAACCATAGGAGCGACAACCACCCAG

wildtype AA sequence

MEKDKVKIHG ILSNTHRQAA RVNLSFDFPF YGHFLREITV ATGGFIYTGE VVHRMLTATQ
YIAPLMANFD PSVSRNSTVR YFDNGTALVV QWDHVHLQDN YNLGSFTFQA TLLMDGRIIF
GYKEIPVLVT QISSTNHPVK VGLSDAFVVV HRIQQIPNVR RRTIYEYHRV ELQMSKITNI
SAVEMTPLPT CLQFNRCGPC VSSQIGFNCS WCSKLQRCSS GFDRHRQDWV DSGCPEESKE
KMCENTEPVE TSSRTTTTVG ATTTQFRVLT TTRRAVTSQF PTSLPTEDDT KIALHLKDNG
ASTDDSAAEK KGGTLHAGLI IGILILVLIV ATAILVTVYM YHHPTSAASI FFIERRPSRW
PAMKFRRGSG HPAYAEVEPV GEKEGFIVSE QC*

mutated AA sequence

MEKDKVKIHG ILSNTHRQAA RVNLSFDFPF YGHFLREITV ATGGFIYTGE VVHRMLTATQ
YIAPLMANFD PSVSRNSTVR YFDNGTALVV QWDHVHLQDN YNLGSFTFQA TLLMDGRIIF
GYKEIPVLVT QISSTNHPVK VGLSDAFVVV HRIQQIPNVR RRTIYEYHRV ELQMSKITNI
SAVEMTPLPT CLQFNRCGPC VSSQIGFNCS WCSKLQRCSS GFDRHRQDWV DSGCPEESKE
KMCENTEPVE TSSRTTTTIG ATTTQFRVLT TTRRAVTSQF PTSLPTEDDT KIALHLKDNG
ASTDDSAAEK KGGTLHAGLI IGILILVLIV ATAILVTVYM YHHPTSAASI FFIERRPSRW
PAMKFRRGSG HPAYAEVEPV GEKEGFIVSE QC*

speed

1.16 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999206846 (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)

chr10:20506418G>AN/A show variant in all transcripts IGV

HGNC symbol

PLXDC2

Ensembl transcript ID

ENST00000377242

Genbank transcript ID

N/A

UniProt peptide

Q6UX71

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1039G>A
cDNA.1880G>A
g.401251G>A

AA changes

V347I Score: 29 explain score(s)

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

347

frameshift

known variant

Reference ID: rs3817405

database	homozygous (A/A)	heterozygous	allele carriers
1000G	898	1040	1938
ExAC	24194	-15621	8573

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.391	0.218
	-2.485	0
(flanking)	-0.278	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	401243	wt: 0.44 / mu: 0.66	wt: AACCACCACAACCGT mu: AACCACCACAACCAT	CCAC\|caca
Donor marginally increased	401251	wt: 0.8847 / mu: 0.9345 (marginal change - not scored)	wt: CAACCGTAGGAGCGA mu: CAACCATAGGAGCGA	ACCG\|tagg
Donor increased	401253	wt: 0.54 / mu: 0.89	wt: ACCGTAGGAGCGACA mu: ACCATAGGAGCGACA	CGTA\|ggag
Donor increased	401256	wt: 0.72 / mu: 0.88	wt: GTAGGAGCGACAACC mu: ATAGGAGCGACAACC	AGGA\|gcga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

347

mutated

all conserved

347

Ptroglodytes

all identical

ENSPTRG00000002342

396

Mmulatta

all identical

ENSMMUG00000015370

396

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000026748

396

Ggallus

all conserved

ENSGALG00000007956

395

Trubripes

not conserved

ENSTRUG00000008838

348

Drerio

all identical

ENSDARG00000059950

390

Dmelanogaster

not conserved

FBgn0028331

497

Celegans

not conserved

C36E8.3

397

Xtropicalis

all conserved

ENSXETG00000016596

371

protein features

start (aa)	end (aa)	feature	details
31	454	TOPO_DOM	Extracellular (Potential).	lost
327	372	DOMAIN	PSI.	lost
383	427	COMPBIAS	Thr-rich.	might get lost (downstream of altered splice site)
455	475	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
476	529	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
506	506	MOD_RES	Phosphoserine (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

1443 / 1443

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

481 / 481

position of stopcodon in wt / mu cDNA

2284 / 2284

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

842 / 842

chromosome

strand

last intron/exon boundary

2168

theoretical NMD boundary in CDS

1276

length of CDS

1443

coding sequence (CDS) position

1039

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

1880

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

401251

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

20506418

original gDNA sequence snippet

CTTCTCGAACCACCACAACCGTAGGAGCGACAACCACCCAG

altered gDNA sequence snippet

CTTCTCGAACCACCACAACCATAGGAGCGACAACCACCCAG

original cDNA sequence snippet

CTTCTCGAACCACCACAACCGTAGGAGCGACAACCACCCAG

altered cDNA sequence snippet

CTTCTCGAACCACCACAACCATAGGAGCGACAACCACCCAG

wildtype AA sequence

MARFPKADLA AAGVMLLCHF FTDQFQFADG KPGDQILDWQ YGVTQAFPHT EEEVEVDSHA
YSHRWKRNLD FLKAVDTNRA SVGQDSPEPR SFTDLLLDDG QDNNTQIERV NLSFDFPFYG
HFLREITVAT GGFIYTGEVV HRMLTATQYI APLMANFDPS VSRNSTVRYF DNGTALVVQW
DHVHLQDNYN LGSFTFQATL LMDGRIIFGY KEIPVLVTQI SSTNHPVKVG LSDAFVVVHR
IQQIPNVRRR TIYEYHRVEL QMSKITNISA VEMTPLPTCL QFNRCGPCVS SQIGFNCSWC
SKLQRCSSGF DRHRQDWVDS GCPEESKEKM CENTEPVETS SRTTTTVGAT TTQFRVLTTT
RRAVTSQFPT SLPTEDDTKI ALHLKDNGAS TDDSAAEKKG GTLHAGLIIG ILILVLIVAT
AILVTVYMYH HPTSAASIFF IERRPSRWPA MKFRRGSGHP AYAEVEPVGE KEGFIVSEQC
*

mutated AA sequence

MARFPKADLA AAGVMLLCHF FTDQFQFADG KPGDQILDWQ YGVTQAFPHT EEEVEVDSHA
YSHRWKRNLD FLKAVDTNRA SVGQDSPEPR SFTDLLLDDG QDNNTQIERV NLSFDFPFYG
HFLREITVAT GGFIYTGEVV HRMLTATQYI APLMANFDPS VSRNSTVRYF DNGTALVVQW
DHVHLQDNYN LGSFTFQATL LMDGRIIFGY KEIPVLVTQI SSTNHPVKVG LSDAFVVVHR
IQQIPNVRRR TIYEYHRVEL QMSKITNISA VEMTPLPTCL QFNRCGPCVS SQIGFNCSWC
SKLQRCSSGF DRHRQDWVDS GCPEESKEKM CENTEPVETS SRTTTTIGAT TTQFRVLTTT
RRAVTSQFPT SLPTEDDTKI ALHLKDNGAS TDDSAAEKKG GTLHAGLIIG ILILVLIVAT
AILVTVYMYH HPTSAASIFF IERRPSRWPA MKFRRGSGHP AYAEVEPVGE KEGFIVSEQC
*

speed

0.97 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems