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: ENST00000359894
Querying Taster for transcript #2: ENST00000520876
MT speed 0 s - this script 4.305206 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PLPPR3	polymorphism_automatic	7.78138398160877e-09	simple_aae		affected		T531A	single base exchange	rs351994		show file
PLPPR3	polymorphism_automatic	7.78138398160877e-09	simple_aae		affected		T503A	single base exchange	rs351994		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999992218616 (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)

chr19:813220T>CN/A show variant in all transcripts IGV

HGNC symbol

PLPPR3

Ensembl transcript ID

ENST00000359894

Genbank transcript ID

NM_024888

UniProt peptide

Q6T4P5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1591A>G
cDNA.1655A>G
g.8759A>G

AA changes

T531A Score: 58 explain score(s)

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

531

frameshift

known variant

Reference ID: rs351994

database	homozygous (C/C)	heterozygous	allele carriers
1000G	356	768	1124
ExAC	964	6517	7481

regulatory features

Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Gabp, Transcription Factor, Gabp TF binding
PolII, Polymerase, RNA Polymerase II
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.533	0.048
	0.674	0.353
(flanking)	0.639	0.411

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	8758	0.32	mu: GCGCAGGCGGGGGCC	GCAG\|gcgg

distance from splice site

676

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

531

mutated

not conserved

531

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000035835

500

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000011591

Drerio

not conserved

ENSDARG00000010144

509

Dmelanogaster

no homologue

Celegans

no alignment

T06D8.3

n/a

Xtropicalis

not conserved

ENSXETG00000021653

502

protein features

start (aa)	end (aa)	feature	details
558	567	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2241 / 2241

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

747 / 747

position of stopcodon in wt / mu cDNA

2305 / 2305

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

65 / 65

chromosome

strand

-1

last intron/exon boundary

980

theoretical NMD boundary in CDS

865

length of CDS

2241

coding sequence (CDS) position

1591

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

1655

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

8759

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

813220

original gDNA sequence snippet

TCCCGGAGGAGGGCGCGCAGACGGGGGCCGGCCTGTCCCCC

altered gDNA sequence snippet

TCCCGGAGGAGGGCGCGCAGGCGGGGGCCGGCCTGTCCCCC

original cDNA sequence snippet

TCCCGGAGGAGGGCGCGCAGACGGGGGCCGGCCTGTCCCCC

altered cDNA sequence snippet

TCCCGGAGGAGGGCGCGCAGGCGGGGGCCGGCCTGTCCCCC

wildtype AA sequence

MISTKEKNKI PKDSMTLLPC FYFVELPIVA SSIVSLYFLE LTDLFKPAKV GFQCYDRTLS
MPYVETNEEL IPLLMLLSLA FAAPAASIMV AEGMLYCLQS RLWGRAGGPA GAEGSINAGG
CNFNSFLRRT VRFVGVHVFG LCATALVTDV IQLATGYHTP FFLTVCKPNY TLLGTSCEVN
PYITQDICSG HDIHAILSAR KTFPSQHATL SAFAAVYVSV SPAPHCPSQA LLLTRGEPSL
TPTPMPQMYF NSVISDTTKL LKPILVFAFA IAAGVCGLTQ ITQYRSHPVD VYAGFLIGAG
IAAYLACHAV GNFQAPPAEK PAAPAPAKDA LRALTQRGHD SVYQQNKSVS TDELGPPGRL
EGAPRPVARE KTSLGSLKRA SVDVDLLAPR SPMAKENMVT FSHTLPRASA PSLDDPARRH
MTIHVPLDAS RSKQLISEWK QKSLEGRGLG LPDDASPGHL RAPAEPMAEE EEEEEDEEEE
EEEEEEEDEG PAPPSLYPTV QARPGLGPRV ILPPRAGPPP LVHIPEEGAQ TGAGLSPKSG
AGVRAKWLMM AEKSGAAVAN PPRLLQVIAM SKAPGAPGPK AAETASSSSA SSDSSQYRSP
SDRDSASIVT IDAHAPHHPV VHLSAGGAPW EWKAAGGGAK AEADGGYELG DLARGFRGGA
KPPGVSPGSS VSDVDQEEPR FGAVATVNLA TGEGLPPLGA ADGALGPGSR ESTLRRHAGG
LGLAEREAEA EAEGYFRKMQ ARRFPD*

mutated AA sequence

MISTKEKNKI PKDSMTLLPC FYFVELPIVA SSIVSLYFLE LTDLFKPAKV GFQCYDRTLS
MPYVETNEEL IPLLMLLSLA FAAPAASIMV AEGMLYCLQS RLWGRAGGPA GAEGSINAGG
CNFNSFLRRT VRFVGVHVFG LCATALVTDV IQLATGYHTP FFLTVCKPNY TLLGTSCEVN
PYITQDICSG HDIHAILSAR KTFPSQHATL SAFAAVYVSV SPAPHCPSQA LLLTRGEPSL
TPTPMPQMYF NSVISDTTKL LKPILVFAFA IAAGVCGLTQ ITQYRSHPVD VYAGFLIGAG
IAAYLACHAV GNFQAPPAEK PAAPAPAKDA LRALTQRGHD SVYQQNKSVS TDELGPPGRL
EGAPRPVARE KTSLGSLKRA SVDVDLLAPR SPMAKENMVT FSHTLPRASA PSLDDPARRH
MTIHVPLDAS RSKQLISEWK QKSLEGRGLG LPDDASPGHL RAPAEPMAEE EEEEEDEEEE
EEEEEEEDEG PAPPSLYPTV QARPGLGPRV ILPPRAGPPP LVHIPEEGAQ AGAGLSPKSG
AGVRAKWLMM AEKSGAAVAN PPRLLQVIAM SKAPGAPGPK AAETASSSSA SSDSSQYRSP
SDRDSASIVT IDAHAPHHPV VHLSAGGAPW EWKAAGGGAK AEADGGYELG DLARGFRGGA
KPPGVSPGSS VSDVDQEEPR FGAVATVNLA TGEGLPPLGA ADGALGPGSR ESTLRRHAGG
LGLAEREAEA EAEGYFRKMQ ARRFPD*

speed

1.18 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: 0.999999992218616 (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)

chr19:813220T>CN/A show variant in all transcripts IGV

HGNC symbol

PLPPR3

Ensembl transcript ID

ENST00000520876

Genbank transcript ID

NM_001270366

UniProt peptide

Q6T4P5

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1507A>G
cDNA.1597A>G
g.8759A>G

AA changes

T503A Score: 58 explain score(s)

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

503

frameshift

known variant

Reference ID: rs351994

database	homozygous (C/C)	heterozygous	allele carriers
1000G	356	768	1124
ExAC	964	6517	7481

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.533	0.048
	0.674	0.353
(flanking)	0.639	0.411

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	8758	0.32	mu: GCGCAGGCGGGGGCC	GCAG\|gcgg

distance from splice site

676

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

503

mutated

not conserved

503

Ptroglodytes

no homologue

Mmulatta

no homologue

Fcatus

no homologue

Mmusculus

not conserved

ENSMUSG00000035835

500

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000011591

Drerio

not conserved

ENSDARG00000010144

510

Dmelanogaster

no homologue

Celegans

no alignment

T06D8.3

n/a

Xtropicalis

not conserved

ENSXETG00000021653

489

protein features

start (aa)	end (aa)	feature	details
558	567	COMPBIAS	Poly-Ser.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2157 / 2157

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

719 / 719

position of stopcodon in wt / mu cDNA

2247 / 2247

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

91 / 91

chromosome

strand

-1

last intron/exon boundary

922

theoretical NMD boundary in CDS

781

length of CDS

2157

coding sequence (CDS) position

1507

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

1597

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

8759

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

813220

original gDNA sequence snippet

TCCCGGAGGAGGGCGCGCAGACGGGGGCCGGCCTGTCCCCC

altered gDNA sequence snippet

TCCCGGAGGAGGGCGCGCAGGCGGGGGCCGGCCTGTCCCCC

original cDNA sequence snippet

TCCCGGAGGAGGGCGCGCAGACGGGGGCCGGCCTGTCCCCC

altered cDNA sequence snippet

TCCCGGAGGAGGGCGCGCAGGCGGGGGCCGGCCTGTCCCCC

wildtype AA sequence

MISTKEKNKI PKDSMTLLPC FYFVELPIVA SSIVSLYFLE LTDLFKPAKV GFQCYDRTLS
MPYVETNEEL IPLLMLLSLA FAAPAASIMV AEGMLYCLQS RLWGRAGGPA GAEGSINAGG
CNFNSFLRRT VRFVGVHVFG LCATALVTDV IQLATGYHTP FFLTVCKPNY TLLGTSCEVN
PYITQDICSG HDIHAILSAR KTFPSQHATL SAFAAVYVSM YFNSVISDTT KLLKPILVFA
FAIAAGVCGL TQITQYRSHP VDVYAGFLIG AGIAAYLACH AVGNFQAPPA EKPAAPAPAK
DALRALTQRG HDSVYQQNKS VSTDELGPPG RLEGAPRPVA REKTSLGSLK RASVDVDLLA
PRSPMAKENM VTFSHTLPRA SAPSLDDPAR RHMTIHVPLD ASRSKQLISE WKQKSLEGRG
LGLPDDASPG HLRAPAEPMA EEEEEEEDEE EEEEEEEEED EGPAPPSLYP TVQARPGLGP
RVILPPRAGP PPLVHIPEEG AQTGAGLSPK SGAGVRAKWL MMAEKSGAAV ANPPRLLQVI
AMSKAPGAPG PKAAETASSS SASSDSSQYR SPSDRDSASI VTIDAHAPHH PVVHLSAGGA
PWEWKAAGGG AKAEADGGYE LGDLARGFRG GAKPPGVSPG SSVSDVDQEE PRFGAVATVN
LATGEGLPPL GAADGALGPG SRESTLRRHA GGLGLAEREA EAEAEGYFRK MQARRFPD*

mutated AA sequence

MISTKEKNKI PKDSMTLLPC FYFVELPIVA SSIVSLYFLE LTDLFKPAKV GFQCYDRTLS
MPYVETNEEL IPLLMLLSLA FAAPAASIMV AEGMLYCLQS RLWGRAGGPA GAEGSINAGG
CNFNSFLRRT VRFVGVHVFG LCATALVTDV IQLATGYHTP FFLTVCKPNY TLLGTSCEVN
PYITQDICSG HDIHAILSAR KTFPSQHATL SAFAAVYVSM YFNSVISDTT KLLKPILVFA
FAIAAGVCGL TQITQYRSHP VDVYAGFLIG AGIAAYLACH AVGNFQAPPA EKPAAPAPAK
DALRALTQRG HDSVYQQNKS VSTDELGPPG RLEGAPRPVA REKTSLGSLK RASVDVDLLA
PRSPMAKENM VTFSHTLPRA SAPSLDDPAR RHMTIHVPLD ASRSKQLISE WKQKSLEGRG
LGLPDDASPG HLRAPAEPMA EEEEEEEDEE EEEEEEEEED EGPAPPSLYP TVQARPGLGP
RVILPPRAGP PPLVHIPEEG AQAGAGLSPK SGAGVRAKWL MMAEKSGAAV ANPPRLLQVI
AMSKAPGAPG PKAAETASSS SASSDSSQYR SPSDRDSASI VTIDAHAPHH PVVHLSAGGA
PWEWKAAGGG AKAEADGGYE LGDLARGFRG GAKPPGVSPG SSVSDVDQEE PRFGAVATVN
LATGEGLPPL GAADGALGPG SRESTLRRHA GGLGLAEREA EAEAEGYFRK MQARRFPD*

speed

1.18 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems