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: ENST00000412055
Querying Taster for transcript #2: ENST00000411976
MT speed 0 s - this script 3.538027 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
PRRT3	polymorphism_automatic	7.99360577730113e-15	simple_aae				S213P	single base exchange	rs55847610		show file
PRRT3	polymorphism_automatic	7.99360577730113e-15	simple_aae				S213P	single base exchange	rs55847610		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.999999999999992 (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)

chr3:9991163A>GN/A show variant in all transcripts IGV

HGNC symbol

PRRT3

Ensembl transcript ID

ENST00000412055

Genbank transcript ID

NM_207351

UniProt peptide

Q5FWE3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.637T>C
cDNA.767T>C
g.2916T>C

AA changes

S213P Score: 74 explain score(s)

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

213

frameshift

known variant

Reference ID: rs55847610

database	homozygous (G/G)	heterozygous	allele carriers
1000G	549	815	1364
ExAC	5883	21001	26884

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.589	0.005
	-0.014	0.001
(flanking)	-0.939	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
Acc marginally increased	2917	wt: 0.2684 / mu: 0.3187 (marginal change - not scored)	wt: CCCACCCCACACCCTTGTTTCCCACTCAGGTACTGTCAAGA mu: CCCACCCCACACCCTTGTTCCCCACTCAGGTACTGTCAAGA	tttc\|CCAC
Acc marginally increased	2923	wt: 0.9866 / mu: 0.9881 (marginal change - not scored)	wt: CCACACCCTTGTTTCCCACTCAGGTACTGTCAAGAGGCCAG mu: CCACACCCTTGTTCCCCACTCAGGTACTGTCAAGAGGCCAG	actc\|AGGT
Donor marginally increased	2920	wt: 0.9596 / mu: 0.9708 (marginal change - not scored)	wt: TTCCCACTCAGGTAC mu: TCCCCACTCAGGTAC	CCCA\|ctca

distance from splice site

379

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

213

mutated

not conserved

213

Ptroglodytes

not conserved

ENSPTRG00000014605

214

Mmulatta

not conserved

ENSMMUG00000018289

214

Fcatus

not conserved

ENSFCAG00000014208

217

Mmusculus

not conserved

ENSMUSG00000045009

204

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000077087

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032926

n/a

protein features

start (aa)	end (aa)	feature	details
28	474	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2946 / 2946

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

982 / 982

position of stopcodon in wt / mu cDNA

3076 / 3076

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

131 / 131

chromosome

strand

-1

last intron/exon boundary

1302

theoretical NMD boundary in CDS

1121

length of CDS

2946

coding sequence (CDS) position

637

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

767

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

2916

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

9991163

original gDNA sequence snippet

GCCCACCCCACACCCTTGTTTCCCACTCAGGTACTGTCAAG

altered gDNA sequence snippet

GCCCACCCCACACCCTTGTTCCCCACTCAGGTACTGTCAAG

original cDNA sequence snippet

GCCCACCCCACACCCTTGTTTCCCACTCAGGTACTGTCAAG

altered cDNA sequence snippet

GCCCACCCCACACCCTTGTTCCCCACTCAGGTACTGTCAAG

wildtype AA sequence

MASSPWGCVC GLLLLLLPLL GTGPALGRGF PRPLENSEIP MIPGAHPKGS VGSEPQAFDV
FPENPRADSH RNSDVRHAPA EEMPEKPVAS PLGPALYGPK AAQGAQRERL PVTDDLQMAQ
GPSSHGWTGP LDSQELLQQE AVAPHPVGHP HLTFIPTTPR RQLRVATVPP SLQHEGQEGQ
WPPRDEGLKA KTKSRVPPTS PSDHQGPPHT LVSHSGTVKR PVLEGQGGFE EHLQEAAQGP
HFTQQDPAAP DVGSVPPVEV VYSQEPGAQP DLALARSLPP AEELPVETPK RAGAEVSWEV
SSPGPPPKQA DLPDAKDSPG PQPTDPPASE APDRPSKPER AAMNGADPIS PQRVRGAVEA
PGTPKSLIPG PSDPGPAVNR TESPMGALQP DEAEEWPGRP QSHPPAPPVQ APSTSRRGLI
RVTTQRALGQ PPPPEPTASS MASAPASSPP ANATAPPLRW GPLRRVLSFS WELHVYGVGV
LFLLPALLAL AALAAAPAGP RLALVAAVLV LVASALRSAY MLTDPYGSQA RLGVRGGLVL
YNLPFPLLLT ALAALTLLGL GAGLPPPLQN PLLLGAVALV HGVGLLATDL LSTWSVLNLL
TQGLSCAWGA AVALGTLCLC RRRLLDGPRG WDASPGPRLL AVAGALGLLA SGLQLAAALW
LYPGPGRVGR FSWAWWGVHF WLRLLELTWA LALALAAVAA ARPRPPTEHA CWAKLMRLAC
PAPSGKSEVP ERPNNCYAGP SNVGAGSLDI SKSLIRNPAE SGQLATPSSG AWGSAASLGR
GPQGGPGLSR NGVGPAPSLS ELDLRPPSPI NLSRSIDAAL FREHLVRDSV FQRCGLRGLA
SPPPGGALRP RRGSHPKAEL DDAGSSLLRG RCRSLSDVRV RGPVPQHVVE APDGAAAAAS
GSSLDSFSRG SLKISWNPWR HGLSSVDSLP LDELPSTVQL LPAPTPAPDS TAARQGDGQG
EVQPRGKPGE SRSASSDTIE L*

mutated AA sequence

MASSPWGCVC GLLLLLLPLL GTGPALGRGF PRPLENSEIP MIPGAHPKGS VGSEPQAFDV
FPENPRADSH RNSDVRHAPA EEMPEKPVAS PLGPALYGPK AAQGAQRERL PVTDDLQMAQ
GPSSHGWTGP LDSQELLQQE AVAPHPVGHP HLTFIPTTPR RQLRVATVPP SLQHEGQEGQ
WPPRDEGLKA KTKSRVPPTS PSDHQGPPHT LVPHSGTVKR PVLEGQGGFE EHLQEAAQGP
HFTQQDPAAP DVGSVPPVEV VYSQEPGAQP DLALARSLPP AEELPVETPK RAGAEVSWEV
SSPGPPPKQA DLPDAKDSPG PQPTDPPASE APDRPSKPER AAMNGADPIS PQRVRGAVEA
PGTPKSLIPG PSDPGPAVNR TESPMGALQP DEAEEWPGRP QSHPPAPPVQ APSTSRRGLI
RVTTQRALGQ PPPPEPTASS MASAPASSPP ANATAPPLRW GPLRRVLSFS WELHVYGVGV
LFLLPALLAL AALAAAPAGP RLALVAAVLV LVASALRSAY MLTDPYGSQA RLGVRGGLVL
YNLPFPLLLT ALAALTLLGL GAGLPPPLQN PLLLGAVALV HGVGLLATDL LSTWSVLNLL
TQGLSCAWGA AVALGTLCLC RRRLLDGPRG WDASPGPRLL AVAGALGLLA SGLQLAAALW
LYPGPGRVGR FSWAWWGVHF WLRLLELTWA LALALAAVAA ARPRPPTEHA CWAKLMRLAC
PAPSGKSEVP ERPNNCYAGP SNVGAGSLDI SKSLIRNPAE SGQLATPSSG AWGSAASLGR
GPQGGPGLSR NGVGPAPSLS ELDLRPPSPI NLSRSIDAAL FREHLVRDSV FQRCGLRGLA
SPPPGGALRP RRGSHPKAEL DDAGSSLLRG RCRSLSDVRV RGPVPQHVVE APDGAAAAAS
GSSLDSFSRG SLKISWNPWR HGLSSVDSLP LDELPSTVQL LPAPTPAPDS TAARQGDGQG
EVQPRGKPGE SRSASSDTIE L*

speed

0.80 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: 0.999999999999992 (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)

chr3:9991163A>GN/A show variant in all transcripts IGV

HGNC symbol

PRRT3

Ensembl transcript ID

ENST00000411976

Genbank transcript ID

N/A

UniProt peptide

Q5FWE3

alteration type

single base exchange

alteration region

CDS

DNA changes

c.637T>C
cDNA.763T>C
g.2916T>C

AA changes

S213P Score: 74 explain score(s)

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

213

frameshift

known variant

Reference ID: rs55847610

database	homozygous (G/G)	heterozygous	allele carriers
1000G	549	815	1364
ExAC	5883	21001	26884

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.589	0.005
	-0.014	0.001
(flanking)	-0.939	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
Acc marginally increased	2917	wt: 0.2684 / mu: 0.3187 (marginal change - not scored)	wt: CCCACCCCACACCCTTGTTTCCCACTCAGGTACTGTCAAGA mu: CCCACCCCACACCCTTGTTCCCCACTCAGGTACTGTCAAGA	tttc\|CCAC
Acc marginally increased	2923	wt: 0.9866 / mu: 0.9881 (marginal change - not scored)	wt: CCACACCCTTGTTTCCCACTCAGGTACTGTCAAGAGGCCAG mu: CCACACCCTTGTTCCCCACTCAGGTACTGTCAAGAGGCCAG	actc\|AGGT
Donor marginally increased	2920	wt: 0.9596 / mu: 0.9708 (marginal change - not scored)	wt: TTCCCACTCAGGTAC mu: TCCCCACTCAGGTAC	CCCA\|ctca

distance from splice site

379

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

213

mutated

not conserved

213

Ptroglodytes

not conserved

ENSPTRG00000014605

214

Mmulatta

not conserved

ENSMMUG00000018289

214

Fcatus

not conserved

ENSFCAG00000014208

217

Mmusculus

not conserved

ENSMUSG00000045009

204

Ggallus

no homologue

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000077087

n/a

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000032926

n/a

protein features

start (aa)	end (aa)	feature	details
28	474	TOPO_DOM	Extracellular (Potential).	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1266 / 1266

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

422 / 422

position of stopcodon in wt / mu cDNA

1392 / 1392

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

127 / 127

chromosome

strand

-1

last intron/exon boundary

1142

theoretical NMD boundary in CDS

965

length of CDS

1266

coding sequence (CDS) position

637

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

763

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

2916

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

9991163

original gDNA sequence snippet

GCCCACCCCACACCCTTGTTTCCCACTCAGGTACTGTCAAG

altered gDNA sequence snippet

GCCCACCCCACACCCTTGTTCCCCACTCAGGTACTGTCAAG

original cDNA sequence snippet

GCCCACCCCACACCCTTGTTTCCCACTCAGGTACTGTCAAG

altered cDNA sequence snippet

GCCCACCCCACACCCTTGTTCCCCACTCAGGTACTGTCAAG

wildtype AA sequence

mutated AA sequence

speed

0.75 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems